runsnp failing

[LLansing]

Nextflow output shows this message for failed runsnp job: [2e/4888ce] NOTE: Process `STANDARD_AMRplusplus_wKraken:FASTQ_RESISTOME_WF:runsnp (NS.1508.003.IDT_i7_165---IDT_i5_165.COR05e_t2_M)\` terminated with an error exit status (1) -- Error is ignored

and the .command.err file shows the following (with absolute paths censored by me after the fact):

+ nxf_launch + /bin/bash -uex /isilon/lacombe-rdc/users/tranlan/amrplusplus/AMRplusplus/work/2e/4888ce3a02f09dbe5aa8aba2b60194/.command.sh + python3 AmrPlusPlus_SNP/SNP_Verification.py -i NS.1508.003.IDT_i7_165---IDT_i5_165.COR05e_t2_M.amr.alignment.sam -o NS.1508.003.IDT_i7_165---IDT_i5_165.COR05e_t2_M_SNPs Traceback (most recent call last): File "/AMRplusplus/work/2e/4888ce3a02f09dbe5aa8aba2b60194/AmrPlusPlus_SNP/SNP_Verification.py", line 110, in config['SOURCE_FILES']['SAM_INPUT'] = arg File "/python-09679a002b117b56bcf8ad7be35338e2/lib/python3.9/configparser.py", line 963, in getitem raise KeyError(key) KeyError: 'SOURCE_FILES'

Fail location in AmrPlusPlus_SNP My amateur suggestion is that the problem is the following:

• the SNP_Verification.py script is expecting to be ran from within the AmrPlusPlus_SNP directory, and as such tries to read the configFile 'config.ini' path with such an expectation. I suspect that the runsnp process calls the SNP_Verification.py script from a higher directory, based on line 105 in resistome.nf

If this is the cause of the problem, I'm not sure I can patch a solution myself and, if this is not the cause of the problem, I'm even more lost.

Thanks for your help

[EnriqueDoster]

Hi @LLansing ,

Thanks for reporting this and providing a useful suggestion! We had to make a few updates to make things work again due to the requirement from AmrPlusPlus_SNP that the command needs to be run within the main directory. We patched something together now that, while not the prettiest code, will work to get the SNP verification working. Please try pulling the latest updates to AMR++ and run your command, but now including the --snp Y flag. Let me know how that goes for you!

Best, Enrique

[LLansing]

Thanks Enrique, I will be able to test it out next week

[LLansing]

SNP seems to have worked, although there is 1 of my samples missing. The missing sample is present in the results/ResistomeCounts as well as in the non-SNP AMR_analytic_matrix.csv

[LLansing]

I'm not sure if this is the same problem as the run I mentioned in the previous comment, but while running the pipeline again, 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'

[LLansing]

Solved at this issue