Issues with samblaster when using BISCUIT

[KChadwick78]

Hi,
I am working on Compute Canada clusters and getting an output error relating to samblaster when trying to align to me reference genome:

samblaster: Inputting from stdin
samblaster: Outputting to stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[gzread] (null)
samblaster: Loaded 172124 header sequence entries.
samblaster: No reads in input SAM file

This is my code:
module load gcc
module load bowtie2/2.4.1
module load samtools/1.16.1
module load samblaster/0.1.26
module load perl/5.30.2

biscuit align /home/chadders/projects/def-frasiert/methyl_seq/ref_genome/Eubalaena_glacialis_HiC.fasta 1151_B_S11_L001-FP.fastq 1151_B_S11_L001-RP.fastq |
samblaster | samtools sort -o my_output.bam -O BAM -

samtools index my_output.bam

I am super new to this and not sure if I have made a misstep in creating the reference index, but the outputs for this all looked ok. I know the fastq files are ok as they ran fine in bismark.

Thanks

[jamorrison]

Hi @KChadwick78,

Based on a little bit of testing on my end, it looks like the FASTQs you used as input weren't in the working directory you ran biscuit from.

I think it's fair to say that [gzread] (null) is not a helpful error message at all for this, so I will fix this to make it more obvious what is going on.

Feel free to reach out if you have further hang ups with running BISCUIT.

[KChadwick78]

Hi Jacob, I went back to look closely at my directory after you mentioning this might be the problem, as I was 99% I was running it from where my files are and realised that I had missed off the '.gz' at the end which is why BISCUIT couldn't find them as files with just the '.fastq' don't exist! Getting to grips with this I can't see the wood for the trees sometimes :) Thanks for your help Kate

…

On Thu, Jul 13, 2023 at 10:18 AM Jacob Morrison ***@***.***> wrote: Hi @KChadwick78 <https://github.com/KChadwick78>, Based on a little bit of testing on my end, it looks like the FASTQs you used as input weren't in the working directory you ran biscuit from. I think it's fair to say that [gzread] (null) is not a helpful error message at all for this, so I will fix this to make it more obvious what is going on. Feel free to reach out if you have further hang ups with running BISCUIT. — Reply to this email directly, view it on GitHub <#38 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7EFUPHK3P64KBIHEG3RE2DXP7YQZANCNFSM6AAAAAA2HRAYYE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[jamorrison]

Glad to hear you were able to resolve the issue! Feel free to reopen (or open another) issue if you run into further issues.