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execution error with reconstruct_contig.py FileNotFoundError: [Errno 2] No such file or directory #83
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Hi @jcleple33 , I'm looking into this now. Pretty sure it's a minor bug in the code... |
Hi @jcleple33 , I believe I've fixed the issue in v6.1.0. Let me know if this works for you! |
Dear Liz, Yes the issue is fixed. However I obtain other errors for the last 9 clusters. I have tried with k 60, 80 and 120 and I got these messages for each of the clusters 1 to 9 (see error messages slurm-19087499_1.out to slurm-19087499_9.out). should I try to increase k over 120? 1 ccs_A/1172_11533 I attached the last one ccs_A/32167_0 as example Sincerely Jean-Charles jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_1.out jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_2.out jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_3.out jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_4.out jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_5.out jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_7.out jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_8.out jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_9.out |
Hi @jcleple33 , The result is here: https://www.dropbox.com/s/divzx2l62gtzxva/32167_0.tar.gz?dl=0 |
Running cogent 6.0.0 / reconstruct_contig.py I got such error on several cluster for which reconstruction failed using kmer 30, 60 and 80:
un example below:
jleple@genologin1 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19002922_10.out
2.17-r941
Traceback (most recent call last):
File "/usr/local/bioinfo/src/Miniconda/Miniconda3-4.4.10/envs/cogent-6.0.0_env/bin/reconstruct_contig.py", line 4, in
import('pkg_resources').run_script('Cogent==6.0.0', 'reconstruct_contig.py')
File "/usr/local/bioinfo/src/Miniconda/Miniconda3-4.4.10/envs/cogent-6.0.0_env/lib/python3.7/site-packages/pkg_resources/init.py", line 665, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/local/bioinfo/src/Miniconda/Miniconda3-4.4.10/envs/cogent-6.0.0_env/lib/python3.7/site-packages/pkg_resources/init.py", line 1463, in run_script
exec(code, namespace, namespace)
File "/usr/local/bioinfo/src/Miniconda/Miniconda3-4.4.10/envs/cogent-6.0.0_env/lib/python3.7/site-packages/Cogent-6.0.0-py3.7.egg/EGG-INFO/scripts/reconstruct_contig.py", line 346, in
os.chdir(args.dirname)
FileNotFoundError: [Errno 2] No such file or directory: 'ccs_A/1982_0'
but ccs_A/1982_0 exists! I do not understand:
jleple@genologin1 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ ls ccs_A/1982_0
CYCLE_DETECTED hello.log in.fa in.trimmed.fa in.weights
Below the command line used to try to reconstruct this files:
reconstruct_contig.py --nx_cycle_detection -k 80 ccs_A/1172_19320"
NB: version of networks is 2.3 as I have an error running process_kmer_to_graph.py with 2.4 (error already reported)
I attached the directory ccsA_/1980_0 as example
Please, could you help me. Thanks in advance!
ccs_A.zip
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