pipeline-nanopore-denovo-isoforms
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Running error at first time instalation
I tried to run ./run_evaluation.sh but error occurs during the process : i change input file name, but no success to run
(denovo-isoforms) dedenmatra@dmatra:~/pipeline-nanopore-denovo-isoforms$ ./run_evaluation.sh
SyntaxError:
Input and output files have to be specified as strings or lists of strings.
File "/home/dedenmatra/pipeline-nanopore-denovo-isoforms/Snakefile", line 21, in
File "/home/dedenmatra/pipeline-nanopore-denovo-isoforms/snakelib/utils.snake", line 18, in
[M::mm_idx_gen::0.0201.07] collected minimizers
[M::mm_idx_gen::0.0262.64] sorted minimizers
[M::main::0.0262.64] loaded/built the index for 7 target sequence(s)
[M::mm_mapopt_update::0.0292.50] mid_occ = 14
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 7
[M::mm_idx_stat::0.0302.41] distinct minimizers: 40410 (62.16% are singletons); average occurrences: 1.876; average spacing: 2.942; total length: 223019
[M::worker_pipeline::8.0128.83] mapped 19730 sequences
[M::main] Version: 2.22-r1101
[M::main] CMD: minimap2 -ax splice -t 10 evaluation/data/SIRV_150601a.fasta evaluation/data/SIRV_PCS109_phmm_fl.fq
[M::main] Real time: 8.019 sec; CPU: 70.741 sec; Peak RSS: 0.802 GB
[bam_sort_core] merging from 0 files and 2 in-memory blocks...
Traceback (most recent call last):
File "/home/dedenmatra/pipeline-nanopore-denovo-isoforms/./scripts/compute_cluster_quality.py", line 467, in