runsnp failing in AMRplusplus with error from AMRplusplus_SNP script

[LLansing]

Reposting an issue I raised on the AMRplusplus repository:

I have ran AMRplusplus and I noticed 3 samples missing from the SNPconfirmed_AMR_analytic_matrix.csv. The 3 missing samples all failed during the run, showing the following message:

[88/801dcb] NOTE: Process STANDARD_AMRplusplus:FASTQ_RESISTOME_WF:runsnp (CRA02e_t2_M) terminated with an error exit status (1) -- Error is ignored [98/073afc] NOTE: Process STANDARD_AMRplusplus:FASTQ_RESISTOME_WF:runsnp (CRA01e_t2_M) terminated with an error exit status (1) -- Error is ignored [5d/62f34d] NOTE: Process STANDARD_AMRplusplus:FASTQ_RESISTOME_WF:runsnp (CRA03u_t2_M) terminated with an error exit status (1) -- Error is ignored

And each show a similar error in the .command.err files:

+ nxf_launch + /bin/bash -uex /AMRplusplus/work/88/801dcb26e38a048e368ce895f969f3/.command.sh + cp -r /AMRplusplus/bin/AmrPlusPlus_SNP/config.ini /AMRplusplus/bin/AmrPlusPlus_SNP/data /AMRplusplus/bin/AmrPlusPlus_SNP/genes-issues.md /AMRplusplus/bin/AmrPlusPlus_SNP/LICENSE /AMRplusplus/bin/AmrPlusPlus_SNP/README.md /AMRplusplus/bin/AmrPlusPlus_SNP/SNP_Verification_Processes /AMRplusplus/bin/AmrPlusPlus_SNP/SNP_Verification.py /AMRplusplus/bin/AmrPlusPlus_SNP/SNP_Verification_Tools /AMRplusplus/bin/AmrPlusPlus_SNP/usage.md . + python3 SNP_Verification.py -c config.ini -a -i CRA02e_t2_M.alignment.sam -o CRA02e_t2_M_AMR_SNPs --count_matrix AMR_analytic_matrix.csv Traceback (most recent call last): File "/AMRplusplus/work/88/801dcb26e38a048e368ce895f969f3/SNP_Verification.py", line 213, in verify(read, gene, config) File "/AMRplusplus/work/88/801dcb26e38a048e368ce895f969f3/SNP_Verification_Processes/init.py", line 26, in verify checkResult = NonsenseCheck(read, gene, mapOfInterest, seqOfInterest) #Checks for nonsense previously found in literature and for new nonsense File "/AMRplusplus/work/88/801dcb26e38a048e368ce895f969f3/SNP_Verification_Processes/NonsenseCheck.py", line 9, in NonsenseCheck return verifyNonsense(read, gene, stopLocation, mapOfInterest) File "/AMRplusplus/work/88/801dcb26e38a048e368ce895f969f3/SNP_Verification_Processes/NonsenseCheck.py", line 37, in verifyNonsense findNonsenseLocation() File "/AMRplusplus/work/88/801dcb26e38a048e368ce895f969f3/SNP_Verification_Processes/NonsenseCheck.py", line 24, in findNonsenseLocation elif stopLocation < queryIndex: TypeError: '<' not supported between instances of 'int' and 'str'

Originally posted by @LLansing in https://github.com/Microbial-Ecology-Group/AMRplusplus/issues/2#issuecomment-1292779248

[Isabella136]

Hi @LLansing Thanks for reporting this issue. I believe that the new changes I've made should fix the problem. Let me know if you run into the same or any other issues.

Best, Nathalie

[LLansing]

@Isabella136 this fix seems to have solved my error, thank you!