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pcantalupo/gist:f399e5952d9c73e02166cf4ecffeae86

Created July 27, 2020 12:03
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gistfile1.txt
$ nextflow run nf-core/rnaseq -c myconfig.config --pseudo_aligner salmon -r dev --reads 'reads/*_tu_KAM56A3_S17.{1,2}.fq.gz' --reverseStranded --fasta GRCh38.d1.vd1.fa --gtf gencode.v22.annotation.gtf --skipBiotypeQC --removeRiboRNA -resume
N E X T F L O W ~ version 20.04.1
Launching `nf-core/rnaseq` [distracted_wiles] - revision: e14e0d4912 [dev]
WARN: It appears you have never run this project before -- Option `-resume` is ignored
Extracting transcript fastas from genome fasta + gtf/gff
WARN: The `into` operator should be used to connect two or more target channels -- consider to replace it with `.set { gtfFile }`
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/rnaseq v1.4.3dev
----------------------------------------------------
Pipeline Release : dev
Run Name : distracted_wiles
Reads : reads/*_tu_KAM56A3_S17.{1,2}.fq.gz
Data Type : Paired-End
Strandedness : Reverse
Trimming : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0 / NextSeq Trim: 0
Aligner : STAR
Fasta Ref : GRCh38.d1.vd1.fa
Pseudo Aligner : Salmon
GTF Annotation : gencode.v22.annotation.gtf
Remove Ribosomal RNA: true
Biotype GTF field : gene_biotype
Save prefs : Ref Genome: No / Trimmed FastQ: No / Alignment intermediates: No
Max Resources : 128 GB memory, 16 cpus, 10d time per job
Container : singularity - nfcore/rnaseq:dev
Output dir : ./results
Launch dir : /zfs1/uchandran/pgc92/projects/murphy_rnaseq/run3
Working dir : /zfs1/uchandran/pgc92/projects/murphy_rnaseq/run3/work
Script dir : /ihome/uchandran/pgc92/.nextflow/assets/nf-core/rnaseq
User : pgc92
Config Profile : standard
----------------------------------------------------
[- ] process > get_software_versions -
[- ] process > get_software_versions -
[- ] process > get_software_versions [ 0%] 0 of 1
[- ] process > get_software_versions [ 0%] 0 of 1
[- ] process > get_software_versions [ 0%] 0 of 1
executor > slurm (1)
executor > slurm (2)
executor > slurm (3)
executor > slurm (4)
executor > slurm (5)
executor > slurm (6)
executor > slurm (7)
executor > slurm (7)
executor > slurm (8)
executor > slurm (9)
executor > slurm (10)
executor > slurm (11)
executor > slurm (12)
executor > slurm (13)
executor > slurm (14)
executor > slurm (15)
executor > slurm (16)
executor > slurm (20)
executor > slurm (21)
executor > slurm (32)
[a0/f3a45e] process > get_software_versions [100%] 1 of 1 ✔
[56/4bdfae] process > makeBED12 (gencode.v22.annotation.gtf) [100%] 1 of 1 ✔
[04/7ed6ba] process > makeSTARindex (GRCh38.d1.vd1.fa) [100%] 1 of 1 ✔
[fd/b864b9] process > makeRSEMReference (GRCh38.d1.vd1.fa) [100%] 1 of 1 ✔
[e4/fe2ce5] process > transcriptsToFasta (GRCh38.d1.vd1.fa) [100%] 1 of 1 ✔
[dd/288bc4] process > makeSalmonIndex (transcripts.fa) [100%] 1 of 1 ✔
