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verified publisher icon rrwick

runtime_error when locale isn't set

Open TomHarrop opened this issue 3 months ago • 0 comments

Hi,

Just reporting this. It could be a conda thing.

The file is test_trim.fastq from this repo.

Cheers, Tom

$ apptainer exec \
    docker://quay.io/biocontainers/filtlong:0.3.1--h077b44d_0 \
    filtlong \
    --min_length 1000 \
    test_trim.fastq 

INFO:    Using cached SIF image

Scoring long reads
  terminate called after throwing an instance of 'std::runtime_error'
  what():  locale::facet::_S_create_c_locale name not valid
Aborted (core dumped)

Works with LC_ALL=C

$ apptainer exec \
    --env LC_ALL=C \
    docker://quay.io/biocontainers/filtlong:0.3.1--h077b44d_0 \
    filtlong \
    --min_length 1000 \
    test_trim.fastq 

INFO:    Using cached SIF image

Scoring long reads
  4 reads (4901 bp)

Outputting passed long reads
@test_trim_1
GCCCTGGCTAGCACTGCACTTCGCACGCAAGTTTCATCCAGTAACGGCGCCGATAGTCCTATTTCGCAGCGCTCTCTATTGTCCGGCGTCCGGGGTAAGGATTTGCAGACATCCCGCCTACTATGATACTATGACTCCTTGTATGTCCTGTCTCAGTTAATGGTTAGACATGTTGAGATGACTGGTTGAACTCAGTAGGTTATGCTAAGACTCCATCAGTTTATTCAACAATTAGAATTGGATCGAAGGGGGATACCCGGCAATGAAGAAGAGCCCGTTAGCCAAAAATAAGGTAGCAACTACAAAGTAGACGCGCAGAGCTAAATAGGTCGTACTTGATATTGCAACATGACCAACCGATGCAAAGTCCGCTCCTGCATATTCGTATAGGATGGGGGCCTCGGGGCCACGAAATGGCTCCATGCTTCGCAATCACCGCACCTTTAAGTAATCGCCGCGTATTTCCAAAAAGCCGGCATGGGTGCAGATTAATTGGGACTTTGTCGAAGACGTTACACAATCCCGCCAACTCGAATGGTTAATGTTCAGCGGATACACGCTCGCTGGCGTCCACGGATCTATCGCTTTGCTCCCGCTCGGCTCCCGAACGACGGGACTCGAGTAACCGATCACTCCGCTTTTCTCAACCTCAGCTTTTGGTGCCACAGCAGAGTGACACTCTCATGTTGGAGTATGGGGGTCCCTGCTAATGACCGCGGACGACTAGCAGTTATTTTCTGCGCGTCACTCAGAATAGCGATTGTATAAGCAAGGCAACCGGCGAGGTCGATAGCGTGTAGCTGCTCGGACGAATCTATATAGGTAGGGGCCTGCCTGTTCTTTCCCCACCCTGTATAGCAACAGAATAGGCTGTCCTAATTTTGGGCCCCACACTTGGAATACCTGTAAAATCTTTAGCTTGGCTATCGATATATCATGTAACGAGCTGTGAAGTACTTTATTCAAGAGAGCACCGTGGGACCGAGATAAGATCGTCAAGGACGTTTACCAATTGAGCGTTGGTCTTATCACTCCGATCGCAGAACTATATCTGGCGATAGTGTATCCGGTAGAGTGCTCCCATTCTAGTCTGTAAGAAATTGGAGCACGACTTTTCCAGTCATTTATCGAAACCGGCCGGTGGAGTAGTAGTAATTACTTTACTCAATACGCTTTGACCTGATTCATGCCCCCAAAAGTGGGGTACGTGAGTCTAAGTACCTGTGGAGTGCTTTTCCGCCGTACATAGTTAAGTATAGACTTATTCTACAGCTACCCGCGCGGGGGAGAAAGGGTCCAG
+
