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olgabot/reflow run error output

Created October 23, 2018 22:01
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how to use trace and len of file to dynamically allocate memory
Raw
reflow run error output
Tue 23 Oct - 14:57  ~/code/kmer-hashing/sourmash/maca/10x_spleen_kidney   origin ☊ olgabot/search-compare-ignore-abundance ✔ 5☀ 
 reflow run ../../../reflow/sourmash_compute_10x.rf -ksizes "21,27,33,51" -num_hashes 5000 -tenx s3://czbiohub-maca/10x_data/10X_P4_7 -output s3://olgabot-maca/10x/sourmash_compute/ksizes=21,27,33,51_num_hashes=1000/Spleen_10X_P4_7.csv
2018/10/23 14:57:48 panic while evaluating <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n "): invalid type
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aad50, 0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
2018/10/23 14:57:48 panic while evaluating <(signature file)>block(<(file, string)>assign((bam, _), <(file, string)>apply(<func(dir dir, pattern string) (file, string)>deref(<module{Groups func(dir dir, re string) [string:dir], Make func(map [string:file]) dir, Pick func(dir dir, pattern string) (file, string), Files func(dir dir) [file], Copy func(dir dir, url string) unit, Fileset func(fileset fileset) dir}>ident("dirs"), Pick)(<dir>ident("tenx"), <string>const("*.bam")))), <int>assign(memory, <int>builtin(len, <file>ident("bam"))), <int>assign(v, <int>builtin(trace, <int>ident("memory"))), <dir>assign(u, <dir>builtin(trace, <dir>ident("tenx"))) in <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n ")): panic while evaluating <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n "): invalid type
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aad50, 0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aab88, 0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066ba40)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
log.Panicf(0xfb0e4d, 0x20, 0xc4206aad10, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
2018/10/23 14:57:48 panic while evaluating <(signature file)>apply(<func(tenx dir, ksizes string) (signature file)>ident("Compute")(<dir>ident("minimal_tenx_dir"), <string>ident("ksizes"))): panic while evaluating <(signature file)>block(<(file, string)>assign((bam, _), <(file, string)>apply(<func(dir dir, pattern string) (file, string)>deref(<module{Groups func(dir dir, re string) [string:dir], Make func(map [string:file]) dir, Pick func(dir dir, pattern string) (file, string), Files func(dir dir) [file], Copy func(dir dir, url string) unit, Fileset func(fileset fileset) dir}>ident("dirs"), Pick)(<dir>ident("tenx"), <string>const("*.bam")))), <int>assign(memory, <int>builtin(len, <file>ident("bam"))), <int>assign(v, <int>builtin(trace, <int>ident("memory"))), <dir>assign(u, <dir>builtin(trace, <dir>ident("tenx"))) in <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n ")): panic while evaluating <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n "): invalid type
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aad50, 0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aab88, 0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066ba40)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
log.Panicf(0xfb0e4d, 0x20, 0xc4206aad10, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aa9c0, 0xd7a240, 0xc4203355a0)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42048a140)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0xc4203355a0)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
log.Panicf(0xfb0e4d, 0x20, 0xc4206aab48, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066ba40)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
log.Panicf(0xfb0e4d, 0x20, 0xc4206aad10, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
panic: invalid type [recovered]
panic: panic while evaluating <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n "): invalid type
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aad50, 0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
[recovered]
