Stacks2fineRAD.py Index error

[smallfishcui]

Hi,

I am running Stacks2fineRAD using the population haplotype file produced by 'population' program in RAD. Then I come across this error, is it a bug? Code: python Stacks2fineRAD.py -i /wrk/cuiwang/DONOTREMOVE/amphibian_project300/data/Fejervarya_multistriata/ipyrad/popmappop/stacks/populations.haplotypes.tsv -n 4 -m 20

Error message: Traceback (most recent call last): File "Stacks2fineRAD.py", line 70, in num_snp_list.append(len(list(alleles_set)[0])) IndexError: list index out of range

Thanks, Cui

[millanek]

Hi Cui

Well, normally the Stacks2fineRAD.py conversion works well, so likely it's something specific to your data. Would you mind emailing me your populations.haplotypes.tsv file (or just a part of it which produces the error)?

Thanks Milan

[smallfishcui]

2018-07-15 10:24 GMT+03:00 Milan Malinsky notifications@github.com:

Hi Cui

Well, normally the Stacks2fineRAD.py conversion works well, so likely it's something specific to your data. Would you mind emailing me your populations.haplotypes.tsv file (or just a part of it which produces the error)?

Thanks Milan

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Catalog Locus ID Cnt trimmed_ZWBHF trimmed_ZWBHM trimmed_ZWCJF trimmed_ZWCJM trimmed_ZWHKF trimmed_ZWHKM trimmed_ZWLDF trimmed_ZWLDM trimmed_ZWLSF trimmed_ZWLSM trimmed_ZWMMF trimmed_ZWMMM trimmed_ZWNBF trimmed_ZWNBM trimmed_ZWNCF trimmed_ZWNCM trimmed_ZWPWF trimmed_ZWPWM trimmed_ZWSWF trimmed_ZWSWM trimmed_ZWWCF trimmed_ZWWCM trimmed_ZWWNF trimmed_ZWWNM trimmed_ZWWYF trimmed_ZWWYM trimmed_ZWYLF trimmed_ZWYLM trimmed_ZWZJF trimmed_ZWZJM