/04//11,-/-)(&&+***)/1,'0(%&$#$&&&1*+0,))'(%(%&%'4433324/.,''(++&12022..0./0&(331110233//1%$'((224.(1++)30/.+,0.1**/10-,-2.,%)****1.-.)0001-,-)+..,-,4,)($*'+0.23+&+)*310.+(%''(,3442////03(,')0,+13./-,*('($$&'',,/+*))(%'$+--.1-/032.2-,,+*%&&'&&(*,'&#('**')((-,)+()'(($'%$##%&),*)&&$"'$%,'$#'$(0,"#$)''*0/452550+,1--02)).+',,,245.-0..(,,.0,*.,+,)&%'(&&-*,&+2)%&,+,1-4.-0/.../*)2420&(&-.++$+)',,(-1+(01/2-+-)(#)+43/+-))('''('$')),-++*-4'%*),)*0--)++-,++(*'+')4200+-++&+$&')#'-03+/01443,*'),10.,+*-+%$%%$##$$&&+$+.-+''*$(+'(-0,/.+*',42131(',('(&)((,,-....1.*,)-3/1,,&##%%().34214-'++''+/0.+*+$+-240*0++..31-,/+-0--)--.,.(&+%%#('*))%)#'('&(*+***),,,....20/.-2,0.)'#%&(*./('$%$%&&'*+())*(#,(''+)(**)'($&(*'$)+,,+.++41*-2,2432213-31-.1.+&%&%&-+./.,,'%&&(-/10***(+1,+-,2)++*.+*,.,)*,,12/-+*&''*)+-+143/(('-,,,),012322,3,+,-0,-11,+3.,13,'#$*#-,++%042+,+&')..$),&#%#%$,)01--3*-(%&&$(%*0&*120.+0/301./'%%%&()+*,01&,01220121,-$&-0332**'++2+230.*$0*&')+)+&/.,'-&,1/+*(**.)+%)%)%.4144235/2222231454542/&24131,403144441*/'00/412111210+)'(+.31/3.0524041.4-1)/43/**)($,))),)-1-/04505-32533155443+,+++11+3+%'#$-./3,+,&%&*,-.--3.,0.%,--000.---,00522/-*)*'+$$$)$$,1123122*),)(2*.22*&$%')(.*$%&')+*'+%**1+)&)$&&*(&-3304*'$'%$)$%%&('')/**0+41012.,.4,)+-2/./.0445.+)+)*%(**'/,*.+((3-+*-('(.+('%&%&*)(*-(%+.112534.-./).3..34
@test_trim_3
CTTGAACAGGCGAGAACGCCAAAGGCATACTGATGGCTAAATGACCTTGACCATATGCCGCGTTGTCGAATGCGAGTGGAAAACACCCAGGCCTAGCTACGGAGACCTTAAAAACCAAAATATTATAGGACGCATGGTTGCTCCCCGCCGAGTTGCGCTTCACCGCGTCACTTTGTTGATATATTTGAATGAATTCTCTGACTGCCAGAAAGACTCATGCACTGCTCTTTAGTAGTGCAGGCCGAGAAAATTCCGAGCGAACCCTGTCCGCGCCTTCCTGACACATCTTTCCTTCCGGAGTGGGCTTAGTATGGCTTCCGAATAGCCGAGCTACGTTGTTTTGATAGGAAAACCGCCAGTTGTTTATAAAAATGGGGTGCCCTATGGACGTCCGATTTGGTATCACTGACTATCTCCGCTTCACTGTACGGGGGATACACCAGAGTAACTGGGCAATAAGTGCCAAAGATTAGTTGCGAACGACTCACGTTCATGGTCAATTCGTTATCCTTAAAGTTATTGCCTGCTACCATAGCTTATCAGAACGAGCGGCCCTTTGAGTCGCCCGTGAGAAGACCGATTCCAGACTAGCAATATAGATTTGTGGGGTTAAAAGGCTGCCTCCGTGTAGTCTTTCAAAAAAGCACGTAAATCTGTAGTGGGCCTTTGGATATTGTAGGGGGAAAAGCGGAGACATTCAAGAGGCAGTTTTTTGCGTTTGTATGGCAGGCCATTTTAGAGCCTTTAAGTGGCACATAACCGCGGAAGCTTGGAATGGAAACGGGATCTAAGTCGCATTCAATTTCTTGATGAGTCTGGCGTTCGGTGGCGTGGCTCTTAGGTGAGAACGACTGACATACCCTGCTGCTGAATCCGTGAGAAACCGAACTTGGCGCAATCTTTAGCAGGCGTACACATGGGCGCGAGACGTGCGGTAGCGAGCAAGAGCTGCTAAGTGAGTCTCCTCCAGCGCTCCCACAGGCCAGGTCATGACACGTTG
+
-/153.461)+-**+,31(-'$&)%3+*3,%.%11012+./*+.-142411001++1+&&.14-'-%,,0+,**(),,,0,)*00+++*+,,+()/14323****(%%/$)*%-.5.++.))*3+.,&'$'&(+-./+*-+-((+(3./..+(&%&(,)/1/.0*+)(+&)-(+-%)&''+-0++'$(+01+3410)/(#&#)&01.'&#%.+13131-%&%$'+//&.*/++,0)&%%$#($,-31/32--+**(&$#"'$&)'$/10114224-1)&*'21**311,''*%*112//*&-)./334443-,3,+,,52)4104234430/&/1234'.1-$-***,&**-*++.,0++,((+0++4531,%+,0**1/**3135344*--$%#$('-+0*(+,0.,,0.-3/,.)+2200501221)&%00*,+/./52,2-./(&%&%#))()'&#'#,+(-24/234231,.