The sorted and not-sorted bam files are the same size
Running manually mpileup produces the same error
Code:
-bash-4.1$ pwd /usit/abel/u1/maxib/1_data/1_project/1st_assembly_strategy -bash-4.1$ du -sh * 7,0G 1_align.sam 84K chrysanthemum_indicum_chloroplast.fasta 3,5K chrysanthemum_indicum_chloroplast.fasta.fai 15G contig.fa 1,8G file.bam 1,8G file_sorted.bam 6,5K file_sorted.bam.bai 0 file.vcf.gz 0 out.fa 512 sam.sh 6,3G scafseq.fa 1,5K test.vcf.gz 0 vcffile
Code:
-bash-4.1$ /usit/abel/u1/maxib/8_samtools/bin/samtools mpileup -v -f chrysanthemum_indicum_chloroplast.fasta file_sorted.bam -o file.vcf.gz [mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 Abandon
Comment