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zjshi / gt-pro

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No output for sample #4

Closed snayfach closed 5 years ago

snayfach commented 5 years ago

Hi Jason,

I've run gtpro using the full kmer database against a sample, but no results are returned. The sample in question is here on the chestnut server: /pollard/shattuck0/snayfach/share/AM45-2_clean_240_100x.fastq

Could you look into the issue?

Thanks, Stephen

zjshi commented 5 years ago

Hi Stephen, I could not reproduce the issue, but I saw it before and I guess it was caused by the 'N' char in read id. It was patched several versions ago, would you please try the newest version to see if the problem still persists, I could also be wrong here.

snayfach commented 5 years ago

git pull Already up-to-date.

gt_pro -d gt-pro2.0/sckmerdb_sp974.bin -t 16 -o gtpro_out/AM45-2/gtpro gtpro_out/AM45-2/AM45-2_clean_240_100x.fastq /global/projectb/scratch/snayfach/projects/mgtyping/gt-pro2.0/gt_pro /global/projectb/scratch/snayfach/projects/mgtyping/gt-pro2.0/sckmerdb_sp974.bin 16 [OK] start to load: /global/projectb/scratch/snayfach/projects/mgtyping/gt-pro2.0/sckmerdb_sp974.bin [Done] 210 seconds elapsed Segmentation fault

snayfach commented 5 years ago

FYI the sample is from an Ion Proton System, not Illumina. These samples consistently failed to run with gtpro. Besides longer read length and higher error rates, I'm not sure what other differences exist

snayfach commented 5 years ago

Samples from Illumina ran to completion without error

zjshi commented 5 years ago

This information is very helpful, thanks! I found it was caused by extra long reads in the dataset, i just pushed a quick fix to the repo, let me know if it solve the problem.