2021-02-26 17:34:41,006 - INFO - Using 40 threads.
2021-02-26 17:34:41,011 - INFO - kallisto bus -i /projappl/project_2003803/INVD/BT18/BT18/human_GRCh38_gencode.v31.600/gencode.v31.fragments.idx -o /tmp/lackmama/5030922/tmpbm3mgh_u -x 10xv3 -t 40 BT18_S3_L001_R1_001.fastq.gz BT18_S3_L001_R2_001.fastq.gz BT18_S3_L002_R1_001.fastq.gz BT18_S3_L002_R2_001.fastq.gz
2021-02-26 17:34:41,241 - INFO - [index] k-mer length: 31
2021-02-26 17:34:41,241 - INFO - [index] number of targets: 845,338
2021-02-26 17:34:41,241 - INFO - [index] number of k-mers: 271,648,279
2021-02-26 17:35:13,848 - INFO - [index] number of equivalence classes: 4,776,424
2021-02-26 17:35:34,174 - INFO - [quant] will process sample 1: BT18_S3_L001_R1_001.fastq.gz
2021-02-26 17:35:34,184 - INFO - BT18_S3_L001_R2_001.fastq.gz
2021-02-26 17:35:34,184 - INFO - [quant] will process sample 2: BT18_S3_L002_R1_001.fastq.gz
2021-02-26 17:35:34,184 - INFO - BT18_S3_L002_R2_001.fastq.gz
2021-02-26 18:05:30,269 - INFO - [quant] finding pseudoalignments for the reads ... done
2021-02-26 18:05:30,366 - INFO - [quant] processed 150,596,634 reads, 26,426,999 reads pseudoaligned
2021-02-26 18:05:35,808 - ERROR - Error decoding run_info.json: Expecting value: line 1 column 1 (char 0)
2021-02-26 18:05:35,808 - INFO - Loading gene metadata
2021-02-26 18:05:36,188 - INFO - Loading fragments-to-gene mappings
2021-02-26 18:05:36,760 - INFO - Indexing genes
2021-02-26 18:05:37,214 - INFO - Loading equivalence classes
2021-02-26 18:05:37,214 - INFO - Mapping equivalence classes to genes
2021-02-26 18:05:37,214 - INFO - Loading fragment IDs
2021-02-26 18:05:37,214 - INFO - Loading BUS records
Traceback (most recent call last):
File "/projappl/project_2003803/bioconda3_env/my_biotools/bin/loompy", line 10, in
sys.exit(cli())
File "/projappl/project_2003803/bioconda3_env/my_biotools/lib/python3.8/site-packages/click/core.py", line 829, in call
return self.main(args, kwargs)
File "/projappl/project_2003803/bioconda3_env/my_biotools/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/projappl/project_2003803/bioconda3_env/my_biotools/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/projappl/project_2003803/bioconda3_env/my_biotools/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/projappl/project_2003803/bioconda3_env/my_biotools/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(args, **kwargs)
File "/projappl/project_2003803/bioconda3_env/my_biotools/lib/python3.8/site-packages/loompy/commands.py", line 34, in fromfq
create_from_fastq(loomfile, sampleid, list(fastqs), indexdir, metadatafile, threads)
File "/projappl/project_2003803/bioconda3_env/my_biotools/lib/python3.8/site-packages/loompy/bus_file.py", line 429, in create_from_fastq
bus = BusFile(
File "/projappl/project_2003803/bioconda3_env/my_biotools/lib/python3.8/site-packages/loompy/bus_file.py", line 239, in init
self.bus_gene = np.array([self.gene_for_ec[x] for x in self.bus["equivalence_class"]], dtype=np.int32)
File "/projappl/project_2003803/bioconda3_env/my_biotools/lib/python3.8/site-packages/loompy/bus_file.py", line 239, in
self.bus_gene = np.array([self.gene_for_ec[x] for x in self.bus["equivalence_class"]], dtype=np.int32)
KeyError: 4628204
I was running the following code on approximately 1600 human cells:
Hi! I'm having issues with generating loom files with the loompy fromfq command. The error appears when loading bus records:
I was running the following code on approximately 1600 human cells:
I'm using loompy v3.0.6 and kallisto v0.46.2 in a conda environment. What could be causing the error?
Thanks for your help! :)