panic: panic while evaluating <(signature file)>block(<(file, string)>assign((bam, _), <(file, string)>apply(<func(dir dir, pattern string) (file, string)>deref(<module{Groups func(dir dir, re string) [string:dir], Make func(map [string:file]) dir, Pick func(dir dir, pattern string) (file, string), Files func(dir dir) [file], Copy func(dir dir, url string) unit, Fileset func(fileset fileset) dir}>ident("dirs"), Pick)(<dir>ident("tenx"), <string>const("*.bam")))), <int>assign(memory, <int>builtin(len, <file>ident("bam"))), <int>assign(v, <int>builtin(trace, <int>ident("memory"))), <dir>assign(u, <dir>builtin(trace, <dir>ident("tenx"))) in <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n ")): panic while evaluating <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n "): invalid type
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aad50, 0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aab88, 0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066ba40)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
log.Panicf(0xfb0e4d, 0x20, 0xc4206aad10, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
[recovered]
panic: panic while evaluating <(signature file)>apply(<func(tenx dir, ksizes string) (signature file)>ident("Compute")(<dir>ident("minimal_tenx_dir"), <string>ident("ksizes"))): panic while evaluating <(signature file)>block(<(file, string)>assign((bam, _), <(file, string)>apply(<func(dir dir, pattern string) (file, string)>deref(<module{Groups func(dir dir, re string) [string:dir], Make func(map [string:file]) dir, Pick func(dir dir, pattern string) (file, string), Files func(dir dir) [file], Copy func(dir dir, url string) unit, Fileset func(fileset fileset) dir}>ident("dirs"), Pick)(<dir>ident("tenx"), <string>const("*.bam")))), <int>assign(memory, <int>builtin(len, <file>ident("bam"))), <int>assign(v, <int>builtin(trace, <int>ident("memory"))), <dir>assign(u, <dir>builtin(trace, <dir>ident("tenx"))) in <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n ")): panic while evaluating <(signature file)>exec(decls(<string>assign(image, <string>ident("kmer_hashing")), <int>assign(mem, <int>ident("memory"))), (signature file), "\n\t\t/opt/conda/bin/sourmash compute \\\n {{protein_flag}} \\\n {{dna_flag}} \\\n --input-is-10x \\\n --processes {{processes}} \\\n --num-hashes {{num_hashes}} \\\n --ksizes {{ksizes}} \\\n --output {{signature}} \\\n {{tenx}}\n "): invalid type
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aad50, 0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aab88, 0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066ba40)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
log.Panicf(0xfb0e4d, 0x20, 0xc4206aad10, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
goroutine 1 [running]:
runtime/debug.Stack(0xc4206aa9c0, 0xd7a240, 0xc4203355a0)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/debug/stack.go:24 +0xa7
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42048a140)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x6e
panic(0xd7a240, 0xc4203355a0)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
log.Panicf(0xfb0e4d, 0x20, 0xc4206aab48, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066ba40)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
log.Panicf(0xfb0e4d, 0x20, 0xc4206aad10, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
goroutine 1 [running]:
log.Panicf(0xfb0e4d, 0x20, 0xc4206aa980, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42048a140)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0xc4203355a0)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
log.Panicf(0xfb0e4d, 0x20, 0xc4206aab48, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066ba40)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0xc420335450)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
log.Panicf(0xfb0e4d, 0x20, 0xc4206aad10, 0x3, 0x3)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/log/log.go:333 +0xda
github.com/grailbio/reflow/syntax.(*Expr).eval.func2(0xc42066b900)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:74 +0x14e
panic(0xd7a240, 0x10a1670)
/Users/marius/.gimme/versions/go1.10.darwin.amd64/src/runtime/panic.go:505 +0x229
github.com/grailbio/reflow/syntax.makeResources.func1(0xf91b65, 0x3, 0x3)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1187 +0x148
