error "unrecognized CIGAR operator" when run gemBS map

[fyymxb]

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]

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 ***@***.***> 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 <#66?email_source=notifications&email_token=AAY4655WTKLFPJFFXMP2ZHLQTTODRA5CNFSM4JNGAOI2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HZGXNGA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAY4654GGQXCJMO3TVAXVELQTTODRANCNFSM4JNGAOIQ> .