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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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Got an error in Running Kallisto #107

Closed zhouxinseeu closed 3 years ago

zhouxinseeu commented 3 years ago

Making Kallisto indices

File "/SGRNJ/Public/Software/tracer/tracer", line 21, in launch() File "/SGRNJ01/Public/Software/tracer/tracerlib/launcher.py", line 43, in launch Task().run() File "/SGRNJ01/Public/Software/tracer/tracerlib/tasks.py", line 373, in run self.quantify(cell) File "/SGRNJ01/Public/Software/tracer/tracerlib/tasks.py", line 627, in quantify self.fragment_length, self.fragment_sd) File "/SGRNJ01/Public/Software/tracer/tracerlib/tracer_func.py", line 1352, in quantify_with_kallisto subprocess.check_call(index_command) File "/SGRNJ/Public/Software/conda_env/vdjpuzzle1/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/SGRNJ/Public/Software/conda_env/vdjpuzzle1/bin/kallisto', 'index', '-i', '/SGRNJ01/RD_dir/pipeline_test/zhouyiqi/users/zhouxin/test/cell1/expression_quantification/kallisto_index/cell1_transcriptome.idx', '/SGRNJ01/RD_dir/pipeline_test/zhouyiqi/users/zhouxin/test/cell1/expression_quantification/kallisto_index/cell1_transcriptome.fa']' returned non-zero exit status -9

and my command is /SGRNJ/Public/Software/tracer/tracer assemble \ --fragment_length 150\ --fragment_sd 5\ --single_end\ --species Hsap\ -c /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/unittest/tcr_fl/20201103/tracer_SGR.conf \ /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/unittest/tcr_fl/pipe/GOT0928_P1_T/03.split_fq/fastq/1.fq cell1 ./

I don't know why cuz this shell can work normally before, but it failed this time. I need your help if it is convenient. Thank you!

mstubb commented 3 years ago

What happens if you run the following command at the command line?

/SGRNJ/Public/Software/conda_env/vdjpuzzle1/bin/kallisto index -i /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/users/zhouxin/test/cell1/expression_quantification/kallisto_index/cell1_transcriptome.idx /SGRNJ01/RD_dir/pipeline_test/zhouyiqi/users/zhouxin/test/cell1/expression_quantification/kallisto_index/cell1_transcriptome.fa

zhouxinseeu commented 3 years ago

Thank you for your reply. I have solved the problem. It took a long time while running kallisto index, so the server killed my program. Maybe a faster software is needed.