Question: CD-HIT fatal error
0
gravatar for a.mostafa5050
2 days ago by
a.mostafa50500 wrote:

Hello everybody, when I run CD-HIT-est, after starting the work and the algorithm starts to compare sequences and do some work, it stops the following error message appears (Fatal Error: file opening failed.. Program halted !!). Here is my script:

module load CD-HIT/4.8.1-foss-2018b
cd-hit-est -i /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/Contigs_and_scafolds/New_folder/contigs_F-1year-Amox.fasta -o /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/Contigs_and_scafolds/New_folder/output -M 0 -T 0

I hope that anyone could help me.

ADD COMMENTlink modified 1 day ago • written 2 days ago by a.mostafa50500
1

Fatal Error: file opening failed

Program is either not able to find/open the input file you have specified in your command line or is unable to create the output file your have specified. Check into both possibilities.

ADD REPLYlink written 2 days ago by genomax92k

I mean it starts and after doing some job, it stops and says (Fatal Error: file opening failed.. Program halted !!)

ADD REPLYlink written 2 days ago by a.mostafa50500

Could you post the output of the program? Maybe it's referring to the output file? Do you have write permission to create a file in that folder?

Also, you need to click on moderate, and move your answer to the comment section.

ADD REPLYlink modified 2 days ago • written 2 days ago by Fatima820

This is the output I got. Starting job 1557338 on c5-43 at Sat Nov 21 00:26:07 CET 2020

1) StdEnv

Program: CD-HIT, V4.8.1 (+OpenMP), Jun 22 2019, 13:22:05 Command: cd-hit-est -i /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/Contigs_and_scafolds_2/contigs_F-1year-Amox_S15.fasta -o /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/CD_HIT_output/ -M 0 -T 0

Started: Sat Nov 21 00:26:08 2020

Output

total number of CPUs in the system is 2 Actual number of CPUs to be used: 2

total seq: 1889 longest and shortest : 5441 and 56 Total letters: 729274 Sequences have been sorted

Approximated minimal memory consumption: Sequence : 0M Buffer : 2 X 13M = 26M Table : 2 X 16M = 33M Miscellaneous : 4M Total : 65M

Table limit with the given memory limit: Max number of representatives: 2414213 Max number of word counting entries: 295874244

comparing sequences from 0 to 472

---------- new table with 472 representatives

comparing sequences from 472 to 826

................... 59.9% 60.0% 60.1% 60.7% 60.8% 60.9% 61.0% 61.1% 61.4% 61.6% 61.7% 61.8% 61.9% 62.5% 62.6% 62.7% 62.8% 62.9% 63.0% 63.2% 63.5% 63.6% 63.7% 63.8% 63.9% 64.1% 64.9% 65.0% 65.1% 65.3% 65.4% 65.5% 65.6% 65.7% 65.8% 65.9% 66.1% 66.6% 66.7% 66.8% 67.0% 67.1% 67.2% 67.4% 67.6% 67.8% 67.9% 68.0% 68.1% 68.2% 68.3% 68.5% 68.6% 68.7% 68.9% 69.1% 69.3% 69.5% 69.7% 69.8% 70.0% 70.1% 70.2% 70.4% 70.5% 70.6% 70.7% 70.8% 71.0% 71.2% 71.4% 71.5% 71.6% 71.7% 71.8% 72.0% 72.2% 72.4% 72.5% 72.7% 72.9% 73.1% 73.2% 73.4% 73.5% 73.6% 73.8% 73.9% 74.2% 74.3% 74.4% 74.5% 74.7% 74.9% 75.1% 75.2% 75.3% 75.4% 75.5% 75.6% 75.8% 75.9% 76.0% 76.1% 76.2% 76.3% 76.4% 76.5% 76.6% 76.7% 76.8% 76.9% 77.0% 77.1% 77.2% 77.3% 77.4% 77.6% 77.7% 77.8% 77.9% 78.1% 78.2% 78.4% 78.5% 78.6% 78.7% 78.9% 79.0% 79.1% 79.2% 79.4% 79.5% 79.6% 79.7% 79.8% 79.9% 80.1% 80.3% 80.4% 80.5% 80.6% 80.7% 80.9% 81.0% 81.1% 81.3% 81.4% 81.5% 81.7% 81.8% 82.0% 82.2% 82.3% 82.4% 82.5% 82.6% 82.8% 83.0% 83.1% 83.2% 83.3% 83.4% 83.5% 83.7% 83.9% 84.0% 84.2% 84.3% 84.4% 84.5% 84.6% 84.8% 85.0% 85.1% 85.2% 85.3% 85.4% 85.5% 85.7% 85.8% 85.9% 86.0% 86.1% 86.2% 86.4% 86.6% 86.7% 86.9% 87.0% 87.1% 87.2% 87.3% 87.5% 87.6% 87.7% 87.8% 87.9% 88.0% 88.1% 88.3% 88.4% 88.5% 88.7% 88.8% 88.9% 89.0% 89.3% 89.4% 89.6% 89.7% 89.8% 89.9% 90.1% 90.3% 90.4% 90.5% 90.6% 90.8% 91.1% 91.4% 91.5% 91.6% 91.9% 92.1% 92.2% 92.3% 92.4% 92.5% 92.7% 92.9% 93.1% 93.2% 93.3% 93.4% 93.6% 93.9% 94.0% 94.2% 94.3% 94.4% 94.6% 94.7% 94.8% 95.0% 95.2% 95.3% 95.4% 95.6% 95.7% 95.9% 96.1% 96.2% 96.5% 96.7% 96.8% 96.9% 97.0% 97.1% 97.2% 97.5% 97.6% 97.8% 97.9% 98.0% 98.1% 98.5% 98.7% 98.8% 99.2% 99.3% 99.4% 99.5% 99.6% 99.7% 99.8% 99.9%---------- new table with 354 representatives

comparing sequences from 826 to 1091

.................... 69.5% 69.7% 70.0% 70.1% 70.2% 70.4% 70.5% 70.6% 70.7% 70.8% 71.0% 71.4% 71.5% 71.6% 71.9% 72.0% 72.2% 72.3% 72.4% 72.5% 72.6% 72.9% 73.2% 73.3% 73.5% 73.7% 73.9% 74.3% 74.4% 74.6% 74.9% 75.0% 75.2% 75.3% 75.4% 75.6% 75.7% 75.9% 76.0% 76.2% 76.3% 76.4% 76.5% 76.6% 76.7% 76.8% 76.9% 77.2% 77.3% 77.4% 77.6% 77.7% 78.0% 78.3% 78.8% 79.0% 79.5% 79.9% 80.2% 80.9% 81.1% 81.5% 82.1% 82.4% 82.5% 82.6% 83.0% 83.5% 83.7% 84.2% 86.9% 89.7% 90.1%---------- new table with 265 representatives

comparing sequences from 1091 to 1889

.......... Fatal Error: file opening failed Program halted !!

---------- new table with 342 representatives

 1889  finished       1433  clusters

Approximated maximum memory consumption: 69M writing new database

ADD REPLYlink written 1 day ago by a.mostafa50500
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