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DMFold Run_DeepMSA2.py error

Posted: Fri Apr 05, 2024 9:18 am
by kehan777
DeepMSA2_noIMG has been complete for test-B!
sed: couldn't write 224 items to stdout: Broken pipe
Segmentation fault

Error: File format problem in trying to open HMM file /tmp/adsb/MSA_46945579/hmmsearch.hmm.
File exists, but appears to be empty?

Failed to open key file /tmp/adsb/MSA_46945579/hmmsearch.0.tbl

WARNING! As most processes are I/O bounded, increasing the number of threads could worsen instead of improves total running timeTraceback (most recent call last):
File "/mnt/e/DMFold/bin/qMSA/scripts/qMSA2.py", line 1064, in <module>
nf=build_MSA(prefix,sequence,tmpdir,db_dict,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/e/DMFold/bin/qMSA/scripts/qMSA2.py", line 916, in build_MSA
hms_nf=search_metaclust(query_fasta,sequence,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/e/DMFold/bin/qMSA/scripts/qMSA2.py", line 806, in search_metaclust
return run_hmsblits(query_fasta,sequence,query_profile_prefix,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/e/DMFold/bin/qMSA/scripts/qMSA2.py", line 724, in run_hmsblits
txt+=trim_eslsfetch(outprefix+".fseqs",outprefix+".match",
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/e/DMFold/bin/qMSA/scripts/qMSA2.py", line 509, in trim_eslsfetch
fp=open(first_file,'r')
^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/adsb/MSA_46945579/hmmsearch.0.match'
Segmentation fault

Error: File format problem in trying to open HMM file /tmp/adsb/MSA_8263872696/hmmsearch.hmm.
File exists, but appears to be empty?

Failed to open key file /tmp/adsb/MSA_8263872696/hmmsearch.0.tbl

Traceback (most recent call last):
File "/mnt/e/DMFold/bin/dMSA/scripts/build_MSA.py", line 1118, in <module>
nf=build_MSA(prefix,sequence,tmpdir,db_dict,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/e/DMFold/bin/dMSA/scripts/build_MSA.py", line 982, in build_MSA
hms_nf=run_hmsblits(query_fasta,sequence,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/e/DMFold/bin/dMSA/scripts/build_MSA.py", line 803, in run_hmsblits
txt+=trim_eslsfetch(outprefix+".fseqs",outprefix+".match",queryseq_fasta=query_fasta,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/e/DMFold/bin/dMSA/scripts/build_MSA.py", line 575, in trim_eslsfetch
fp=open(first_file,'r')
^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/adsb/MSA_8263872696/hmmsearch.0.match';

It looks like it may be related to insufficient memory on my desktop, Can I adjust which parameters of which file to slow down threads and avoid reporting errors?

Re: DMFold Run_DeepMSA2.py error

Posted: Sat Apr 06, 2024 1:09 pm
by jlspzw
Dear user,

You can check the config.py, see the dMSA_cpu setting, etc.

Please try to reduce the CPU number to see if memory can be reduced.

BTW how large is your memory on your Desktop, and how large are your sequences?

Best Regards
Wei Zheng

Re: DMFold Run_DeepMSA2.py error

Posted: Sat Apr 13, 2024 2:33 am
by kehan777
Thank you for your reply´╝îI will try what you suggested

13th Gen Intel(R) Core(TM) i5-13600KF 3.50 GHz
Total Cores 14
# of Performance-cores 6
# of Efficient-cores 8
Total Threads 20
Max Turbo Frequency 5.1 GHz
Performance-core Max Turbo Frequency 5.10 GHz
Efficient-core Max Turbo Frequency 3.90 GHz
Performance-core Base Frequency 3.50 GHz
Efficient-core Base Frequency 2.60 GHz
Total L2 Cache20 MB
Processor Base Power 125 W
Maximum Turbo Power 181 W

Memory 48.0 GB; GPU 4070Ti; Hard Disk Drive 14.5T
>protein-A
GLEKDFLPLYFGWFLTKKSSETLRKAGQVFLEELGNHKAFKKELRHFISGDEPKEKLELVSYFGKRPPGVLHCTTKFCDYKAAGAEEYAQQEVVKRSYGKAFKLSISALFVTPKTAGAQVVLTDQELQLWPSDLDKPSASEGLPPGSRAHVTLGCAADVQPVQTGLDLLDILQQVKGGSQGEAVGELPRGKLYSLGKGRWMLSLTKKMEVKAIFTGYYG
>protein-B
EVQLEESGGGLVQPGGSLRLSCAVSGITLDDFGIGWFRQAPGKEREGVACISPGYEHIYYADSAKGRFTISRDNAKNTVYLQMNNLKPWDTGVYYCAADNDLPDRLWGGSDWSDPSPYDYWGQGTQVTVSS


BTW, Please tell me, are the following modifications correct?
#!/usr/bin/env python
# This is the setting file of the program
import os

rootpath = "/mnt/e/DMFold"
databasesrootpath = os.path.join(rootpath,"database")

para_json = dict(
# main program parameter
programrootpath=rootpath,


qMSApkg=os.path.join(rootpath, "bin/qMSA"),
dMSApkg=os.path.join(rootpath, "bin/dMSA"),
python_DeepPotential=os.path.join(rootpath, "~/miniconda/bin/python")

# submit job parameter
run_type='local', # 'local' or 'sbatch'

##### change those with you sbatch parameters
partition='xxx_cpu',
gpu_partition='xxx_gpu',
account='xxx',

mMSAcpu=4, #modifed
qMSAcpu=4, #modifed
dMSAcpu=4, #modifed

Re: DMFold Run_DeepMSA2.py error

Posted: Mon Apr 15, 2024 1:12 pm
by jlspzw
Dear user,

Your change is correct. Please let us know if you have any questions.

Best
Wei