questionssamtools sort not working
I just found a new issue:
samtools sort output is not sorted. Seems it did not do anything. The content is still the same as the unsorted bam or sam files. Here is how I tested it:
- Upload a sam file 2.sam;
- samtools sort /data/2.sam -o /samtools/examples/2.bam
- samtools index /samtools/examples/2.bam
Then I got the error:
[E::hts_idx_push] NO_COOR reads not in a single block at the end 1 -1 [E::sam_index] Read 'M02034:479:000000000-D7LT7:1:1101:13367:1705' with ref_name="DELLA-4B-Kronos", ref_length=301, flags=73, pos=62 cannot be indexed samtools index: failed to create index for "/samtools/examples/2.bam": No such file or directory
Then I checked the contents of the 2.bam with
samtools view /samtools/examples/2.bam and the reads order are the same as the sam file.
Thank you @robertaboukhalil! Really appreciate your biowasm project! Really cool and useful!
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