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smangul1 / MiCoP

MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.
GNU General Public License v3.0
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Failing to open file when using --paired #5

Closed SimenHyllHansen closed 5 years ago

SimenHyllHansen commented 5 years ago

Hi! I have paired-end files (R1 and R2), and I am trying to run them with the --paired option. I get an error which seems to suggest that the program thinks there is only a single file with the name of both files (`F08060-L1_S17_L002_R1_001.fastq F08060-L1_S17_L002_R2_001.fastq').

Running on a single file works fine.

Any ideas?

python run-bwa.py F08060-L1_S17_L002_R1_001.fastq F08060-L1_S17_L002_R2_001.fastq --fungi --output alignmentstest.sam --paired
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[E::main_mem] fail to open file `F08060-L1_S17_L002_R1_001.fastq F08060-L1_S17_L002_R2_001.fastq'.
nlapier2 commented 5 years ago

Thanks for reporting this bug! I've pushed a commit that should fix this. Let me know if that works for you.

Best, Nathan

SimenHyllHansen commented 5 years ago

Great, it works now! Thanks a lot!