Bowtie2 error; list index out of range

Microbial community profiling MetaPhlAn
1

Hello,
I am trying to run metaphlan3 but keep an error

Traceback (most recent call last):
File “/home/scebmeta/bin/miniconda3/envs/metaphlan3/bin/metaphlan”, line 10, in
sys.exit(main())
File “/home/scebmeta/bin/miniconda3/envs/metaphlan3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 1060, in main
min_alignment_len=pars[‘min_alignment_len’], read_min_len=pars[‘read_min_len’], min_mapq_val=pars[‘min_mapq_val’])
File “/home/scebmeta/bin/miniconda3/envs/metaphlan3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 434, in run_bowtie2
nreads, avg_read_length = list(map(float, read_fastx_stderr[0].decode().split()))
IndexError: list index out of range

my command was, started only for one sample

bowtie2db="/media/scebmeta/SSD/DB/"
metaphlan KN100_R1.unmapped.fastq.gz KN100_R2.unmapped.fastq.gz --bowtie2db $bowtie2db --bt2_ps very-sensitive --ignore_eukaryotes --ignore_archaea --input_type fastq -t rel_ab_w_read_stats --bowtie2out profiled_very_sensitive/1x.bowtie2_out.bz2 --nproc $(nproc) -o profiled_very_sensitive/1x.txt
…
FYI: installed in a conda environment and database in a separate folder
Please can you help me to figure it out?
Thanks,
Khem

2

I got the same error. Anyone figured it out? Thanks ！

3

Hello,

I have got exactly the same error than you. However, metaphlan3 worked for a kind of fastq files.

I use in command line:
metaphlan example.fastq --unknown_estimation --nproc 10 -t rel_ab_w_read_stats --bowtie2db ~/database_metaphlan --input_type fastq -o ~/example.txt

head of the fastq that worked for metaphlan:
@A01619:68:HCLH5DSX3:4:1101:28818:1016:N:0:AGTGGCAA+TACTGCTC#0/1
ATTCGTGCAATTCGTGTTCCGAAAAAAAATACGTAATTCGCGTGCAGAGAAATATCTATTGCTGTGAGGCATAGTGACTACCATTGCTTGCAACGAAGAAATCTGTGTAAATCTGTGAGATCTGTGGGACATTAGAATAAACTCCCCATTC
+
FFFF:FFFFFFFFF:FFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF

head of fastq that didn’t work:
@SRR3736984.1 HISEQ:210:C2PGDACXX:1:1101:1886:2247 length=100
CACCGATGCAAACACCACCGTAAGTATTCCTGCCACCGCGATAGCAAGAGAGCTCATGGCGCCCTCTATCTCGCCCATCTCAATAGCCTTTGCTGTTCCT
+SRR3736984.1 HISEQ:210:C2PGDACXX:1:1101:1886:2247 length=100
@@@DDADD=DAFBGGFHIIIGIIBFFHGGG49@BHGGEFFAA@@==DHGE.;CEE>BECBB<?BBBCCCCCC?BBBCCCC@ACC>>CAC>CC:4@C:C

Have you got any idea about the problem ?
Thanks.

4

Would it be possible to share with us the beginning and end of the bowtie2out file?