Issue with "Error: reads file does not look like a FASTA file"

Microbial community profiling MetaPhlAn
1

Hello,

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?)

2

Which is the command line you used? It looks like you specified --input_type fasta instead of fastq

3

Ahh, yeah, well that did turn out to be the issue, quite embarrassing but I didn’t notice that. Thanks for the help!