&)*-$),%&,+-0+(()-(&2&,/-+.-234232200122.,,+**+1+10-,*0/2)2)+-2.//,-++3+'.-0-03312,)*+,-*#'&'%-%(%%$%()(-+.4/(+($(+011..//214234410//.(*+).,/2+,,545105335,((''#$%()-0)(+.*'%+&+224310),2130%$'(#$%*.12.100+%01,,4434-,4,2*3+(30).,++)'()(&-.0()*).-%210-/*(//101--0(&%)(,)&((()(&++-,&*.--...,'%&),240/42.($$%(&(44210,+-/1)'()(%&&&.,31/2&%#%%%033425.4204%.35120.(+..0-1$(,*(()*+*001342342*+0+*-(&&)--*+.01'/%()(),.-+..*.../02../12013)),1.)/1/22331.,%)((+,330.,$%*)2./51332,3,+)&/00132)'%(')'($%%%'%),0*24/03%//433311*0-.1,*,,,)(&$
@test_trim_4
AGGATGAAAGTGCCTTTCTTAACCATTTGTGCGCTGTCGAAGTTTACGAGGCCGCGGAGCCTGCTGCCGACATATGACCCCCGTGATCTTTGCTATATTCGGCTGCCGCCCGCTAACCGTATTAGTCGCCACTTTAGGCGACAAGTATTCCTGTACAGGCTGGTTCTTTCTGCTATCATCACACCGTGGGAATCGAGAGCCGGAATCGCTGCTGCTTCCAAAGGAGTGATGTTTATTTGACAACAGGGGTCCATAGGGTGTAGTAGAATTGTCCCGTTGGGCTTTAATTCGGGCTAGAGCCTTAGTCTAGGTTGAGTACATTTGATACACAACTTATGGCTCTAACGTCATCATCTTCCGCGCGCCTTCCGTTTCGGGCACTGGGTTAATTATTGAGGTCGAGGACAAAGACGAGTGGAGGTCAACCTTATCAGTATGATCTCAATTTATATATGCACAGCGCCAAACACCGACTCAAGGTACGCCACTGGCCACTCGGCACGCGGGCTCAAACTCAAACCAAGGTGACGTGGTACCCAGACTCCTAGATTGCAAGACTATCCCCAATGCTTTTGGCGGTCTCATCTACTCGAAAATTGTCTGTGCGGGGGCGTGGCATTTCTCCCACCTGCGGCCCTAAGGAGGAAGCATAGTACATCACTGGAAGCGACAAATGGACATGTGAATCTTTTGCCAGTATCTGAAGCGCTCCCCGCAGCCTTACCAACTTACAACTAAAGGCACCTCGAATCGCCTGGCGACGGCTCATTCGCGCTTCGATAAGGTCCTATAATCTAGGTGGTACCCGTACTCACAGTACGATATCGTTGGCCGGTAGTGAATAATCTACTATTCTAAACACGACTCTGGACTGTTTTGTAAATGGACACCGCCATACTTATTTGACTTCCTTTCACATTGTAGATGGGAGCCCGCTTGCGGACGGCTTTTATCGTTTGCACAACACAGGAAGGATCCATACTTATGGTGATTTTTTCTAACTACGCTGCATATGGAAAAGAGTCCAGGTGCTTGCAGAAGCTGCAAAAAAGGACGCCACGTCGCCCGTAACGAAGGGCAGGGCGGGTCTTTGATATACGCTCGCCATCTTGAAATAGGCTTCCCACGGACTGAACGGCGCCGCGCTCGGCAAGCATTTCGTGCCCGTCAAGGAAGCGCGTATCTATGGGTCAGTATTAGCATGTGACAGTTGACTTTGAGAGCCACAGCGTCTCACCCCTCGGGTCCCATAGTTATTTATCGACTATGGCCCGTGCAAGCAGTTTCCTTAGAGAATCGTTCAATTCATCCTTGAATATCTTCGTGACTATTATCACTAGTAAACAGTGCTCGCTCCGTTCTCCACCGCCTAGCACCGACGGTATTACCTCGGTACACCCCTACTCCGAAATGCACAATTACCATACTTCCATGCTCAGGTGCCATCGTATGAAGCCTACGCGTCTCGTAACGGGACAAGCCCTGAAATTACGGGGACAACACGAGCACATTTGTGTAGCTATGCCAGATGGGAATTAGGCTCATTCGGAAATTTGTTGCGAGAATCTTTCCGTCCTGATGATTGAAGGGAATGGCAACGGGGAGATTCTTTTCTCGCCGCAGGAAAGAATGACCGGTAACTTGAGGTCCCGCAAAAATTGAGCGGAGATCTGCAAGAATAGAATTAATTACATCCTGTCGACCTCGTTAGAAGGAGTAATACATACCGGAGGATCAAAGGGGCAGTAACTTAAAGCATGAGTTAGTGAACAACGTTGCCGGTCTTCAAAAGTTCAACTAGGTGCTGGGATCTGGTGTAGGAGCTGGCTAAAGGATCCTCGGCTAGGTGCCGGGCTCTCAAGCCCGGCGACAGTCTTTGATCACCACGGACTTGTTTACG
+
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

TomHarrop avatar Oct 06 '25 04:10 TomHarrop