Unexpected KeyError in line 328 of /opt/quagmir/Snakefile @ Cancer Genomics Cloud #2
Description
Hi there,
I am testing QuagmiR on CGC.
However, it errors out and the error message is not very revealing.
It said (see details below): KeyError in line 328 of /opt/quagmir/Snakefile
I suspected the 'N' in the key (sometimes 'N' is not included in k-mer/hash table initializations)
Any advise for me?
Feel free to msg me if you want to get added to the test project.
Best,
Luke
2018-08-29T18:36:10.457014569Z Provided cores: 1
2018-08-29T18:36:10.457065529Z Rules claiming more threads will be scaled down.
2018-08-29T18:36:10.457522991Z Job counts:
2018-08-29T18:36:10.457535760Z count jobs
2018-08-29T18:36:10.457541613Z 1 all
2018-08-29T18:36:10.457546176Z 1 analyze_isomir
2018-08-29T18:36:10.457550756Z 1 collapse_fastq
2018-08-29T18:36:10.457554934Z 1 gff_file
2018-08-29T18:36:10.457559050Z 1 group_outputs
2018-08-29T18:36:10.457563486Z 5
2018-08-29T18:36:10.458066024Z rule collapse_fastq:
2018-08-29T18:36:10.458077760Z input: data/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq
2018-08-29T18:36:10.458081571Z output: collapsed/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq.collapsed
2018-08-29T18:36:10.458084786Z wildcards: A=CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq
2018-08-29T18:36:14.443285821Z 1 of 5 steps (20%) done
2018-08-29T18:36:14.444275189Z rule analyze_isomir:
2018-08-29T18:36:14.444286611Z input: collapsed/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq.collapsed, data/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq, /sbgenomics/Projects/60ad4b57-f744-4ddc-9bbe-6abbf7e4b72f/QuagmiR_Refs/motif_list_hsa.fa
2018-08-29T18:36:14.444294648Z output: results/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq.isomir.tsv, results/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq.isomir.sequence_info.tsv, results/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq.isomir.nucleotide_dist.tsv
2018-08-29T18:36:14.444298216Z log: logs/29-Aug-2018@06:36:10PM
2018-08-29T18:36:14.444301447Z wildcards: A=CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq
2018-08-29T19:22:27.718088086Z 2 of 5 steps (40%) done
2018-08-29T19:22:27.720182002Z rule gff_file:
2018-08-29T19:22:27.720194929Z input: data/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq, /sbgenomics/workspaces/60ad4b57-f744-4ddc-9bbe-6abbf7e4b72f/tasks/31bcf717-142a-4a98-8c08-f7c23811eee2/quagmir-1-0/miRBase21-master.tsv, results/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq.isomir.sequence_info.tsv
2018-08-29T19:22:27.720202815Z output: results/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq.gff
2018-08-29T19:22:27.720206118Z log: logs/29-Aug-2018@06:36:10PM
2018-08-29T19:22:27.720209290Z wildcards: A=CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq
2018-08-29T19:22:30.857336650Z Error in job gff_file while creating output file results/CC3T7ANXX_s1_1_GSLv3-7_13_SL301606.01.fastq.gff.
2018-08-29T19:22:30.857939131Z RuleException:
2018-08-29T19:22:30.857950845Z KeyError in line 328 of /opt/quagmir/Snakefile:
2018-08-29T19:22:30.857956309Z 'ACNNC'
2018-08-29T19:22:30.857961124Z File "/opt/quagmir/Snakefile", line 1244, in __rule_gff_file
2018-08-29T19:22:30.857966241Z File "/opt/conda/envs/quagmir/lib/python3.5/site-packages/pandas/core/series.py", line 2220, in apply
2018-08-29T19:22:30.857980667Z File "pandas/src/inference.pyx", line 1088, in pandas.lib.map_infer (pandas/lib.c:62658)
2018-08-29T19:22:30.857984151Z File "/opt/quagmir/Snakefile", line 328, in get_id
2018-08-29T19:22:30.858549694Z Will exit after finishing currently running jobs.
2018-08-29T19:22:30.862334424Z Exiting because a job execution failed. Look above for error message