Problems with C-QUARK standalone

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skyto
Posts: 4
Joined: Tue Jun 29, 2021 8:25 am

Problems with C-QUARK standalone

Post by skyto »

Hello!
I have installed C-QUARK on the fresh OS (Ubuntu 20.04.1) and tried to satisfy all the dependencies it has. Nevertheless it still produce many errors while running and doesn't produce any result. I downloaded and checked libraries and C-QUARK itself two times. Some errors from example run are written here. Almost complete log-file is in the attachment. May there be any help or solution?

1) Error in /mnt/disk/C-QUARK-1.0/contact/DeepMSA/bin/hhblits: could not open file 'hms0_64267115.hhm'
grep: /tmp/skyto/CQexample_MSA/MSAexample/hmmsearch.a3m: No such file or directory
/mnt/disk/C-QUARK-1.0/contact/DeepMSA/bin/rmRedundantSeq 99 60 /tmp/skyto/CQexample_MSA/MSAexample/hmmsearch.aln > /tmp/skyto/CQexample_MSA/MSAexample/hmmsearch.60.aln
Traceback (most recent call last):
File "/mnt/disk/C-QUARK-1.0/contact/DeepMSA/scripts/build_MSA.py", line 1119, in <module>
ncpu=ncpu, overwrite_dict=parse_overwrite_option(overwrite))
File "/mnt/disk/C-QUARK-1.0/contact/DeepMSA/scripts/build_MSA.py", line 986, in build_MSA
shutil.copyfile(hmmsearch_prefix+".a3m",prefix+".hmsa3m")
File "/usr/lib/python2.7/shutil.py", line 96, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: '/tmp/skyto/CQexample_MSA/MSAexample/hmmsearch.a3m'

2) Compilation is falling back to object mode WITH looplifting enabled because Function "cal_large_matrix1" failed type inference due to: No implementation of function Function(<built-in function zeros>) found for signature:
>>> zeros(list(int64)<iv=None>)

3) Traceback (most recent call last):
File "deeppre.py", line 239, in <module>
model.load_state_dict(torch.load(saved_model, map_location=lambda storage, loc: storage))
File "/home/skyto/.local/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1406, in load_state_dict
raise RuntimeError('Error(s) in loading state_dict for {}:\n\t{}'.format(
RuntimeError: Error(s) in loading state_dict for ResNet:
Unexpected running stats buffer(s) "bn1.running_mean" and "bn1.running_var" for InstanceNorm2d with track_running_stats=False. If state_dict is a checkpoint saved before 0.4.0, this may be expected because InstanceNorm2d does not track running stats by default since 0.4.0. Please remove these keys from state_dict. If the running stats are actually needed, instead set track_running_stats=True in InstanceNorm2d to enable them. See the documentation of InstanceNorm2d for details.

4) cannot load homolist bhomolisti.txt

5) ---------- input of mk_contactmap.pl ----------------->
Wcon= 0.355
Lch= 108
confcomm= /mnt/disk/C-QUARK-1.0/common/conf27.comm
svmseq= restriplet,tripletres,resplm,respre,deepplm
aLo(type1,2,3,4)= 1, 2, 4.5, 7.5
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
restriplet not exist, skip! ----------==========
tripletres not exist, skip! ----------==========
resplm not exist, skip! ----------==========
respre not exist, skip! ----------==========
deepplm not exist, skip! ----------==========
cp /mnt/disk/C-QUARK-1.0/QUARKmod/QUARK_REMC QUA_CQ_example_1 .....
run simulations ...........
Segmentation fault (core dumped)
mk=0
mk=0, without trajectories geneated!
Attachments
c-quark_log.zip
(14.56 KiB) Downloaded 21 times
jlspzw
Posts: 31
Joined: Tue May 04, 2021 5:04 pm

Re: Problems with C-QUARK standalone

Post by jlspzw »

Hi skyto,

The problem occurs on DeepMSA stage, I guess you may try to clean /tmp/skyto/ during the job running, based on you log file, it seems DeepMSA running correctly, but some output files are lost during the job running. So please clean the example folder (only left the seq.fasta file) and re-run the program, make sure no file operation (like rm) to this folder, /tmp/skyto/ and make sure you have enough space in the device. If you still has problem, then you can go to DeepMSA folder manually run the DeepMSA main program following the DeepMSA readme, see if you still has this problem, if the problem still exist, let us know your further information.

