ALIGNMENT PIPELINE ERROR #711
Description
After uploading the Fastq file and ref genome (.gnk), submit the Alignments mission. Then it shows ERROR, and I open the 'bwa_align.error' file and see the following error. I'm not sure what's going on and hope to get your answer.
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The input is probably truncated.
Killed
Segmentation fault (core dumped)
Traceback (most recent call last):
File "/home/ubuntu/millstone/genome_designer/pipeline/read_alignment.py", line 156, in align_with_bwa_mem
opt_processing_mask=opt_processing_mask)
File "/home/ubuntu/millstone/genome_designer/pipeline/read_alignment.py", line 278, in process_sam_bam_file
subprocess.check_call(sort_rmdup_cmd, shell=True, stderr=error_output)
File "/usr/lib/python2.7/subprocess.py", line 540, in check_call
raise CalledProcessError(retcode, cmd)
CalledProcessError: Command '/home/ubuntu/millstone/genome_designer/conf/../tools/samtools/samtools sort -o /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/197f3ad5/alignment_groups/a706a96f/sample_alignments/72eb1c40/bwa_align.bam /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/197f3ad5/alignment_groups/a706a96f/sample_alignments/72eb1c40/bwa_align.sorted.tmp.bam|/home/ubuntu/millstone/genome_designer/conf/../tools/samtools/samtools rmdup - /home/ubuntu/millstone/genome_designer/conf/../temp_data/projects/197f3ad5/alignment_groups/a706a96f/sample_alignments/72eb1c40/bwa_align.sorted.bam' returned non-zero exit status 139
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