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dyxstat / HiCBin

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
GNU Affero General Public License v3.0
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run jgi_summarize_bam_contig_depths error #3

Closed JLUVicent closed 2 years ago

JLUVicent commented 2 years ago

when I run ./jgi_summarize_bam_contig_depths --outputDepth coverage410.txt --pairedContigs pair410.txt test/sorted.bam,I get an error Please execute 'samtools sort' on unsorted input bam files and try again! . But I have run the command samtools sort -o sorted.bam -n align_test.bam, I still make the mistake. I don't know what to do. I would appreciate it if you could give me some advice. Thank you!

dyxstat commented 2 years ago

Hi,

Can you try 'samtools sort align_test.bam -o sorted.bam' since '-n' option is used to sort bam file by the read name?

Best, Yancey

JLUVicent commented 2 years ago

Thank you very much for your answer. I have solved my problem !