1 0 - - - - - - - - - - - - - - - - TAACCT/TAACCT TAACCT/TAACCT TAACCT/TAACCT TAACCT/TAACCT - - - - CCTATC/TCTATC CCTATC/CCTATC CCTATC/CCTATC CCTATC/CCTATC - - 2 0 - - - - - - - - - - - - - - - - - - - - TGAA/TGGG CAGG/TAGG TGAG/TGGG TNAG/TNGG TAGG/TAGG TNNG/TNNG - - - - 4 0 - - - - - - - - - - - - - - - - - - - - - - - - ACGTAGG/ACGTAGG TTAAAGG/TTAAAGG - - ACGTAGG/ACGTAGG TCGAGAT/TCGAGAT 7 0 AGGNNG/GGANNG NNNNNG/NNNNNG - - - - GNNNNG/GNNNNG GCGGGG/GGAATG GGAATG/GGAATG GGAATG/GGAATG - - - - GGAATG/GGAATG GGAATC/GGAATC GGAATG/GGAATG GGAATG/GGAATG GGAATG/GGAATG GGAATG/GGAATG AGGGGG/GCGGGG AGGGGG/GCGGGG - - GGAATG/GGAATG GGAATG/GGAATG GGAATG/GGAATG GGAATG/GGAATG - - 8 0 - - - - - - - - G/G G/T - - - - G/G G/G G/G G/G G/G G/G - - - - - - - - - - 9 0 TA/TG TA/TA - - TA/TA TA/TA TA/TA CA/TA - - - - - - - - - - - - TA/TA TA/TA - - - - - - TA/TA TA/TA 10 0 ATAA/ATAA ATAA/ATAA ATAA/ATAA ATAA/ATAA - - ATAA/ATAA ATAA/ATAA - - ATAA/ATAA ATAA/ATAA - - - - TCGT/TCGT TCGT/TCGT TCGT/TCGT TCGT/TCGT - - - - ATAA/ATAA NNNN/NNNN - - - - 13 0 - - - - - - - - - - / / - - - - - - - - - - - - - - - - - - 14 0 consensus consensus consensus consensus - - consensus consensus - - consensus consensus - - consensus consensus consensus consensus consensus consensus consensus consensus consensus consensus consensus consensus - - consensus consensus 15 0 - - - - - - - - - - - - - - - - / / - - - - - - - - - - - - 16 0 AT/AT AT/AT - - - - - - - - - - - - - - - - - - - - - - AT/GG AT/GG - - - - 18 0 - - - - - - - - A/G N/N - - - - - - - - A/A A/A - - - - G/G G/G - - - - 19 0 - - - - - - - - - - - - - - - - AA/AA AA/AA - - - - - - AG/GG AG/GG - - - - 21 0 - - - - - - - - - - A/T A/T - - - - - - - - - - - - - - - - - - 22 0 - - - - - - - - - - - - - - - - - - - - - - - - CCC/TTC TTC/CCC TTC/CCC CCA/TTA - - 23 0 - - - - - - - - - - - - AA/AC AC/GC - - - - - - - - - - - - - - - - 24 0 - - - - - - ACTGGCTT/ATAAAGCT ANNAAGNA/GNNGGGNT - - - - - - - - GTAGAGTA/GTAGAGTA GTAGAGTA/GTAGAGTA - - - - - - GTAGAGTA/GTAGAGTA NTAGAGTA/NTAGAGTT - - - - 25 0 - - - - - - - - - - - - - - - - - - - - - - - - consensus consensus consensus consensus - - 27 0 T/T T/T - - - - - - - - - - - - - - C/T C/T - - - - - - T/T T/T - - - - 29 0 NCTN/NCTN NCTN/NCTN NCTN/NCTN NCTN/NCTN ACTC/GCTA ACTC/GCTA NCTN/NCTN ACTC/GCTA ACTA/ACTA ACTA/GCTA ACTC/GCTA NCTN/NCTN ACTC/GCTA NCTN/NCTN ACTA/ACTA ACTN/ACTN ACTA/ACTA ACTN/ACTN ACCA/ACTA ACTA/ACTA ACTC/GCTA NCTN/NCTN ACTC/GCTA NCTN/NCTN ACTA/GTTA ACTN/GTTN NNTA/NNTA ACTA/GCTA NCTN/NCTN NCTN/NCTN 32 0 - - - - - - - - - - - - - - - - - - A/G A/A - - - - - - - - - - 34 0 C/G C/G - - - - - - - - - - - - - - - - - - - - - - - - - - - - 38 0 GCAC/GCAC GCAC/GCAC GCAC/GCAC GCAC/GCAC GCAC/GCAC GCAC/GCAC - - - - - - GCAC/GCAC GCAC/GCAC TATA/TCTA TATA/TCTA TATA/TCTA TATA/TCTA TATA/TCTA TATA/TCTA GCAC/GCAC GCAC/GCAC - - GCAC/GCAC GCNN/GCNN GCAC/GCAC GCAC/GCAC GCAC/GCAC GCAC/GCAC 41 0 - - - - - - - - - - - - - - CAT/CAT CAT/CAT CAT/CAT CAT/CAT - - - - - - CAT/TCC CAT/CAT - - - - 42 0 - - - - - - - - - - - - - - - - - - - - - - - - / / - - - - 43 0 - - - - - - - - - - - - - - CT/TC CT/TC - - - - - - - - - - - - - - 45 0 G/G G/G G/G G/G - - G/G G/G - - - - - - - - A/A A/A - - - - G/G G/G G/G G/G G/G G/G G/G G/G 46 0 / / / / / / / / - - / / / / - - - - - - / / / / / / / / / / 48 0 - - - - - - - - - - - - - - - - consensus consensus - - - - - - - - - - - - 49 0 CAC/CGA CNC/CNC - - - - CAC/CGA CAC/CGA - - - - - - - - CAC/CAC CAC/CAC - - CAN/CGN CAN/CGN - - CAC/TAC CAC/TAC - - - - 50 0 - - - - - - - - - - - - CNAACN/GNTACN CAAACG/CAACTA - - - - - - - - - - CAAACG/CCTACG CAAACG/GCTACG - - - - 51 0 - - - - ACCCATAG/GCCTATAG ACCCATAG/GCCTATAG - - - - - - - - - - - - - - ACCCATAG/GCCTATAG NCCNATAG/NCCNGCGA - - ACCCGCGA/ACCCGCGA ACCCGCGA/ACCCGCGA - - NCCNATAG/NCCNATAG NATNATAG/NATNATAG 55 0 GCCGNA/TCGGNA GCNATG/TCNGTA - - - - - - - - - - - - GACGCA/GACGCA GACGCA/GACGCA - - - - - - - - GCCGCA/GCCGCA GCCGCA/GCCGCA - - - -

[millanek]

A few other people contacted me with a similar problem, probably something to do with using a newer version of Stacks. The problem were the missing data fields encoded as "/". This has now been fixed, so the conversion should run smoothly.