I’m trying to use Metaphlan3 to look at the bacterial and viral (phage primarily) abundance in several samples, but when I try to run them I get the following error:
Error: reads file does not look like a FASTA file terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT)
I’ve been trying to do some trouble shooting, and based on advice elsewhere tried unzipping my fastq.gz file (which didn’t work). I’ve also used
head ERR2059930_1.fastq and
read_fastx.py -l 70 ERR2059930_1.fastq | tail and the file looks normal to me (output attached below):
$ head ERR2059930_1.fastq @ERR2059930.1 K00171:212:H55NMBBXX:3:1101:32613:2615/1 GTAGTACGGATTATGAAGATTATTAAGAGAAACGGCTCAGAAGTAGATTTTGATTTAAATAAAATCGCTGTAGCCGTAACAAAGGCAAATGCAGCCTGCGA + AAA-AFFF-FJ<JAJJJFJJJJJJJJJJJF-<A-<F<7<7FJFA-AAFJFF<FFJJ<F-FFJJJJAA-AA-AA7A<AFFJFFJFJJJFF<JJJJ<JF))A< @ERR2059930.2 K00171:212:H55NMBBXX:3:1101:32674:2615/1 TTTGTCTGTATGACTTATTTTCACGAAATCCGGTCCGACCTTCATATCAATGCCAATTTCTTCCAGCTTCATCAGAATCGCTTCCAGGTGCTGAGGGATGA + AAA<AAJJJ-FJFAA7AJJ<FAJJJJJJJFAJJJFAJJFF-FJ<JF-7AA<FJFF7JJJ<JA7--7AFJJAAFAJAA<7FJJJAFJFF<JFFJJJAFAFJA @ERR2059930.3 K00171:212:H55NMBBXX:3:1101:22313:2633/1 TCACATCGGTGTACCCTTCGACGATCACGACCTGGCGTTTCTTCACGATCTGCGGCTTGGCCAGGTCGATGCCGTAGAGCACCTGGTTCTTGTGGTAGAGC $ read_fastx.py -l 70 ERR2059930_1.fastq | tail 31111853+ AAFFFAFJFJJJJFJJJJJJJJJJJFJJFJFAJJJAFJJJJAFJJJJJJFJJJ7FF-FJFAJJJFJJFAFJJFJFJ<A<FAFJJJJJJJFJJJFJJJFJJJ @ERR2059930.31111852_K00171:212:H55NMBBXX:4:2228:31964:49247/1 TCTGATCGGCGCTTGTGTAGCGGCGGGTGCCACAGTGGGCGCCGTGCCAATTCCGATCGCCGATTCGCTGGTGCGCTCTCCGTTGGAACTCGGCGAACTGC + AAFFFJJFJA-F7AJFJFAJJJFFFFF-FFAAAAJA-FJJJ-F<FFA-7JJ<<-<-----7A-7--<-F<<-AA--77<7--F7-AF<-<FF<JJFJ<<F< @ERR2059930.31111853_K00171:212:H55NMBBXX:4:2228:31984:49247/1 GGGGATATGTCTGGGAAAACGACTGTGCAGAAGGGGTCGCTATACCACGCGAAATTCTTGTGGAAGGTGTCTACAAAGCCGTCAATATCTGCCAGCAGCGT + AAAFFJJJFJJJJJJJJJJFJJF<FFJJFAJJJJFJA<FFFFF<J--7A-AFFJJAA<<FFJJ-AAAJFAFJ<JJFJJJJJFJFJF<FJJJFFFJJ<FAF-
Any help would be greatly appreciated.
(also, on a side note, I noticed in some other comments that Metaphlan3 doesn’t work great with phage currently, if phage abundance is important to my project should I be looking at a different tool?)