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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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Tracer using Singularity #87

Closed tiagobrc closed 5 years ago

tiagobrc commented 5 years ago

Hi, Thanks for developing Tracer.

I am trying to use the Docker Image with SIngularity and I am having a stranger issue within the igBlast.

Here is the command and error:

singularity exec -H /ru-auth/local/home/trezende/trezende/Johanne/ /ru-auth/local/home/trezende/localPrograms/tracer.simg tracer assemble --loci A B -p 6 -c tracer.conf -s Mmus fastq/Plate_5_B12_S216_R1_001.fastq.gz fastq/Plate_5_B12_S216_R2_001.fastq.gz Plate_5_B12_S216 tracer/

##Running IgBLAST##
CMD failed:
/ncbi-igblast-1.7.0/bin/igblastn -germline_db_V /tracer/resources/Mmus/igblast_dbs/TCR_V.fa -germline_db_D /tracer/resources/Mmus/igblast_dbs/TCR_D.fa -germline_db_J /tracer/resources/Mmus/igblast_dbs/TCR_J.fa -domain_system imgt -organism mouse -ig_seqtype TCR -show_translation -num_alignments_V 5 -num_alignments_D 5 -num_alignments_J 5 -outfmt 3 -auxiliary_data optional_file/mouse_gl.aux -query /ru-auth/local/home/trezende/trezende/Johanne/tracer/Plate_5_B12_S216/Trinity_output/Plate_5_B12_S216_TCR_A.Trinity.fasta

BLAST query/options error: Germline annotation database mouse/mouse_TR_V could not be found in [internal_data] directory
Please refer to the BLAST+ user manual.

Can you help me figure out the problem?

Thanks.

tiagobrc commented 5 years ago

I solved the problem by setting up the IGDATA variable inside the container. with export IGDATA=/<path_to_igblast>/igblast/1.4.0/bin