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bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics
GNU Affero General Public License v3.0
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Matam assembly error #77

Closed mkarlik93 closed 5 years ago

mkarlik93 commented 5 years ago

Dear all,

I am trying to assemble merged ilumina reads, I got this error:

header = line[1:].split()[0] IndexError: list index out of range

loic-couderc commented 5 years ago

Hi @mkarlik93,

Could you please join the full error message.

From this error message, I guess the error is coming from the function reading the FASTQ file. Have you any sequences without SEQID in your FASTQ ? (only '@' will be present on the header) You can use the following command line to check. (Be aware than if you are unlucky, the '@' can come from the quality lines)

grep -c '^@$' PATH_TO_YOUR_FASTQ
mkarlik93 commented 5 years ago

Hi @loic-couderc,

Thanks for quick reply,

but what if I have reads only in fasta format? Is there any way to specify format of the input ?

loic-couderc commented 5 years ago

MATAM is normally able to handle reads in FASTA or FASTQ format. If you want more helps, please, join the full error message. It will be hard to determine what's wrong otherwise.

ppericard commented 5 years ago

No answer for 2 months. Closing this temporarily