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GregoryFaust / samblaster

samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
MIT License
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Aligning in Biscuit with samblaster and samtools #57

Open KChadwick78 opened 1 year ago

KChadwick78 commented 1 year ago

Hi, I am 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

GregoryFaust commented 1 year ago

Does your reference genome really have 172,124 contigs? If so, samblaster should still work fine, it's just a question.

It appears as if the input SAM file only has a header and no alignments. Have you checked for that?