"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
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3.3 years ago
gordo2b • 0

Hey!

I am trying to run velocyto on my BAM file, however I was getting some errors that implied a truncation or corruption of the BAM file. I tested that this wasn't velocyto related by running samtools index on the file, which achieved a highly similar error (below), so it's most likely the file itself which is the problem.

samtools index WT_UT_possorted_genome_bam.bam
[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 index: failed to create index for "WT_UT_possorted_genome_bam.bam"


I've tried some suggested approaches for checking the state of my BAM including samtools quickcheck -v (seems fine) and manually checking for the correct BAM footer (matches what it should look like):

tail -c 28 WT_UT_possorted_genome_bam.bam | hexdump -C
00000000  1f 8b 08 04 00 00 00 00  00 ff 06 00 42 43 02 00  |............BC..|
00000010  1b 00 03 00 00 00 00 00  00 00 00 00              |............|
0000001c


I would ask is the file definitely corrupted, and if not is there any way to check further or fix the file?

Poster suggested solutions:

samtools quickcheck -qvvv WT_UT_possorted_genome_bam.bam
verbosity set to 3
checking WT_UT_possorted_genome_bam.bam
opened WT_UT_possorted_genome_bam.bam
WT_UT_possorted_genome_bam.bam is sequence data
WT_UT_possorted_genome_bam.bam has 66 targets in header.
WT_UT_possorted_genome_bam.bam has good EOF block.


Just displaying command and error content (several lines of BAM output follow this error):

samtools view WT_UT_possorted_genome_bam.bam | tail
[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
[main_samview] truncated file.

samtools • 9.4k views
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Run samtools quickcheck -qvvv your.bam.

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Hmm, based on qhat you posted the file looks ok based on https://github.com/samtools/samtools/issues/785 . You could do samtools view testWT_UT_possorted_genome_bam.bam | tail which then should give you the last line of the non-corrupted part of the file. Then inspect the n+1st line and see what is going on.

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Added to post, view is also having issues, but not clear why. Thanks for the input btw!

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Strange. I suggest you recreate that file. Might be the simpler workaround than digging out the cause of that error. I guess that if one of the maintainers of samtools in https://github.com/samtools/samtools/issues/785 did not have a good response we will not find one either.

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I normally would, hoped not to in this case as this bam is linked to an output that already has already been through a lot of processing. I'll have a think about a way around it. Thanks again for the input!

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Would you happen to have an update on this? Running into the same problem and the bam files themself seem fine.

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If these errors come up how can the file be fine?

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They've all been downloaded from TCGA with a lot of post-processing that worked on them. I'm trying to use diffbind for some count matrices, so I'm super confused about why they're showing up as truncated now :/

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Probably something went wrong during the "lot of post-processing". Look, if you need help then please open a new question and include all relevant code. Anecdotal descriptions are rarely fruitful.

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Got the similar errors when running samtools depth, also the quickcheck didn't show any issues.

[E::bgzf_read] Read block operation failed with error 1 after 198 of 248 bytes


Maybe my bam file is too large (139G) ?

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It means the file is corrputed, this is unrelated to size.

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Yeah I think it really is... I tried one more time and samtools stoped at the same place

[E::bgzf_uncompress] Inflate operation failed: 1
[E::bgzf_read] Read block operation failed with error 1 after 198 of 248 bytes
samtools depth: couldn't read from input file


I may need to redo the alignment...