CIGAR and sequence length are inconsistent

[Unaimend]

So I got this error while assembling a dataset, could some tell me how to investigate the source of this error?

[main] Version: 0.7.10-r789
[main] CMD: /scratch/SlurmTMP/sukem127.571191/OPERA-MS//tools_opera_ms/bwa index -p /scratch/SlurmTMP/sukem127.571191/RESULTS//intermediate_files/coverage_estimation/final.contigs.fa /scratch/SlurmTMP/sukem127.571191/RESULTS/intermediate_files/megahit_assembly/final.contigs.fa
[main] Real time: 698.433 sec; CPU: 687.584 sec
[M::main_mem] read 1333334 sequences (200000100 bp)...
[M::mem_process_seqs] Processed 1333334 reads in 246.059 CPU sec, 12.599 real sec
[samopen] SAM header is present: 189153 sequences.
Line 251087, sequence length 101 vs 150 from CIGAR
Parse error at line 251087: CIGAR and sequence length are inconsistent

[jsgounot]

Hi,

thanks for using OPERA-MS. I will need some materials to investigate this. Do you mind sharing the opera-ms command line which led to this result ? Additionally, could you run this script with your result folder as argument and send me the logs archive ?

Regards,
Jean-Sebastien

[Unaimend]

Thanks for your quick reply
Here is the command line
perl OPERA-MS/OPERA-MS.pl
--short-read1 $_my_first_read
--short-read2 $_my_second_read
--long-read $_my_long_read
--no-ref-clustering
--num-processors 30
--out-dir RESULTS 2> log.err

Regards,
Thomas Dost

[Unaimend]

OPERA-MS-LOG.tar.gz

And here are the requested log files

[jsgounot]

Hi, sorry for the very long reply. Were you able to find a solution to this issue ?

[Unaimend]

No, I did not investigate this issue any further since I was not able to generate "good" reads with PbSim. After switching to badreads I did not have any problems. But I will look into after finishing my Bachelor Thesis.