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Gu-Lab-RBL-NCI / QuagmiR

A python-based isomiR quantification and analysis pipeline that utilizes a number of recent and novel miRNA biological insights to produce useful analytics
https://github.com/Gu-Lab-RBL-NCI/QuagmiR
MIT License
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Unexpected KeyError in line 328 of /opt/quagmir/Snakefile @ Cancer Genomics Cloud #2

Open Shengpei-Luke-Chen opened 6 years ago

Shengpei-Luke-Chen commented 6 years ago

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

Shengpei-Luke-Chen commented 6 years ago

Hi there,

I just want you to know: I bypassed this error, simply by filter out any reads has N (with seqtk).

Best, Luke