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Generade-nl / EelSeeds

Scripts used to extract seeds for the European eel genome assembly
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Use of uninitialized value in binLongEelReads.perl #2

Open mictadlo opened 6 years ago

mictadlo commented 6 years ago

Hi, I did the following steps

> jellyfish count -m 25 -t 8 -s 200M -C -o jellyfish/SZ004_001.jf <(zcat SZ004_NoIndex_L001_R1_001.fastq.gz) <(zcat SZ004_NoIndex_L001_R2_001.fastq.gz)
> jellyfish count -m 25 -t 8 -s 200M -C -o jellyfish/SZ004_002.jf <(zcat SZ004_NoIndex_L001_R1_002.fastq.gz) <(zcat SZ004_NoIndex_L001_R2_002.fastq.gz)

...

> jellyfish dump -c -t -L 25 jellyfish/SZ004_001.jf >   SZ004_001.jf.dump
> jellyfish dump -c -t -L 25 jellyfish/SZ004_002.jf >   SZ004_002.jf.dump

...

> flash <(zcat SZ004_NoIndex_L001_R1_001.fastq.gz) <(zcat SZ004_NoIndex_L001_R2_001.fastq.gz) --threads 8 --min-overlap 15 --max-overlap 200 --max-mismatch-density=0.1 --output-prefix=flash/SZ004_001_15FLASh
> flash <(zcat SZ004_NoIndex_L001_R1_002.fastq.gz) <(zcat SZ004_NoIndex_L001_R2_002.fastq.gz) --threads 8 --min-overlap 15 --max-overlap 200 --max-mismatch-density=0.1 --output-prefix=flash/SZ004_002_15FLASh

...

> perl ./selectMergedEelReads.perl flash/SZ004_001_15FLASh.extendedFrags.fastq jellyfish/SZ004_001.jf.dump 260 25 0
> perl ./selectMergedEelReads.perl flash/SZ004_002_15FLASh.extendedFrags.fastq jellyfish/SZ004_002.jf.dump 260 25 0
...
> cat flash/*.extendedFrags.fastq_260_25_0.fasta > flash/all.extendedFrags.fastq_260_25_0.fasta

> rename.sh in=flash/all.extendedFrags.fastq_260_25_0.fasta out=flash/all.extendedFrags.fastq_260_25_0_renamed.fasta  # Part of BBmap

> perl binLongEelReads.perl flash/all.extendedFrags.fastq_260_25_0_renamed.fasta
Use of uninitialized value $seq in scalar chomp at binLongEelReads.perl line 20, <INPUT> line 463787803.
Use of uninitialized value $seqlength in numeric ge (>=) at binLongEelReads.perl line 22, <INPUT> line 463787803.

What did I miss?

Thank you in advance.