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April 16, 2020 19:35
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| $ nextflow run nf-core/rnaseq -profile docker --aligner hisat2 -r 1.4.2 --pseudo_aligner salmon --reads 'data/*_{1,2}_10k.fastq' --reverseStranded --max_cpus 6 --max_memory 32 -c config_bkv.txt | |
| NOTE: Nextflow is not tested with Java 13.0.2 -- It's recommended the use of version 8 up to 12 | |
| N E X T F L O W ~ version 20.01.0 | |
| Launching `nf-core/rnaseq` [cheesy_northcutt] - revision: 3b6df9bd10 [1.4.2] | |
| Extracting transcript fastas from genome fasta + gtf/gff | |
| ---------------------------------------------------- | |
| ,--./,-. | |
| ___ __ __ __ ___ /,-._.--~' | |
| |\ | |__ __ / ` / \ |__) |__ } { | |
| | \| | \__, \__/ | \ |___ \`-._,-`-, | |
| `._,._,' | |
| nf-core/rnaseq v1.4.2 | |
| ---------------------------------------------------- | |
| Pipeline Release : 1.4.2 | |
| Run Name : cheesy_northcutt | |
| Reads : data/*_{1,2}_10k.fastq | |
| Data Type : Paired-End | |
| Strandedness : Reverse | |
| Trimming : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0 / NextSeq Trim: 0 | |
| Aligner : HISAT2 | |
| Fasta Ref : refs/bkv.fa | |
| Pseudo Aligner : Salmon | |
| GTF Annotation : refs/GCF_000837865.1_ViralProj14074_genomic.gtf | |
| Remove Ribosomal RNA: false | |
| Biotype GTF field : gene_biotype | |
| Save prefs : Ref Genome: No / Trimmed FastQ: No / Alignment intermediates: No | |
| Max Resources : 32 memory, 6 cpus, 10d time per job | |
| Container : docker - nfcore/rnaseq:1.4.2 | |
| Output dir : ./results | |
| Launch dir : /Users/pgc92/projects/nextflow_nfcore_rnaseq/bkv | |
| Working dir : /Users/pgc92/projects/nextflow_nfcore_rnaseq/bkv/work | |
| Script dir : /Users/pgc92/.nextflow/assets/nf-core/rnaseq | |
| User : pgc92 | |
| Config Profile : docker | |
| ---------------------------------------------------- | |
| executor > local (12) | |
| [d1/21f419] process > get_software_versions [100%] 1 of 1 ✔ | |
| [98/e74888] process > makeBED12 [100%] 1 of 1 ✔ | |
| [50/08b28c] process > makeHisatSplicesites [100%] 1 of 1 ✔ | |
| [75/0b2dd9] process > makeHISATindex [100%] 1 of 1 ✔ | |
| [aa/e720f4] process > transcriptsToFasta [100%] 1 of 1 ✔ | |
| [f1/0491d4] process > makeSalmonIndex [100%] 1 of 1 ✔ | |
| [57/2acf16] process > fastqc [100%] 1 of 1 ✔ | |
| [97/26f5e8] process > trim_galore [100%] 1 of 1 ✔ | |
| [9e/24debe] process > hisat2Align [100%] 1 of 1 ✔ | |
| [2c/47d31b] process > hisat2_sortOutput [ 0%] 0 of 1 | |
| [- ] process > rseqc - | |
| [- ] process > preseq - | |
| [- ] process > markDuplicates - | |
| [- ] process > qualimap - | |
| [- ] process > dupradar - | |
| [- ] process > featureCounts - | |
| [- ] process > merge_featureCounts - | |
| [- ] process > stringtieFPKM - | |
| [- ] process > sample_correlation - | |
| [03/39dd7c] process > salmon [ 0%] 0 of 1 | |
| [- ] process > salmon_tx2gene - | |
| [- ] process > salmon_tximport - | |
| [- ] process > salmon_merge - | |
| [- ] process > multiqc - | |
| [95/7e7e17] process > output_documentation [100%] 1 of 1 ✔ | |
| [HISAT2 index build] Available memory: 32 B | |
| [HISAT2 index build] Less than 200 GB available, so NOT using splice sites and exons in HISAT2 index. | |
| executor > local (12) | |
| [d1/21f419] process > get_software_versions [100%] 1 of 1 ✔ | |
