Zhanglab forum

Hi IT experts,

Recently, I tried to use CR-I-TASSER package for model building of Cryo-EM map, whereas, it reported a serious error that was described below:
Iteration 1
Prefiltering database
.
HMMs passed 1st prefilter (gapless profile-profile alignment) : 39
HMMs passed 2nd prefilter (gapped profile-profile alignment) : 39
HMMs passed 2nd prefilter and not found in previous iterations : 39
Scoring 39 HMMs using HMM-HMM Viterbi alignment
.
Error in /data/wangning/3D-EM-computation/CR-I-TASSER-Suites/CR-I-TASSER-1.0/contact/DeepMSA/bin/hhblits: could not open file 'hms0_1330134275.hhm'
grep: /tmp/wangning/CITseq.fasta_MSA/MSAseq.fasta/hmmsearch.a3m: No such file or directory
/data/wangning/3D-EM-computation/CR-I-TASSER-Suites/CR-I-TASSER-1.0/contact/DeepMSA/bin/rmRedundantSeq 99 60 /tmp/wangning/CITseq.fasta_MSA/MSAseq.fasta/hmmsearch.aln > /tmp/wangning/CITseq.fasta_MSA/MSAseq.fasta/hmmsearch.60.aln
Traceback (most recent call last):
File "/data/wangning/3D-EM-computation/CR-I-TASSER-Suites/CR-I-TASSER-1.0/contact/DeepMSA/scripts/build_MSA.py", line 1119, in <module>
ncpu=ncpu, overwrite_dict=parse_overwrite_option(overwrite))
File "/data/wangning/3D-EM-computation/CR-I-TASSER-Suites/CR-I-TASSER-1.0/contact/DeepMSA/scripts/build_MSA.py", line 986, in build_MSA
shutil.copyfile(hmmsearch_prefix+".a3m",prefix+".hmsa3m")
File "/usr/lib64/python2.7/shutil.py", line 82, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: '/tmp/wangning/CITseq.fasta_MSA/MSAseq.fasta/hmmsearch.a3m'

It seemed likely that hhblits can't find hms0_1330134275.hhm file. Please give me some suggestions. I don't know so much about perl programming language. Thanks in advance.

Sincerely
Ning

Hello Ning,

Could you send your query sequence to me (xizha@umich.edu) to have a test? You don't have to send the density map since this error happens in MSA step.

Best,
Xi

Hi Xi,

Thanks for your reply. Yes, MSA calculation caused this error. Actually, I just used the example sequence (GYYELYRRSTIGNSLVDALDTLISDGRIEASLAMRVLETFDKVVAETLKDNTQSKLTVKGNLDTYGFCDDVWTFIVKNCQVTVEDQSVISVDKLRIVACNS) to try to go through the tutorial quickly. Maybe the tmp file holder which is located at root directory "/" need an additional storage, I supposed. Any suggestion is welcome.

Sincerely,
Ning

What are the specific requirements for storage space in the temporary file holder when performing MSA calculations, and how can I check if the current space is sufficient?
slope game

MSA calculations require sufficient temporary storage space, often in /tmp or /. Use df -h to check available space. If limited, redirect temp files usingbasketball stars TMPDIR=/path/to/larger/storage. Clear unused files regularly or allocate more space to prevent errors. Refer to the MSA tool’s documentation for additional storage management tips.