Comments (8)
This operates on FILENAMES
Looking at the code as it is written, it has the assumption that read filenames are in the format
_{R1,R2,1,2}.fastq.gz
NNNN-NNNNN_S33_R1_001.fastq.gz
and NNNN-NNNNN_S33_R2_001.fastq.gz
will be split to NNNN-NNNNN_S33_R1
and NNNN-NNNNN_S33_R2
which don't match
A fudge solution would be to make softlinks that remove the _001 until the sanger-pathogens team have bandwidth to correct the code
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I was implementing a seroba component on flowcraft and getting this error when some particular components came before seroba. Thank you @tseemann and @aunderwo for your discussion! Without it I could not have figured it out! And @tseemann, I'm renaming all the input files to ${sample_id}_{1,2}.fq.gz to make it work. :)
Thanks!!!
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I don't feel I should have to rename my files for a tool to work :(
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The code is
seroba/seroba/tasks/sero_run.py
Lines 10 to 12 in 37a5737
Is this operating on the read FILENAMES or the READ IDs ?
Mine are NNNN-NNNNN_S33_R2_001.fastq.gz
and R2
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Thanks once again @aunderwo
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Argh. Our other system is to use SAMPLE/{R1,R2}.fq.gz
but that fails too.
Names for forwards and reverse reads does not match. Cannot continue
:(
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Even I have the same issue. I am using Docker image and renamed files as read_1.fq.gz and read_2.fq.gz as suggested by @cimendes. The issue isn't resolved. Any suggestions on how to resolve this?
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renaming the files to $name_1.fastq.gz and $name_2.fastq.gz worked.
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