Auto-detection of file type failed

[flopezo]

Hello,

I'm getting an "Auto-detection of file type for file ... failed" error. I'm trying to classify reads in gzip-compressed FASTQ files. I used the same reads with Kraken without a problem.

Please see below a few example reads. Any help is greatly appreciated.

@HWI-D00304:259:CBCU1ANXX:4:1101:1471:1965 1:N:0:ATTCAGAAATAGAGGC
NGATTCCGTCAAACATTTTTCCATTACATTCGGCGGCAATGCATGAATATATTTATTGATTCCATAGTTGGATTCCGCTGAAGTTACAATAGCAAGAACAAGGATGAAACCGAGTACGATGAACG
+
#<<?AGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEFGGGGGGGGGGGFGGGGGEGGGGFGGGGGGGGEGGGFGDBGGEGGGGGGGGGGEGGDGGDBGGGGGGGGGGGGGGG<EGBD.8C@E
@HWI-D00304:259:CBCU1ANXX:4:1101:2115:1976 1:N:0:ATTCAGAAATAGATGC
NTCGCGGCGTTAAATCTATGATTTCGCAATGAGAAAAAAAAAAAAAAGAAGATTCCTTTGCCTGCCATCCGCCCTTTTTCGTCACAATTTGTTAACAATCGTTTACTATCTACCCTTTTTCATCG
+
#=<AB0;EGGEGC@GGGGGGECGGGGGGGGGGGEGGGGAGG<GAGGG/0<9;=@9<@FG0990DGG000;//C>>GC/DB/:/.6;DEG//787C///8@.:@D.6/////6//8/86D/6//6/
@HWI-D00304:259:CBCU1ANXX:4:1101:2139:1998 1:N:0:ATTCAGAAATAGAGGC
NGCTGATCGAGAAAATCTACGGCACCGACGAGTACTATAGTTGCCTCGGCACCAGCTGGAATCCTTTTCAATATGTGCTCGTTTTGTCCCTTTTTAAGATCCTCGTTGCTGCTTGTGAATGTTAA
+
#<<ABFGGGGGGGGGGFGGGGGGGGGG<GGCDGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGG0FGGGGGGGGGEFGGGGGGGGGGGGFDGCFGGGGGGGGGGGGGEGGGECD=EGGB
@HWI-D00304:259:CBCU1ANXX:4:1101:2618:1986 1:N:0:ATTCAGAAATAGAGGC
NCGATGAATCTTGCTCATAAATAGACGTTTCAAAATGATTTGGTTGAATTTTGCATTGGTTCTACGTGCCAAAAACCGATAGAGTTTTACAAGAAGTCGTAAATAAACATCTTGCGACTTCGGTT
+
#<=AB?DGFGGGGGGE1FBFGGGGGGGFGGGGGG@GG1CFGGGGGGGGGGGGGGGGGGGCG>GCGGFGGGGGGGGGGGBGGGFG=@FFGGEEEGFF0;EF@@@FG>GGGGGGGCG>DGGGGGG>G

[flopezo]

It works when I run Kaiju like so:

kaiju -x -z 24 -t /path/to/nodes.dmp -f /path/to/kaiju_db_nr_euk.fmi -i <(zcat /path/to/reads_1.fastq.gz) -o kaiju.out

[pmenzel]

Are you running the latest version from GitHub (using git clone) ? That should work with gz compressed files without the bash process substitution..

[flopezo]

No, I installed Kaiju using conda. I will try with the latest version from GitHub. Thank you.