ValueError: too many values to unpack
Closed this issue · 11 comments
Hi Lyam,
I'm trying to run metaTOR from a dedicated conda environment with all required dependencies installed.
metaTOR.sh align starts running but exit with a Python error at the network creation step:
any idea on how to fix that?
Python 3.6.6
Mapping reads...
70604753 reads; of these:
70604753 (100.00%) were unpaired; of these:
65283672 (92.46%) aligned 0 times
4041938 (5.72%) aligned exactly 1 time
1279143 (1.81%) aligned >1 times
7.54% overall alignment rate
70604753 reads; of these:
70604753 (100.00%) were unpaired; of these:
64590673 (91.48%) aligned 0 times
4480279 (6.35%) aligned exactly 1 time
1533801 (2.17%) aligned >1 times
8.52% overall alignment rate
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
Alignment done.
Merging bam files...
Done.
Generating network from alignments...
Traceback (most recent call last):
File "/mibi/users/jnesme/Bin/metaTOR/network.py", line 821, in <module>
main()
File "/mibi/users/jnesme/Bin/metaTOR/network.py", line 810, in main
my_assembly, = reference_file
ValueError: too many values to unpack (expected 1)
Pyton 3.6.6 and all dependencies installed:
Requirement already up-to-date: numpy in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.15.3)
Requirement already up-to-date: scipy in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from -r requirements.txt (line 2)) (1.1.0)
Requirement already up-to-date: matplotlib in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from -r requirements.txt (line 3)) (3.0.0)
Requirement already up-to-date: biopython in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from -r requirements.txt (line 4)) (1.72)
Requirement already up-to-date: pysam in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from -r requirements.txt (line 5)) (0.15.1)
Requirement already up-to-date: seaborn in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from -r requirements.txt (line 6)) (0.9.0)
Requirement already satisfied, skipping upgrade: cycler>=0.10 in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from matplotlib->-r requirements.txt (line 3)) (0.10.0)
Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from matplotlib->-r requirements.txt (line 3)) (1.0.1)
Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from matplotlib->-r requirements.txt (line 3)) (2.2.2)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.1 in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from matplotlib->-r requirements.txt (line 3)) (2.7.3)
Requirement already satisfied, skipping upgrade: pandas>=0.15.2 in /usr/local/home/jnesme/.local/lib/python3.6/site-packages (from seaborn->-r requirements.txt (line 6)) (0.20.1)
Requirement already satisfied, skipping upgrade: six in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from cycler>=0.10->matplotlib->-r requirements.txt (line 3)) (1.11.0)
Requirement already satisfied, skipping upgrade: setuptools in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->-r requirements.txt (line 3)) (40.4.3)
Requirement already satisfied, skipping upgrade: pytz>=2011k in /mibi/users/jnesme/miniconda2/envs/metator_env/lib/python3.6/site-packages (from pandas>=0.15.2->seaborn->-r requirements.txt (line 6)) (2018.5)
Hello, I modified the incriminating line (network.py:810):
my_assembly, =
with
my_assembly, _ =
did that fix your issue?
Thanks for the heads-up, I updated the link. Does it work better now?
I could download it yes. However, the filename isn't the same and it decompress in a dir called "hmm_databases" where default hmm directory location expects "modele_HMM"
I'll update the default hmm directory name. Does it work seamlessly if you just run
./meta3c.sh dependencies
though? And in the meantime you can rename the directory and proceed to the rest of the pipeline.
that's what I've been doing but I'm waiting for the partitioning step to end though
I'll then clone the updated metaTOR git directory and try running it to see if all is working as intended. I've already resumed some runs by just copying the "output" directory and using the same project name with -p
I guess this would still work for annotation step ?
hum, (with previous git version):
./meta3c.sh partition -p 5KB.metaTOR.1
ends with:
Resolving partitions... paste: /mibi/users/jnesme/Bin/metaTOR/output/5KB.metaTOR.1/partition/iteration/1.community : No such file or directory
but the file exists and is non empty ?:
head /mibi/users/jnesme/Bin/metaTOR/output/5KB.metaTOR.1/partition/iteration/1.community
0
1
2
3
4
5
6
7
8
9
about the current release:
meta3c.sh dependencies ends now with:
`
hmm_databases.tgz 100%[==============================================>] 48.45M 1.90MB/s in 29s
2018-10-24 19:15:18 (1.66 MB/s) - ‘hmm_databases.tgz’ saved [50804980/50804980]
hmm_databases/
hmm_databases/conj.hmm
hmm_databases/essential.hmm
hmm_databases/pog.hmm
hmm_databases/SGC.hmm
hmm_databases/VOG.hmm
mv: cannot move ‘hmm_databases’ to ‘’: No such file or directory
OK
`
also, louvain should be put in a directory named "tools" (and also run make in louvain).
I'm now running ./meta3c.sh partition with current version. Let's see what happens.
Edit: still ends with the same error
Could you upload your config_current.sh
file? I seem to have trouble reproducing your issues. Also did you check you had all write/read/etc. access in the directory in question?
Cheers
here it is, with ".txt" extension added so i could upload here.
config_current.sh.txt
Could you try again with this new commit? I simply unquoted the incriminating expression:
paste "$(printf "${partition_dir}/iteration/%s.community " $(seq 1 "$repet"))" >"${tmp_dir}"/"${project}"_iterations_"${repet}".txt
into:
paste $(printf "${partition_dir}/iteration/%s.community " $(seq 1 "$repet")) >"${tmp_dir}"/"${project}"_iterations_"${repet}".txt
Cheers
With the last few weeks' overhaul, this bug is probably unlikely to resurface again so I'm going to close this for now.