To samtools-help,
1) I am trying to convert a cram to bam with samtools view v1.5, but eventually
I get the error below for some of the files, whereas others are successfully
converted:
Block CRC32 failure
[main_samview] truncated file.
Has anyone had this problem? I am quite sure the files are not
truncated/corrupted. How do people usually check that?
2) Furthermore, when typing the command below:
samtools view -H
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/gambian_genome_variation_project/data/FULA/SC_GMFUL5306338/alignment/SC_GMFUL5306338.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram
Then I get this error:
[E::hts_hopen] Failed to open file
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/gambian_genome_variation_project/data/FULA/SC_GMFUL5306338/alignment/SC_GMFUL5306338.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram
[E::hts_open_format] Failed to open file
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/gambian_genome_variation_project/data/FULA/SC_GMFUL5306338/alignment/SC_GMFUL5306338.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram
samtools view: failed to open
"ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/gambian_genome_variation_project/data/FULA/SC_GMFUL5306338/alignment/SC_GMFUL5306338.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram";
for reading: Exec format error
Here my samtools version:
samtools --version
samtools 1.5
Using htslib 1.5
Copyright (C) 2017 Genome Research Ltd.
I also tried doing a git pull just now, but I get the same error with version
1.6-1-gdd8cab5.
It works fine with another file from the same set:
samtools view -H
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/gambian_genome_variation_project/data/FULA/SC_GMFUL5306366/alignment/SC_GMFUL5306366.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram
Tommy
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