Question: Issue With CRAM -> BAM -> FASTQ Conversion
gravatar for Denis.keimakh
5 weeks ago by
Denis.keimakh0 wrote:

Please help! I am trying to obtain fastq files from the GDSC, all we have in the lab is CRAM files. Unfortunately, the reference genome seems to not exist when pulled from an online source. I have attempted to use the Samtools code which allows me to put in my own reference but I get an error message

code used:

 samtools view -b  -T /GRCh37.p13.genome.fa -o /EGAR00001252191_13305_1.bam /EGAR00001252191_13305_1.cram

error message:

[W::find_file_url] Failed to open reference "": Protocol not supported
[E::cram_get_ref] Failed to populate reference for id 0
[E::cram_decode_slice] Unable to fetch reference #0 10507..19965
[E::cram_next_slice] Failure to decode slice
[main_samview] truncated file.

Samtools v1.9, OS: Ubuntu 18.04.2 LTS

Any ideas? Thank you in advance!

view cram bam fastq samtools • 246 views
ADD COMMENTlink modified 4 weeks ago by jkbonfield150 • written 5 weeks ago by Denis.keimakh0

I assume this data is coming from European Genome Phenome Archive? You should email datasharing at to get assistance with reference.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by genomax70k


how have you installed samtools? Is htslib installed as well?


fin swimmer

ADD REPLYlink written 5 weeks ago by finswimmer12k
gravatar for jkbonfield
4 weeks ago by
jkbonfield150 wrote:

Has your copy of samtools (htslib actually) been compiled with curl support? If you just did "make" the answer will probably be no. You need ./configure;make. It's dumb and an annoyance of mine that we have two different build routes that by default choose two different combinations of features. Argh. This is almost certainly what the "protocol not supported" means as without curl it won't be able to handle https; only http.

If you do indeed have a curl capable samtools, then is it maybe failing due to a firewall rule? You can use htslib's "hts_file -vvvvv -c in.cram > /dev/null" to read a CRAM file with maximum verbosity enabled, which may shed some light on the manner. (Sadly samtools itself doesn't have any way to enter htslib debug mode, unless you attach a debugger to it.)

ADD COMMENTlink written 4 weeks ago by jkbonfield150
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