metaWRAP: Error binning module
Hi,
I have run the binning module.
MetaBat2 run without problems and output around 200 bins, but both MaxBin2 and Concoct called for errors, see below the error file:
Creating depth matrix file: binning/work_files/mb2_master_depth.txt
Closing most bam files
Closing last bam file
Finished
readline() on closed filehandle FILE at /home/people/alpal/.conda/envs/metawrap-env/bin/run_MaxBin.pl line 1334.
cp: cannot stat 'binning/work_files/maxbin2_out/bin*.fasta': No such file or directory
Output depth matrix to binning/work_files/tmp
Calculating intra contig depth variance
Output matrix to binning/work_files/tmp
Opening 24 bams
Consolidating headers
Processing bam files
Creating depth matrix file: binning/work_files/tmp
Closing most bam files
Closing last bam file
Finished
Traceback (most recent call last):
File "/home/people/alpal/.conda/envs/metawrap-env/bin/concoct", line 4, in <module>
__import__('pkg_resources').run_script('concoct==0.4.0', 'concoct')
File "/home/people/alpal/.conda/envs/metawrap-env/lib/python2.7/site-packages/pkg_resources/__init__.py", line 748, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/people/alpal/.conda/envs/metawrap-env/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1517, in run_script
exec(code, namespace, namespace)
File "/home/people/alpal/.conda/envs/metawrap-env/lib/python2.7/site-packages/concoct-0.4.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/concoct", line 10, in <module>
from concoct.cluster import cluster
File "/home/people/alpal/.conda/envs/metawrap-env/lib/python2.7/site-packages/concoct-0.4.0-py2.7-linux-x86_64.egg/concoct/cluster.py", line 4, in <module>
from sklearn.mixture import GMM
File "/home/people/alpal/.conda/envs/metawrap-env/lib/python2.7/site-packages/sklearn/__init__.py", line 134, in <module>
from .base import clone
File "/home/people/alpal/.conda/envs/metawrap-env/lib/python2.7/site-packages/sklearn/base.py", line 11, in <module>
from scipy import sparse
File "/home/people/alpal/.conda/envs/metawrap-env/lib/python2.7/site-packages/scipy/sparse/__init__.py", line 229, in <module>
from .csr import *
File "/home/people/alpal/.conda/envs/metawrap-env/lib/python2.7/site-packages/scipy/sparse/csr.py", line 15, in <module>
from ._sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \
ImportError: /home/people/alpal/.conda/envs/metawrap-env/lib/python2.7/site-packages/scipy/sparse/../../../../libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/people/alpal/.conda/envs/metawrap-env/lib/python2.7/site-packages/scipy/sparse/_sparsetools.so
In the log file for MaxBin2, it says:
----- Starting binning with MaxBin2... -----
------------------------------------------------------------------------------------------------------------------------
Cannot run IDBA-UD. Please indicate the file directory in 'setting' file.
------------------------------------------------------------------------------------------------------------------------
----- MaxBin2 finished successfully, and found 0 bins! -----
Both MaxBin2 and concoct abundance files seems to be fine:
head mb2_abund_list.txt
mb2_AAGAGGCATCGCATAA_merged_TM_paired.txt
mb2_ACTCGCTATCGCATAA_merged_TM_paired.txt
...
head mb2_AAGAGGCATCGCATAA_merged_TM_paired.txt
contig-1 53.4517
contig-2 1.2245
contig-3 18.5064
head concoct_depth.txt
contig-1 53.4517 0.103837 0.025839 0.21196 0.135306 0.112696 0.0226196 23.9448 0.0491105 0.0210677 0.0967119 0.082113 0.0973345 0.137699 0.088772 0.0479484 0.176484 0.129474 0.0901337 0.0602444 0.0725666 0.603433 0.131319 0.0282016
contig-2 1.2245 2.09769 1.36187 0.96547 1.05846 1.11671 5.11016 0.975225 0.149114 6.51347 5.00844 0.588666 3.05451 0.642295 0.947799 2.12208 1.30022 1.26318 1.13096 0.930848 1.14926 4.7246 1.36526 1.47942
contig-3 18.5064 0.194334 0.0958584 0.162577 0.224753 0.175527 0.103175 18.4421 0.0364323 0.0595865 0.479316 0.17967 0.20679 0.303299 0.164022 0.462451 0.129024 0.173942 0.190543 0.104959 0.118599 0.744656 0.907991 0.0647205
Do you know what could it be going on?
Thanks in advance.
About this issue
- Original URL
- State: open
- Created 6 years ago
- Comments: 19
Thanks for that Gisle! Looks like accidentally removed
libopenblasas a dependency when I was playing around with the dependency versions… The error should be gone inmetawrap=1.0.5.