search

jlab-code / MethylStar

A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
GNU General Public License v3.0
30 stars 6 forks source link

Error: samtools broken pipe #17

Closed devenderarora closed 2 years ago

devenderarora commented 2 years ago

Dear Sir, I am running deduplication step and encountered the error reported in log file:

Output will be written into the directory: /520_info1/project/arora/2.pig/wgbs/wg/bismark-deduplicate/ Processing paired-end Bismark output file(s) (SAM format): /520_info1/project/arora/2.pig/wgbs/wg/bismark-mappers/1_6.bam

If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

Checking file >>/520_info1/project/arora/2.pig/wgbs/wg/bismark-mappers/1_6.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1

Now testing Bismark result file /520_info1/project/arora/2.pig/wgbs/wg/bismark-mappers/1_6.bam for positional sorting (which would be bad...) ...passed! Output file is: 1_6.deduplicated.bam

skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:1 LN:274330532 skipping header line: @SQ SN:2 LN:151935994

Although this finally output bam file but while running bismark-meth extractor I again encountered with:

samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1

May I know what wrong going on with the steps. I am running with samtools 1.14 version.

devenderarora commented 2 years ago

Fixed the issue with older version of samtools.