Juicer cannot find **.fastq.bam file

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Lu Yin

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Jul 19, 2022, 5:36:31 PM7/19/22

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Dear Aiden lab,

For the hg19 test data, it ran successfully with the --assembly flag, but for my actual data, it has been in the queue for a long time and it seemed the mergsort stage is failing. The mergesort-16732090.err says:

samtools sort: failed to read header from "/data/cchen347/ZingeriaProject2021-/HiC/juicer/run003/splits/**.fastq.sam3".

The ** in the names of the files produced seem odd.

Also I did not change anything when I switched from running the test data to my actual except the file names/paths and the chr.sizes option (the -p flag). Could you tell me what this means? For the hg19 test data, it ran successfully for me by specifying this option as "hg19", but for my actual data I do not think I have such a file.

Lu Yin

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Jul 25, 2022, 12:07:17 PM7/25/22

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Hello Aiden lab,

I'm writing to follow-up on the **.fastq.sam3 issue. This issue did not happen with the hg19 test data but occured with my actual data which was of a grass species I'm working with. Could you offer me some insights as to where it might have gone wrong? I did not change any parameters between the two runs and the only thing I can think of is the -p flag which I specified as "hg19" for the test data but I did not know what it meant and I specified it as "Zingeria" for my actual data.