execution error with reconstruct_contig.py FileNotFoundError: [Errno 2] No such file or directory

[jcleple33]

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

[Magdoll]

Hi @jcleple33 , I'm looking into this now. Pretty sure it's a minor bug in the code...

[Magdoll]

Hi @jcleple33 , I believe I've fixed the issue in v6.1.0.
the run result is here

Let me know if this works for you!
-Liz

[jcleple33]

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
2 ccs_A/1172_11657
3 ccs_A/1172_9583
4 ccs_A/16661_7
5 ccs_A/282_0
6 ccs_A/30518_0
7 ccs_A/3144_5
8 ccs_A/32104_357
9 ccs_A/32167_0

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
2.17-r941
/bin/bash : ligne 1 : 116440 Erreur de segmentation reconstruct_contig.py --nx_cycle_detection -k 120 ccs_A/1172_11533

jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_2.out
2.17-r941
/bin/bash : ligne 1 : 5057 Erreur de segmentation reconstruct_contig.py --nx_cycle_detection -k 120 ccs_A/1172_11657

jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_3.out
2.17-r941
[M::mm_idx_gen::0.0081.06] collected minimizers
[M::mm_idx_gen::0.0160.91] sorted minimizers
[M::main::0.0160.91] loaded/built the index for 20 target sequence(s)
[M::mm_mapopt_update::0.0170.91] mid_occ = 19
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 20
[M::mm_idx_stat::0.0180.92] distinct minimizers: 13108 (67.98% are singletons); average occurrences: 2.661; average spacing: 2.931
[M::worker_pipeline::0.2680.99] mapped 20 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax splice -t 1 cogent.fa in.trimmed.fa
[M::main] Real time: 0.270 sec; CPU: 0.268 sec; Peak RSS: 0.007 GB
[M::mm_idx_gen::0.0091.07] collected minimizers
[M::mm_idx_gen::0.0161.04] sorted minimizers
[M::main::0.0161.04] loaded/built the index for 19 target sequence(s)
[M::mm_mapopt_update::0.0171.04] mid_occ = 16
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 19
[M::mm_idx_stat::0.0181.04] distinct minimizers: 17268 (80.07% are singletons); average occurrences: 1.885; average spacing: 2.928
[M::worker_pipeline::0.1991.00] mapped 20 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax splice -t 1 cogent.fa in.trimmed.fa
[M::main] Real time: 0.201 sec; CPU: 0.201 sec; Peak RSS: 0.006 GB
[M::mm_idx_gen::0.0041.12] collected minimizers
[M::mm_idx_gen::0.0061.07] sorted minimizers
[M::main::0.0061.07] loaded/built the index for 5 target sequence(s)
[M::mm_mapopt_update::0.0071.06] mid_occ = 6
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 5
[M::mm_idx_stat::0.0071.06] distinct minimizers: 5681 (81.89% are singletons); average occurrences: 1.374; average spacing: 2.905
[M::worker_pipeline::0.0341.01] mapped 5 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax splice -t 1 cogent.fa in.trimmed.fa
[M::main] Real time: 0.036 sec; CPU: 0.035 sec; Peak RSS: 0.005 GB
/bin/bash : ligne 1 : 39105 Erreur de segmentation reconstruct_contig.py --nx_cycle_detection -k 120 ccs_A/1172_9583

jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_4.out
2.17-r941
CYCLE detected through simple_cycles! Raise CycleDetectedException!
CYCLE detected through simple_cycles! Raise CycleDetectedException!
CYCLE detected through simple_cycles! Raise CycleDetectedException!
CYCLE detected through simple_cycles! Raise CycleDetectedException!

jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_5.out
2.17-r941
/bin/bash : ligne 1 : 170766 Erreur de segmentation reconstruct_contig.py --nx_cycle_detection -k 120 ccs_A/282_0
jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_6.out
2.17-r941
skipping split_0 because done already
skipping split_1 because done already
skipping split_2 because done already
skipping split_3 because done already
skipping split_4 because done already
skipping split_5 because done already
skipping split_6 because done already
skipping split_7 because done already
skipping split_8 because done already
CYCLE detected through simple_cycles! Raise CycleDetectedException!
skipping split_0 because done already
skipping split_1 because done already
skipping split_2 because done already
skipping split_3 because done already
skipping split_4 because done already
skipping split_5 because done already
skipping split_6 because done already
skipping split_7 because done already
skipping split_8 because done already
skipping split_0 because done already
skipping split_1 because done already
skipping split_2 because done already
skipping split_3 because done already
skipping split_4 because done already
skipping split_5 because done already
skipping split_6 because done already
skipping split_7 because done already
skipping split_8 because done already
CYCLE detected through simple_cycles! Raise CycleDetectedException!
skipping split_0 because done already
skipping split_1 because done already
skipping split_2 because done already
skipping split_3 because done already
skipping split_4 because done already
skipping split_5 because done already
skipping split_6 because done already
skipping split_7 because done already
skipping split_8 because done already
CYCLE detected through simple_cycles! Raise CycleDetectedException!
skipping split_0 because done already
skipping split_1 because done already
skipping split_2 because done already
skipping split_3 because done already
skipping split_4 because done already
skipping split_5 because done already
skipping split_6 because done already
skipping split_7 because done already
skipping split_8 because done already
CYCLE detected through simple_cycles! Raise CycleDetectedException!

jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_7.out
2.17-r941
CYCLE detected through simple_cycles! Raise CycleDetectedException!
CYCLE detected through simple_cycles! Raise CycleDetectedException!

jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_8.out
2.17-r941
/bin/bash : ligne 1 : 102490 Erreur de segmentation reconstruct_contig.py --nx_cycle_detection -k 120 ccs_A/32104_357

jleple@genologin2 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19087499_9.out
2.17-r941
/bin/bash : ligne 1 : 137602 Erreur de segmentation reconstruct_contig.py --nx_cycle_detection -k 120 ccs_A/32167_0

32167_0.zip

[Magdoll]

Hi @jcleple33 ,
interesting I am able to run 32167_0 with just reconstruct_contigs.py 32167_0/...no issue found...!

The result is here: https://www.dropbox.com/s/divzx2l62gtzxva/32167_0.tar.gz?dl=0