Error reading file issues while indexing

[srbehera]

I used excord to create the bed.gz file and then run giggle index. But I am getting the following error giggle: Error reading file "A94_Exp5_6/cache.0.idx": End of file

The command that is used: giggle index -i A94_Exp5_6.bed.gz -o A94_Exp5_6 -s -f

[ryanlayer]

What was your excord command?

[ryanlayer]

Can you try putting A94_Exp5_6.bed.gz into a folder by itself then running giggle index -i "folder/*gz" -o A94_Exp5_6 -s -f

[srbehera]

I tried that initially, but it gave me the same error. So I was checking only one file at a time. Here is my excord script

#!/bin/bash
input="/DIR_PATH/P70_06.txt"
excord="/DIR_PATH/excord"
ref="/DIR_PATH/genome_mainchrs.fa"
out="/DIR_PATH/output/"
while IFS= read -r line
do
  f="$(basename -- $line .bam)"
  samtools view -b $line | ${excord} --discordantdistance 500 --fasta ${ref} /dev/stdin | LC_ALL=C sort --buffer-size 2G -k1,1 -k2,2n -k3,3n | bgzip -c > ${out}${f}.bed.gz
done < "$input"

[ryanlayer]

Can you send me your file?

On Wed, Sep 14, 2022 at 12:45 PM Sairam @.***> wrote:

I tried that initially, but it gave me the same error. So I was checking only one file at a time. Here is my excord script

#!/bin/bash input="/DIR_PATH/P70_06.txt" excord="/DIR_PATH/excord" ref="/DIR_PATH/genome_mainchrs.fa" out="/DIR_PATH/output/" while IFS= read -r line do f="$(basename -- $line .bam)" samtools view -b $line | ${excord} --discordantdistance 500 --fasta ${ref} /dev/stdin | LC_ALL=C sort --buffer-size 2G -k1,1 -k2,2n -k3,3n | bgzip -c > ${out}${f}.bed.gz done < "$input"

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[srbehera]

Sure. I am sending you the link to the box folder.