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cancerit / telomerecat

Telomerecat: The telomere computational analysis tool
GNU General Public License v3.0
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--Reference option for decoding cram not recognized #37

Open zlskidmore opened 3 years ago

zlskidmore commented 3 years ago

Hi,

I am running telomerecat using the following command 

telomerecat bam2length --reference all_sequences.fa -p 4 -v 1 --temp_dir tmp_tumor --output telomerecat_tumor.csv tumor.cram

However I see the following error

DEBUG: Starting telbam generation for 57 inputs
DEBUG: Multiprocessing execution of telbam generation, 2 threads per process, 2 in parallel
[E::easy_errno] Libcurl reported error 77 (Problem with the SSL CA cert (path? access rights?))
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/f98db672eb0993dcfdabafe2a882905c": Input/output error
[E::fai_build3_core] Failed to open the file /gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa
[E::refs_load_fai] Failed to open reference file '/gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa'
[E::cram_get_ref] Failed to populate reference for id 1
[E::cram_decode_slice] Unable to fetch reference #1:10016-42034

It looks like it's trying and failing to use the information in the cram header and ignoring the --reference option

any thoughts? I'm using the current version pip installs, 4.0.0

keiranmraine commented 3 years ago

Sorry for the delay. Can you confirm you have a all_sequences.fa.dict?

zlskidmore commented 3 years ago

I do not, I have all_sequences.fa.fai and all_sequences.dict, I'll try a mv and see if it resolves the issue

keiranmraine commented 3 years ago

It would be good to know if this resolved the problem.