#3 Error when running
I'm getting the next output. In the result folder, some files are OK but other are empty.
================================================================
Program: CD-HIT, V4.6, Mar 30 2017, 14:33:45
Command: ./cd-hit/cd-hit-est -i
./result/wheat.candidateTE8.fasta -o
./result/wheat.clusteredCandidateTE8.fasta -c 0.80 -n
5 -d 0 -T 0 -aL 0.99 -s 0.8 -M 0
Started: Thu Mar 30 17:40:41 2017
Output
Option -T is ignored: multi-threading with OpenMP is NOT enabled!
total seq: 0
longest and shortest : 0 and 18446744073709551615
Total letters: 0
Sequences have been sorted
Approximated minimal memory consumption:
Sequence : 0M
Buffer : 1 X 12M = 12M
Table : 1 X 0M = 0M
Miscellaneous : 0M
Total : 12M
Table limit with the given memory limit:
Max number of representatives: 4000000
Max number of word counting entries: 50000000
0 finished 0 clusters
Apprixmated maximum memory consumption: 12M
writing new database
writing clustering information
program completed !
Total CPU time 0.01
Error using fastaread (line 158)
Input does not exist or is not a valid FASTA file.
Error in detectMITE (line 60)
Cluster = fastaread(['./result/' genome '.clusteredCandidateTE' num2str(count) '.fasta.clstr']);
Error in do_MITE_detection (line 141)
detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen
,p_FlankSeq_Len,genome,p_cpu);
Content of one of the clstr file.
It seems like it is iterating through 8 candidates but from 4th on they are empty files
Last edit: JuanC 2017-03-30
Hello JuanC,
The error is produced when some temporary file is empty (means no candidate was found in that stage), this bug is fixed in the new version, please use the new one.
Thanks for your bug report!
Congting Ye
Hi,
I'm still getting this error even though I'm quite sure I'm using the newest version of detectMITE. It gives results for only the first 8 out of 15 iterations. Any idea what the problem might be? Thanks!!
I'm running this on our server which is SUSE Linux Enterprise Server 12 SP3, and I'm using Matlab version R2016a and cd-hit v4.6.1-2012-08-27.
Hi Virginia Markham,
According to the error info you post, I figure out that you were using an old version of detectMITE. The code "Cluster = fastaread(['./result/' genome '.clusteredCandidateTE' num2str(count) '.fasta.clstr']);" is at line 60 of the old verion (such as detectMITE.20160818.tar.gz), but at line 62 of the newest version. Please go the link (https://sourceforge.net/projects/detectmite/files/detectMITE.20170425.tar.gz/download) to download the newest version.
Error using fastaread (line 158)
Input does not exist or is not a valid FASTA file.
Error in detectMITE (line 60)
Cluster = fastaread(['./result/' genome '.clusteredCandidateTE' num2str(count) '.fasta.clstr']);
Error in do_MITE_detection (line 141)
detectMITE(data_file,p_TIR_Len,p_TSD_minLen ,p_TSD_maxLen ,p_MITE_minLen ,p_MITE_maxLen
,p_FlankSeq_Len,genome,p_cpu);
Thanks so much for your response! Sorry, I should have been more clear. This is my first time posting on sourceforge, apologies for my mistakes. That error you mention ( "Cluster = fastaread(['./result/' ...") is from Juan C. I did not get that error. In fact, I did not get any error message at all. But like Juan C., only my first few iterations are giving clusters. I have 15 iterations and the first 8 look good (for example: "80597 finished 51831 clusters"), but the last 7 are not giving results ("0 finished 0 clusters").
These output files are empty:
my_genome.mite.fasta
my_genome.miteSet.fasta
result/my_genome.candidateTE*_*.fasta
result/my_genome.clusteredCandidateTE*_*.fasta
result/my_genome.clusteredCandidateTE*_*.fasta.clstr
result/my_genome.miteCandidate*.fasta
result/my_genome.miteCandidate*_*.fasta
These output files are not empty:
result/my_genome.candidateTE*.fasta
result/my_genome.clusteredCandidateTE*.fasta
result/my_genome.clusteredCandidateTE*.fasta.clstr
Do you have any ideas about what I'm doing wrong? Thanks so much in advance, I really appreciate it. My output is very long so I am only posting the beginning and the end, with an "etc." in the middle:
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016a (9.0.0.341360) 64-bit (glnxa64)
February 11, 2016
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Starting parallel pool (parpool) using the 'local' profile ... connected to 16 workers. ===============================================================
Program: CD-HIT, V4.6, Jan 23 2019, 14:52:54
Command: ./cd-hit/cd-hit-est -i
./result/Bd21.candidateTE1.fasta -o
./result/Bd21.clusteredCandidateTE1.fasta -c 0.80 -n 5
-d 0 -T 0 -aL 0.99 -s 0.8 -M 0
Started: Mon Jan 28 13:12:47 2019 ================================================================
Output
Option -T is ignored: multi-threading with OpenMP is NOT enabled!
total seq: 80597
longest and shortest : 149 and 50
Total letters: 7739197
Sequences have been sorted
Approximated minimal memory consumption:
Sequence : 18M
Buffer : 1 X 13M = 13M
Table : 1 X 1M = 1M
Miscellaneous : 1M
Total : 33M
Table limit with the given memory limit:
Max number of representatives: 4000000
Max number of word counting entries: 104574500
comparing sequences from 0 to 80597
.......... 10000 finished 7548 clusters
.......... 20000 finished 14234 clusters
.......... 30000 finished 18927 clusters
.......... 40000 finished 26529 clusters
.......... 50000 finished 33365 clusters
.......... 60000 finished 38920 clusters
.......... 70000 finished 45481 clusters
.......... 80000 finished 51523 clusters
Apprixmated maximum memory consumption: 67M
writing new database
writing clustering information
program completed !
================================================================
....[etc.]...
================================================================
Output
----------------------------------------------------------------
Option -T is ignored: multi-threading with OpenMP is NOT enabled!
total seq: 0
longest and shortest : 0 and 18446744073709551615
Total letters: 0
Sequences have been sorted
Approximated minimal memory consumption:
Sequence : 0M
Buffer : 1 X 12M = 12M
Table : 1 X 0M = 0M
Miscellaneous : 0M
Total : 12M
Table limit with the given memory limit:
Max number of representatives: 4000000
Max number of word counting entries: 50000000
Apprixmated maximum memory consumption: 12M
writing new database
writing clustering information
program completed !
Total CPU time 0.01
IdleTimeout has been reached.
Parallel pool using the 'local' profile is shutting down.
Last edit: Virginia Markham 2019-02-02
In your case, this indicates that no candidate MITEs was detected from your input. I guess that you may run detectMITE using a small fasta file for test, a small input often results in nothing detected. You could run detectMITE with Arabidopsis genome to test whether it could run correctly.
Thanks for your interest in detectMITE!
Hm okay, I'll try that. Thanks!!