Thank you use our software.

Best
IT team
skyto
Posts: 4
Joined: Tue Jun 29, 2021 8:25 am

Re: Problems with C-QUARK standalone

Post by skyto »

Cleaning working directories didn't help. I think i've already done this. Running DeepMSA manually is very hard and complicated as i can see, because readme-file contains only one command (it gives expected result), while C-QUARK invokes dozens of them.
jlspzw
Posts: 31
Joined: Tue May 04, 2021 5:04 pm

Re: Problems with C-QUARK standalone

Post by jlspzw »

Dear user,

During the program running, there are many files created by the program will locate in /tmp/skyto and /tmp/. Do NOT and make sure your system will NOT clean those two folders!

It is not difficult to run DeepMSA

you can do

export HHLIB=/mnt/disk/C-QUARK-1.0/contact/DeepMSA

then run

/mnt/disk/C-QUARK-1.0/contact/DeepMSA/scripts/build_MSA.py /mnt/disk/C-QUARK-1.0/example/seq.fasta -hhblitsdb=/mnt/disk/ITLIB/uniclust30/uniclust30_2017_04 -jackhmmerdb=/mnt/disk/ITLIB/uniref90/uniref90.fasta -hmmsearchdb=/mnt/disk/ITLIB/metaclust/metaclust.fasta

see what is the output

Best
ITteam
jlspzw
Posts: 31
Joined: Tue May 04, 2021 5:04 pm

Re: Problems with C-QUARK standalone

Post by jlspzw »

If the python has issue, then you can try

/bin/python2 /mnt/disk/C-QUARK-1.0/contact/DeepMSA/scripts/build_MSA.py /mnt/disk/C-QUARK-1.0/example/seq.fasta -hhblitsdb=/mnt/disk/ITLIB/uniclust30/uniclust30_2017_04 -jackhmmerdb=/mnt/disk/ITLIB/uniref90/uniref90.fasta -hmmsearchdb=/mnt/disk/ITLIB/metaclust/metaclust.fasta
skyto
Posts: 4
Joined: Tue Jun 29, 2021 8:25 am

Re: Problems with C-QUARK standalone

Post by skyto »

Unfortunately, no difference at all.
jlspzw
Posts: 31
Joined: Tue May 04, 2021 5:04 pm

Re: Problems with C-QUARK standalone

Post by jlspzw »

Let me know what's the error information when you run deepmsa solely.

Thank you
skyto
Posts: 4
Joined: Tue Jun 29, 2021 8:25 am

Re: Problems with C-QUARK standalone

Post by skyto »

The same error:
Error in /home/skyto/C-QUARK-1.0/contact/DeepMSA/bin/hhblits: could not open file 'hms0_64267115.hhm'
grep: /tmp/skyto/MSA_6484835649/hmmsearch.a3m: No such file or directory
/home/skyto/C-QUARK-1.0/contact/DeepMSA/bin/rmRedundantSeq 99 60 /tmp/skyto/MSA_6484835649/hmmsearch.aln > /tmp/skyto/MSA_6484835649/hmmsearch.60.aln
Traceback (most recent call last):
File "/home/skyto/C-QUARK-1.0/contact/DeepMSA/scripts/build_MSA.py", line 1119, in <module>
ncpu=ncpu, overwrite_dict=parse_overwrite_option(overwrite))
File "/home/skyto/C-QUARK-1.0/contact/DeepMSA/scripts/build_MSA.py", line 986, in build_MSA
shutil.copyfile(hmmsearch_prefix+".a3m",prefix+".hmsa3m")
File "/usr/lib/python2.7/shutil.py", line 96, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: '/tmp/skyto/MSA_6484835649/hmmsearch.a3m'
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