I am running AMR++ pipeline on 177 paired samples. The entirety of the run is successful except that 18 samples fail the runsnp step of the pipeline with the following error in the nextflow output:
[c8/b4aa4e] NOTE: Process STANDARD_AMRplusplus:FASTQ_RESISTOME_WF:runsnp (SRR13495884) terminated with an error exit status (1) -- Error is ignored
and in the .command.err files, they all end with a similar cut error:
...
++ awk -v RS=, '/SRR13495950/{print NR; exit}' AMR_analytic_matrix.csv
+ cut -d , -f AMR_analytic_matrix.csv
cut: invalid byte, character or field list
Try 'cut --help' for more information.
++ kill 60302
This results in those 18 samples missing from the SNPconfirmed_AMR_analytic_matrix.csv file.
A previous run of the pipeline with the same data had 25 samples with this error, and only 3 erroneous samples in common between the two runs. This makes it seem like the error is somewhat random.
I am running AMR++ pipeline on 177 paired samples. The entirety of the run is successful except that 18 samples fail the
runsnpstep of the pipeline with the following error in the nextflow output:and in the
.command.errfiles, they all end with a similarcuterror:This results in those 18 samples missing from the
SNPconfirmed_AMR_analytic_matrix.csvfile.A previous run of the pipeline with the same data had 25 samples with this error, and only 3 erroneous samples in common between the two runs. This makes it seem like the error is somewhat random.