[35/4d5a07] process > fastqc (TPF-18-103) [100%] 1 of 1 ✔
[a0/9057a2] process > trim_galore (TPF-18-103) [100%] 1 of 1 ✔
[30/b0c65e] process > sortmerna_index (silva-bac-16s-id90) [100%] 8 of 8 ✔
[50/ac1806] process > sortmerna (TPF-18-103) [100%] 1 of 1 ✔
[6d/ec36dd] process > star (TPF-18-103) [100%] 1 of 1 ✔
[7f/ae84c5] process > rseqc (TPF-18-103-fwAlignedByCoord.out) [100%] 1 of 1 ✔
[de/15c90f] process > preseq (TPF-18-103-fwAlignedByCoord.out) [100%] 1 of 1 ✔
[f6/0ce538] process > markDuplicates (TPF-18-103-fwAlignedByCoord.out) [100%] 1 of 1 ✔
[52/6d4efb] process > qualimap (TPF-18-103-fwAligned.sortedByCoord.out) [100%] 1 of 1 ✔
[37/cd48f4] process > dupradar (TPF-18-103-fwAligned.sortedByCoord.out.markDups) [100%] 1 of 1 ✔
[70/6803c9] process > featureCounts (TPF-18-103-fwAlignedByCoord.out) [100%] 1 of 1 ✔
[9f/49ed41] process > merge_featureCounts (TPF-18-103-fwAlignedByCoord.out_gene.featureCounts) [100%] 1 of 1 ✔
[af/11a5c0] process > rsem (TPF-18-103-fwAligned.toTranscriptome.out) [100%] 1 of 1 ✔
[- ] process > merge_rsem_genes -
[df/516d60] process > stringtieFPKM (TPF-18-103-fwAlignedByCoord.out) [100%] 1 of 1 ✔
[- ] process > sample_correlation -
[75/e6b738] process > salmon (TPF-18-103) [100%] 1 of 1 ✔
[15/d33931] process > salmon_tx2gene (1) [100%] 1 of 1 ✔
[41/6fdc2e] process > salmon_tximport (1) [100%] 1 of 1 ✔
[5b/d99001] process > salmon_merge (1) [100%] 1 of 1 ✔
[- ] process > multiqc [ 0%] 0 of 1
[05/856fed] process > output_documentation [100%] 1 of 1 ✔
[nf-core/rnaseq] 1/1 samples passed minimum 5% aligned check
TPF-18-103-fw: 94.02%
[nf-core/rnaseq] Pipeline completed with errors
Error executing process > 'merge_rsem_genes (TPF-18-103-fw.genes)'
Caused by:
No signature of method: nextflow.processor.TaskPath.get() is applicable for argument types: (Integer) values: [0]
Possible solutions: getAt(int), grep(), head(int), getAt(java.lang.String), grep(java.lang.Object), wait()
Source block:
"""
echo "gene_id\tgene_symbol" > gene_ids.txt
echo "transcript_id\tgene_symbol" > transcript_ids.txt
cut -f 1 ${rsem_res_gene.get(0)} | grep -v "^#" | tail -n+2 | sed -E "s/(_PAR_Y)?(_|\$)/\\1\\t/" >> gene_ids.txt
cut -f 1 ${rsem_res_isoform.get(0)} | grep -v "^#" | tail -n+2 | sed -E "s/(_PAR_Y)?(_|\$)/\\1\\t/" >> transcript_ids.txt
mkdir tmp_genes tmp_isoforms
for fileid in $rsem_res_gene; do
basename \$fileid | sed s/\\.genes.results\$//g > tmp_genes/\${fileid}.tpm.txt
grep -v "^#" \${fileid} | cut -f 5 | tail -n+2 >> tmp_genes/\${fileid}.tpm.txt
done
for fileid in $rsem_res_isoform; do
basename \$fileid | sed s/\\.isoforms.results\$//g > tmp_isoforms/\${fileid}.tpm.txt
grep -v "^#" \${fileid} | cut -f 5 | tail -n+2 >> tmp_isoforms/\${fileid}.tpm.txt
done
paste gene_ids.txt tmp_genes/*.tpm.txt > rsem_tpm_gene.txt
paste transcript_ids.txt tmp_isoforms/*.tpm.txt > rsem_tpm_isoform.txt
"""
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
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