Closed tdelisper closed 10 months ago
If you are running multiple samples, do other samples work?
Could you check you input input/SRR8375411_?.fastq.gz
Are both files valid gzip files with the same number of lines?
Also if you could supply your project.yaml config, that might be helpful.
EOY cleanup. Please feel free to re-open.
Hello, I am running a Bulk RNA-seq analysis using STAR and hg38 and I have this error during alignment:
File "/mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/anaconda/lib/python3.7/site-packages/bcbio/distributed/ipythontasks.py", line 54, in _setup_logging yield config File "/mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/anaconda/lib/python3.7/site-packages/bcbio/distributed/ipythontasks.py", line 300, in process_alignment return ipython.zip_args(apply(sample.process_alignment, args)) File "/mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/anaconda/lib/python3.7/site-packages/bcbio/distributed/ipythontasks.py", line 82, in apply return object(args, kwargs) File "/mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/sample.py", line 140, in process_alignment data = align_to_sort_bam(fastq1, fastq2, aligner, data) File "/mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/alignment.py", line 87, in align_to_sort_bam names, align_dir, data) File "/mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/alignment.py", line 164, in _align_from_fastq out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data) File "/mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/anaconda/lib/python3.7/site-packages/bcbio/ngsalign/star.py", line 118, in align do.run(cmd.format(locals()), run_message, None) File "/mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/anaconda/lib/python3.7/site-packages/bcbio/provenance/do.py", line 26, in run _do_run(cmd, checks, log_stdout, env=env) File "/mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/anaconda/lib/python3.7/site-packages/bcbio/provenance/do.py", line 106, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) subprocess.CalledProcessError: Command 'set -o pipefail; /mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/galaxy/../anaconda/bin/STAR --genomeDir /mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/genomes/Hsapiens/hg38/star/ --readFilesIn <(gunzip -c /mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/ALS_GSE124439/bcbio/SraRunTable-124439/input/SRR8375411_1.fastq.gz) <(gunzip -c /mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/ALS_GSE124439/bcbio/SraRunTable-124439/input/SRR8375411_2.fastq.gz) --runThreadN 16 --outFileNamePrefix /mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/ALS_GSE124439/bcbio/SraRunTable-124439/work/bcbiotx/tmpngmy3f66/SRR83754111pass/SRR8375411 --outReadsUnmapped Fastx --outFilterMultimapNmax 10 --outStd BAM_Unsorted --limitOutSJcollapsed 2000000 --outSAMtype BAM Unsorted --outSAMmapqUnique 60 --outSAMunmapped Within --outSAMattributes NH HI NM MD AS --sjdbGTFfile /mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/genomes/Hsapiens/hg38/rnaseq/ref-transcripts.gtf --sjdbOverhang 124 --outSAMattrRGline ID:SRR8375411 PL:illumina PU:SRR8375411 SM:SRR8375411 --quantMode TranscriptomeSAM | /mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 2G -T /mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/ALS_GSE124439/bcbio/SraRunTable-124439/work/bcbiotx/tmpngmy3f66/SRR83754111pass/SRR8375411_star/SRR8375411-sorttmp -o /mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/ALS_GSE124439/bcbio/SraRunTable-124439/work/bcbiotx/tmpngmy3f66/SRR83754111pass/SRR8375411_star/SRR8375411.bam /dev/stdin > /mnt/hcctcga_a/groups/hcctcga/lab_members/tdelisper/ALS_GSE124439/bcbio/SraRunTable-124439/work/bcbiotx/tmpngmy3f66/SRR83754111pass/SRR8375411_star/SRR8375411.bam [W::bgzf_read_block] EOF marker is absent. The input may be truncated samtools sort: truncated file. Aborting ' returned non-zero exit status 1.
Probably the error occurs during the generation of BAM file. Any suggestion of how to solve it?
Thank you, Triantafyllos