Hi all,

I am analyzing some data from GSE156255 and I keep getting an error when ordering the bam files. I tried to look it up but I could not find anyone asking for error -1.

Here is what I get:

What I have done so far:

• Alignment of sequences using Hisat2.
• Converting sam files to bam using samtools view -bS file.sam > file.bam and,
• samtools sort file.bam -o file_sorted.bam

After running the latter, I get the following error:

W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_uncompress] Inflate operation failed: progress temporarily not possible, or in() / out() returned an error
[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
samtools sort: truncated file. Aborting

I also tried to specify another folder to write the temporary files, but I again get an error

 samtools sort file.bam -T /home/username/temp -o file_sorted.bam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::hts_open_format] Failed to open file /home/mol8008_21/temp.0000.bam
samtools sort: failed to create temporary file "/home/mol8008_21/temp.0000.bam": No such file or directory

Any ideas on how to solve this? Thank you in advance!!