| [98/e74888] process > makeBED12 [100%] 1 of 1 ✔ | |
| [50/08b28c] process > makeHisatSplicesites [100%] 1 of 1 ✔ | |
| [75/0b2dd9] process > makeHISATindex [100%] 1 of 1 ✔ | |
| [aa/e720f4] process > transcriptsToFasta [100%] 1 of 1 ✔ | |
| [f1/0491d4] process > makeSalmonIndex [100%] 1 of 1 ✔ | |
| [57/2acf16] process > fastqc [100%] 1 of 1 ✔ | |
| [97/26f5e8] process > trim_galore [100%] 1 of 1 ✔ | |
| [9e/24debe] process > hisat2Align [100%] 1 of 1 ✔ | |
| [- ] process > hisat2_sortOutput - | |
| [- ] process > rseqc - | |
| [- ] process > preseq - | |
| [- ] process > markDuplicates - | |
| [- ] process > qualimap - | |
| [- ] process > dupradar - | |
| [- ] process > featureCounts - | |
| [- ] process > merge_featureCounts - | |
| [- ] process > stringtieFPKM - | |
| [- ] process > sample_correlation - | |
| [03/39dd7c] process > salmon [100%] 1 of 1, failed: 1 ✘ | |
| [- ] process > salmon_tx2gene - | |
| [- ] process > salmon_tximport - | |
| [- ] process > salmon_merge - | |
| [- ] process > multiqc - | |
| [95/7e7e17] process > output_documentation [100%] 1 of 1 ✔ | |
| [HISAT2 index build] Available memory: 32 B | |
| [HISAT2 index build] Less than 200 GB available, so NOT using splice sites and exons in HISAT2 index. | |
| [HISAT2 index build] Use --hisat_build_memory [small number] to skip this check. | |
| [0;35m[nf-core/rnaseq] Pipeline completed with errors | |
| executor > local (12) | |
| [d1/21f419] process > get_software_versions [100%] 1 of 1 ✔ | |
| [98/e74888] process > makeBED12 [100%] 1 of 1 ✔ | |
| [50/08b28c] process > makeHisatSplicesites [100%] 1 of 1 ✔ | |
| [75/0b2dd9] process > makeHISATindex [100%] 1 of 1 ✔ | |
| [aa/e720f4] process > transcriptsToFasta [100%] 1 of 1 ✔ | |
| [f1/0491d4] process > makeSalmonIndex [100%] 1 of 1 ✔ | |
| [57/2acf16] process > fastqc [100%] 1 of 1 ✔ | |
| [97/26f5e8] process > trim_galore [100%] 1 of 1 ✔ | |
| [9e/24debe] process > hisat2Align [100%] 1 of 1 ✔ | |
| [- ] process > hisat2_sortOutput - | |
| [- ] process > rseqc - | |
| [- ] process > preseq - | |
| [- ] process > markDuplicates - | |
| [- ] process > qualimap - | |
| [- ] process > dupradar - | |
| [- ] process > featureCounts - | |
| [- ] process > merge_featureCounts - | |
| [- ] process > stringtieFPKM - | |
| [- ] process > sample_correlation - | |
| [03/39dd7c] process > salmon [100%] 1 of 1, failed: 1 ✘ | |
| [- ] process > salmon_tx2gene - | |
| [- ] process > salmon_tximport - | |
| [- ] process > salmon_merge - | |
| [- ] process > multiqc - | |
| [95/7e7e17] process > output_documentation [100%] 1 of 1 ✔ | |
| [HISAT2 index build] Available memory: 32 B | |
| [HISAT2 index build] Less than 200 GB available, so NOT using splice sites and exons in HISAT2 index. | |
| [HISAT2 index build] Use --hisat_build_memory [small number] to skip this check. | |
| [0;35m[nf-core/rnaseq] Pipeline completed with errors | |
| WARN: Killing pending tasks (1) | |
| WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info. | |
| Error executing process > 'salmon (SRR11074361)' | |
| Caused by: | |
| Process `salmon (SRR11074361)` terminated with an error exit status (1) | |
| Command executed: | |
| salmon quant --validateMappings \ | |
| --seqBias --useVBOpt --gcBias \ | |
| --geneMap GCF_000837865.1_ViralProj14074_genomic.gtf \ | |
| --threads 6 \ | |
| --libType=ISR \ | |