github.com/grailbio/reflow/syntax.makeResources(0xc4206ab3e8, 0xf933c1)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1191 +0x68
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066b900, 0xc420485ab0, 0xc420644520, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:269 +0x2455
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42066ba40, 0xc420485ab0, 0xc420644160, 0xc42055c220, 0x1c, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:175 +0xaad
github.com/grailbio/reflow/syntax.closure.Apply(0xc42066bb80, 0xc420485ab0, 0xc420368e60, 0xc42055c220, 0x1c, 0xc42055cd40, 0x1e, 0xc42002fe00, 0x2d, 0xc420644140, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/expr.go:834 +0x1af
github.com/grailbio/reflow/syntax.(*Expr).eval.func5(0xc420335120, 0x1, 0x1, 0xc4201bd890, 0xc42048e360, 0xef9080, 0xc4201bd890)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:153 +0x2c9
github.com/grailbio/reflow/syntax.evalK.Continue(0xfcd018, 0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:1092 +0x657
github.com/grailbio/reflow/syntax.(*Expr).k(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0xc4206406c0, 0xc420335110, 0x1, 0x1, 0xf52040, ...)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:988 +0xa6
github.com/grailbio/reflow/syntax.(*Expr).eval(0xc42048a140, 0xc420485ab0, 0xc420369e60, 0xc42055cd40, 0x1e, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/eval.go:143 +0x14c1
github.com/grailbio/reflow/syntax.(*ModuleImpl).Make(0xc420282a80, 0xc420485ab0, 0xc4201d8180, 0x0, 0x0, 0x0, 0x0)
/Users/marius/go/src/github.com/grailbio/reflow/syntax/module.go:360 +0x4db
github.com/grailbio/reflow/tool.(*Cmd).evalV1(0xc4201ee900, 0xc420485ab0, 0x7ffc8e07906d, 0x27, 0xc4201ce030, 0x8, 0x8, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:130 +0x44b
github.com/grailbio/reflow/tool.(*Cmd).Eval(0xc4201ee900, 0xc4201ce030, 0x8, 0x9, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
/Users/marius/go/src/github.com/grailbio/reflow/tool/eval.go:79 +0x79a
github.com/grailbio/reflow/tool.(*Cmd).run(0xc4201ee900, 0x10ad860, 0xc4203c6bc0, 0xc4201ce020, 0x9, 0x9)
/Users/marius/go/src/github.com/grailbio/reflow/tool/run.go:154 +0x213
github.com/grailbio/reflow/tool.(*Cmd).Main(0xc4201ee900)
/Users/marius/go/src/github.com/grailbio/reflow/tool/main.go:312 +0xbc1
main.main()
/Users/marius/go/src/github.com/grailbio/reflow/cmd/reflow/main.go:64 +0x411
Raw
sourmash_compute_10x.rf
param (
// S3 path to 10x folder
tenx string
// Full s3 file location to put the sourmash signature
output string
// Size of kmer(s) to use
ksizes = "21,33,51"
// Number of kmer hashes to use
num_hashes = 1000
// Calculate protein signature
protein = true
// Calculate DNA signature
dna = true
// Number of processes
processes = 8
)
// Instantiate the system modules "files" (system modules begin
// with $), assigning its instance to the "files" identifier. To
// view the documentation for this module, run "reflow doc
// $/files".
val files = make("$/files")
val dirs = make("$/dirs")
BAM_FILENAME := "possorted_genome_bam.bam"
BARCODES := "barcodes.tsv"
val kmer_hashing = "czbiohub/kmer-hashing"
val protein_flag = if protein { "--protein" } else { "--no-protein" }
val dna_flag = if dna { "--dna" } else { "--no-dna" }
// Compute a minhash signature for a sample
@requires(cpu := processes, disk := GiB)
func Compute(tenx dir, ksizes string) = {
val (bam, _) = dirs.Pick(tenx, "*.bam")
val memory = 2*len(bam)
v := trace(memory)
u := trace(tenx)
exec(image := kmer_hashing, mem := memory) (signature file) {"
/opt/conda/bin/sourmash compute \
{{protein_flag}} \
{{dna_flag}} \
--input-is-10x \
--processes {{processes}} \
--num-hashes {{num_hashes}} \
--ksizes {{ksizes}} \
--output {{signature}} \
{{tenx}}
"}
}
// Instantiate Go system module "strings"
val strings = make("$/strings")
val tenx_folder = dir(tenx)
val (bam, _) = dirs.Pick(tenx_folder, "*.bam")
val (bai, _) = dirs.Pick(tenx_folder, "*.bai")
val (barcodes, _) = dirs.Pick(tenx_folder, BARCODES)
val renamed = map([(BAM_FILENAME, bam),
(BAM_FILENAME + ".bai", bai),
(BARCODES, barcodes)])
val minimal_tenx_dir = dirs.Make(renamed)
val signature = Compute(minimal_tenx_dir, ksizes)
val Main = files.Copy(signature, output)
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