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Running error at first time instalation

Open dedenmatra opened this issue 3 years ago • 0 comments

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 main(args) File "/home/dedenmatra/pipeline-nanopore-denovo-isoforms/./scripts/compute_cluster_quality.py", line 345, in main clusters = parse_inferred_clusters_tsv(args.clusters, args) File "/home/dedenmatra/pipeline-nanopore-denovo-isoforms/./scripts/compute_cluster_quality.py", line 18, in parse_inferred_clusters_tsv infile = open(tsv_file, "r") FileNotFoundError: [Errno 2] No such file or directory: 'evaluation/pipeline-isONclust2_SIRV_E0/final_clusters/clusters.tsv'

dedenmatra avatar Oct 13 '21 05:10 dedenmatra