| --index salmon_index \ | |
| -1 SRR11074361_1_10k_val_1.fq.gz -2 SRR11074361_2_10k_val_2.fq.gz \ | |
| -o SRR11074361 | |
| Command exit status: | |
| 1 | |
| Command output: | |
| (empty) | |
| Command error: | |
| Version Info: ### PLEASE UPGRADE SALMON ### | |
| ### A newer version of salmon with bug fixes is available. #### | |
| ### | |
| The newest version, available at https://github.com/COMBINE-lab/salmon/releases | |
| contains new features, improvements, and bug fixes; please upgrade at your | |
| earliest convenience. | |
| ### | |
| Sign up for the salmon mailing list to hear about new versions, features and updates at: | |
| https://oceangenomics.com/subscribe | |
| ### | |
| ### salmon (mapping-based) v0.14.1 | |
| ### [ program ] => salmon | |
| ### [ command ] => quant | |
| ### [ validateMappings ] => { } | |
| ### [ seqBias ] => { } | |
| ### [ useVBOpt ] => { } | |
| ### [ gcBias ] => { } | |
| ### [ geneMap ] => { GCF_000837865.1_ViralProj14074_genomic.gtf } | |
| ### [ threads ] => { 6 } | |
| ### [ libType ] => { ISR } | |
| ### [ index ] => { salmon_index } | |
| ### [ mates1 ] => { SRR11074361_1_10k_val_1.fq.gz } | |
| ### [ mates2 ] => { SRR11074361_2_10k_val_2.fq.gz } | |
| ### [ output ] => { SRR11074361 } | |
| Logs will be written to SRR11074361/logs | |
| [2020-04-16 19:34:49.898] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. | |
| [2020-04-16 19:34:49.898] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 | |
| [2020-04-16 19:34:49.898] [jointLog] [info] Usage of --validateMappings, without --hardFilter implies use of range factorization. rangeFactorizationBins is being set to 4 | |
| [2020-04-16 19:34:49.898] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.2. | |
| [2020-04-16 19:34:49.898] [jointLog] [info] parsing read library format | |
| [2020-04-16 19:34:49.898] [jointLog] [info] There is 1 library. | |
| [2020-04-16 19:34:49.965] [stderrLog] [info] Loading Suffix Array | |
| [2020-04-16 19:34:49.960] [jointLog] [info] Loading Quasi index | |
| [2020-04-16 19:34:49.963] [jointLog] [info] Loading 32-bit quasi index | |
| [2020-04-16 19:34:49.970] [jointLog] [info] done | |
| [2020-04-16 19:34:49.970] [jointLog] [info] Index contained 2 targets | |
| [2020-04-16 19:34:49.968] [stderrLog] [info] Loading Transcript Info | |
| [2020-04-16 19:34:49.970] [stderrLog] [info] Loading Rank-Select Bit Array | |
| [2020-04-16 19:34:49.970] [stderrLog] [info] There were 2 set bits in the bit array | |
| [2020-04-16 19:34:49.970] [stderrLog] [info] Computing transcript lengths | |
| [2020-04-16 19:34:49.970] [stderrLog] [info] Waiting to finish loading hash | |
| [2020-04-16 19:34:49.970] [stderrLog] [info] Done loading index | |
| [2020-04-16 19:34:50.075] [jointLog] [warning] salmon was only able to assign 5 fragments to transcripts in the index, but the minimum number of required assigned fragments (--minAssignedFrags) was 10. This could be indicative of a mismatch between the reference and sample, or a very bad sample. You can change the --minAssignedFrags parameter to force salmon to quantify with fewer assigned fragments (must have at least 1). | |
| Work dir: | |
| /Users/pgc92/projects/nextflow_nfcore_rnaseq/bkv/work/03/39dd7c9568dfcf40e23ad037295928 | |
| Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` |
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