search

heathsc / gemBS

gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).
GNU General Public License v3.0
32 stars 21 forks source link

error "unrecognized CIGAR operator" when run gemBS map #66

Open fyymxb opened 4 years ago

fyymxb commented 4 years ago

Hello, For some data sets, I occasionally met error error "unrecognized CIGAR operator" when run gemBS map. The debug imformation is as follows: Bisulfite Mapping... 2019-11-14 10:16:56,579 DEBUG: Using bundled binary : /home/XUB/.local/lib/python3.6/site-packages/gemBS/gemBSbinaries/gem-mapper 2019-11-14 10:16:56,580 DEBUG: Using bundled binary : /home/XUB/.local/lib/python3.6/site-packages/gemBS/gemBSbinaries/readNameClean 2019-11-14 10:16:56,580 DEBUG: Using bundled binary : /home/XUB/.local/lib/python3.6/site-packages/gemBS/bin/samtools 2019-11-14 10:16:56,581 INFO: Starting: /home/XUB/.local/lib/python3.6/site-packages/gemBS/gemBSbinaries/gem-mapper -I ./../indexes/ucsc.hg19.BS.gem --i1 /public/data/cfNDA-methylation/20190929_HTLM5DSXX-X101SC19090311-Z01_Result/Rawdata/ori-lib6-18-cfDNA_L3_1.fq.gz --i2 /public/data/cfNDA-methylation/20190929_HTLM5DSXX-X101SC19090311-Z01_Result/Rawdata/ori-lib6-18-cfDNA_L3_2.fq.gz -p --bisulfite-conversion inferred-C2T-G2A -t 48 --report-file ./mapping/18_cfDNA/18.json -r @RG\tID:18\tSM:\tBC:18_cfDNA\tPU:18 | /home/XUB/.local/lib/python3.6/site-packages/gemBS/gemBSbinaries/readNameClean | /home/XUB/.local/lib/python3.6/site-packages/gemBS/bin/samtools sort -T ./mapping/18_cfDNA/18 -@ 48 -o ./mapping/18_cfDNA/18_cfDNA.bam - 2019-11-14 10:16:56,581 DEBUG: Setting process log file to ./mapping/18_cfDNA/gem_mapper_18.err 2019-11-14 10:16:56,581 DEBUG: Starting subprocess 2019-11-14 10:16:56,585 DEBUG: Setting process log file to ./mapping/18_cfDNA/gem_mapper_18.err 2019-11-14 10:16:56,586 DEBUG: Setting process input to parent output 2019-11-14 10:16:56,586 DEBUG: Starting subprocess 2019-11-14 10:16:56,590 DEBUG: Setting process log file to ./mapping/18_cfDNA/gem_mapper_18.err 2019-11-14 10:16:56,590 DEBUG: Setting process input to parent output 2019-11-14 10:16:56,590 DEBUG: Starting subprocess 2019-11-14 11:17:29,856 DEBUG: Process '/home/XUB/.local/lib/python3.6/site-packages/gemBS/bin/samtools' finished with 1 2019-11-14 11:17:29,857 ERROR: Process '/home/XUB/.local/lib/python3.6/site-packages/gemBS/bin/samtools' finished with 1 2019-11-14 11:17:29,858 ERROR: [E::sam_parse1] unrecognized CIGAR operator 2019-11-14 11:17:29,858 ERROR: [W::sam_read1] Parse error at line 537509071 2019-11-14 11:17:29,858 ERROR: samtools sort: truncated file. Aborting The version of gemBS is 3.3.3. But for some other data sets, it can be mapped successfully.

Bo

heathsc commented 4 years ago

Would it be possible to get a (ideally small) FASTQ pair that shows this problem that you could share with me?

Thanks, Simon

On Thu, Nov 14, 2019 at 6:23 AM fyymxb notifications@github.com wrote:

Hello, For some data sets, I occasionally met error error "unrecognized CIGAR operator" when run gemBS map. The debug imformation is as follows: Bisulfite Mapping... 2019-11-14 10:16:56,579 DEBUG: Using bundled binary : /home/XUB/.local/lib/python3.6/site-packages/gemBS/gemBSbinaries/gem-mapper 2019-11-14 10:16:56,580 DEBUG: Using bundled binary : /home/XUB/.local/lib/python3.6/site-packages/gemBS/gemBSbinaries/readNameClean 2019-11-14 10:16:56,580 DEBUG: Using bundled binary : /home/XUB/.local/lib/python3.6/site-packages/gemBS/bin/samtools 2019-11-14 10:16:56,581 INFO: Starting: /home/XUB/.local/lib/python3.6/site-packages/gemBS/gemBSbinaries/gem-mapper -I ./../indexes/ucsc.hg19.BS.gem --i1 /public/data/cfNDA-methylation/20190929_HTLM5DSXX-X101SC19090311-Z01_Result/Rawdata/ori-lib6-18-cfDNA_L3_1.fq.gz --i2 /public/data/cfNDA-methylation/20190929_HTLM5DSXX-X101SC19090311-Z01_Result/Rawdata/ori-lib6-18-cfDNA_L3_2.fq.gz -p --bisulfite-conversion inferred-C2T-G2A -t 48 --report-file ./mapping/18_cfDNA/18.json -r @rg https://github.com/rg\tID:18\tSM:\tBC:18_cfDNA\tPU:18 | /home/XUB/.local/lib/python3.6/site-packages/gemBS/gemBSbinaries/readNameClean | /home/XUB/.local/lib/python3.6/site-packages/gemBS/bin/samtools sort -T ./mapping/18_cfDNA/18 -@ 48 -o ./mapping/18_cfDNA/18_cfDNA.bam - 2019-11-14 10:16:56,581 DEBUG: Setting process log file to ./mapping/18_cfDNA/gem_mapper_18.err 2019-11-14 10:16:56,581 DEBUG: Starting subprocess 2019-11-14 10:16:56,585 DEBUG: Setting process log file to ./mapping/18_cfDNA/gem_mapper_18.err 2019-11-14 10:16:56,586 DEBUG: Setting process input to parent output 2019-11-14 10:16:56,586 DEBUG: Starting subprocess 2019-11-14 10:16:56,590 DEBUG: Setting process log file to ./mapping/18_cfDNA/gem_mapper_18.err 2019-11-14 10:16:56,590 DEBUG: Setting process input to parent output 2019-11-14 10:16:56,590 DEBUG: Starting subprocess 2019-11-14 11:17:29,856 DEBUG: Process '/home/XUB/.local/lib/python3.6/site-packages/gemBS/bin/samtools' finished with 1 2019-11-14 11:17:29,857 ERROR: Process '/home/XUB/.local/lib/python3.6/site-packages/gemBS/bin/samtools' finished with 1 2019-11-14 11:17:29,858 ERROR: [E::sam_parse1] unrecognized CIGAR operator 2019-11-14 11:17:29,858 ERROR: [W::sam_read1] Parse error at line 537509071 2019-11-14 11:17:29,858 ERROR: samtools sort: truncated file. Aborting The version of gemBS is 3.3.3. But for some other data sets, it can be mapped successfully.

Bo

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/heathsc/gemBS/issues/66?email_source=notifications&email_token=AAY4655WTKLFPJFFXMP2ZHLQTTODRA5CNFSM4JNGAOI2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HZGXNGA, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAY4654GGQXCJMO3TVAXVELQTTODRANCNFSM4JNGAOIQ .