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Old 05-30-2016, 05:09 AM   #1
halocaridina
Junior Member
 
Location: US

Join Date: Jan 2013
Posts: 2
Default REPET v2.5 and errors related to Matcher

Thank you in advance for any info you might supply. I also emailed the developers but I thought I might also post here in case someone has experienced this issue.

I installed REPET v2.5 and all of the dependencies without issues. Then I began going through the TEdenovo_tuto.txt tutorial using the supplied DmelChr4.fa file. Nearly everything has gone as expected though there are two instances where I encounter fatal errors. These two instances also appear to be related to the software matcher that comes with REPET and occur also in REPET v2.4 (which I quickly downloaded, configured and tried).

The first error is when executing the following at Step 3 of the TEdenovo_tuto.txt tutorial:

Code:
TEdenovo.py -P DmelChr4 -C TEdenovo.cfg -S 3 -s Blaster -c Grouper
results in:

Code:
[19:32:06] [DmelChr4_TEdenovo]$ TEdenovo.py -P DmelChr4 -C TEdenovo.cfg -S 3 -s Blaster -c Grouper

START TEdenovo.py (2016-05-29 19:32:09)
version 2.5
project name = DmelChr4
project directory = /home/srsantos/DmelChr4_TEdenovo
beginning of step 3
self-alignment with Blaster
clustering with Grouper
submitting job(s) with groupid 'DmelChr4_TEdenovo_Blaster_Grouper_Matcher' (2016-05-29 19:32:09)
waiting for 1 job(s) with groupid 'DmelChr4_TEdenovo_Blaster_Grouper_Matcher' (2016-05-29 19:32:09)
job 'Matcher_1' in error, re-submitting (1)
job 'Matcher_1' in error, re-submitting (2)
-----------------------------
[19:32:24] [DmelChr4_TEdenovo]$
Resulting directory structure of DmelChr4_Blaster_Grouper/ is:

Code:
[19:32:58] [DmelChr4_Blaster_Grouper]$ ll
total 52K
drwxr-xr-x.  3 srsantos adm 4.0K May 29 19:32 ./
drwxr-xr-x. 18 srsantos adm 4.0K May 29 19:32 ../
-rwxr-xr-x.  1 srsantos adm 4.3K May 29 19:32 ClusterLauncher_DmelChr4_TEdenovo_Blaster_Grouper_Matcher_Matcher_1_2016-5-29_1337.py*
lrwxrwxrwx.  1 srsantos adm   82 May 29 19:32 DmelChr4.align.not_over.filtered -> /home/srsantos/DmelChr4_TEdenovo/DmelChr4_Blaster/DmelChr4.align.not_over.filtered
lrwxrwxrwx.  1 srsantos adm   63 May 29 19:32 DmelChr4_chunks.fa -> /home/srsantos/DmelChr4_TEdenovo/DmelChr4_db/DmelChr4_chunks.fa
drwxr-xr-x.  2 srsantos adm 4.0K May 29 19:32 DmelChr4_TEdenovo_Blaster_Grouper_Matcher_Matcher_1_20160529-193209/
-rw-------.  1 srsantos adm   66 May 29 19:32 Matcher_1.e113
-rw-------.  1 srsantos adm   66 May 29 19:32 Matcher_1.e114
-rw-------.  1 srsantos adm   66 May 29 19:32 Matcher_1.e115
-rw-------.  1 srsantos adm  468 May 29 19:32 Matcher_1.o113
-rw-------.  1 srsantos adm  468 May 29 19:32 Matcher_1.o114
-rw-------.  1 srsantos adm  468 May 29 19:32 Matcher_1.o115
lrwxrwxrwx.  1 srsantos adm   15 May 29 19:32 TEdenovo.cfg -> ../TEdenovo.cfg*
-----------------------------
[19:32:59] [DmelChr4_Blaster_Grouper]$
Cat of Matcher_1.o113:

Code:
[19:32:59] [DmelChr4_Blaster_Grouper]$ cat Matcher_1.o113
('Linux', 'xxxxxxx.edu', '2.6.32-573.3.1.el6.x86_64', '#1 SMP Thu Aug 13 12:55:33 CDT 2015', 'x86_64')
beginTime=1464568329.757138
work in dir '/home/srsantos/DmelChr4_TEdenovo/DmelChr4_Blaster_Grouper'
current status: waiting
updated status: running
tmpDir is : /home/srsantos/DmelChr4_TEdenovo/DmelChr4_Blaster_Grouper
cDir is : /home/srsantos/DmelChr4_TEdenovo/DmelChr4_Blaster_Grouper
ERROR: job returned 256
current status: running
updated status: error
-----------------------------
[19:35:28] [DmelChr4_Blaster_Grouper]$
Cat of Matcher_1.e113:

Code:
[19:35:28] [DmelChr4_Blaster_Grouper]$ cat Matcher_1.e115
Died: Unknown qualifier -m
-----------------------------
[19:36:00] [DmelChr4_Blaster_Grouper]$
Examination of the ClusterLauncher_DmelChr4_TEdenovo_Blaster_Grouper_Matcher_Matcher_1_2016-5-29_1337.py script shows a -m flag associated with the matcher command in it of (last line in the below):

Code:
.
.
	iJob = Job(jobname = "Matcher_1", groupid = "DmelChr4_TEdenovo_Blaster_Grouper_Matcher", launcherFile = "/home/srsantos/DmelChr4_TEdenovo/DmelChr4_Blaster_Grouper/ClusterLauncher_DmelChr4_TEdenovo_Blaster_Grouper_Matcher_Matcher_1_2016-5-29_1337.py", node = os.getenv("HOSTNAME"))
	iDb = DbFactory.createInstance()
	iTJA = TableJobAdaptator(iDb, "jobs")
	print "current status: %s" % iTJA.getJobStatus(iJob)
	iTJA.changeJobStatus(iJob, "running")
	print "updated status: %s" % iTJA.getJobStatus(iJob)
	sys.stdout.flush()
	iDb.close()

	os.symlink("/home/srsantos/DmelChr4_TEdenovo/DmelChr4_Blaster_Grouper/DmelChr4.align.not_over.filtered", "DmelChr4.align.not_over.filtered")
	log = os.system("matcher -m DmelChr4.align.not_over.filtered -j -a -d 10 -g 1 -v -1")
.
.

The second error occurs at Step 8 of the TEdenovo_tuto.txt tutorial, specifically executing:

Code:
TEdenovo.py -P DmelChr4 -C TEdenovo.cfg -S 8 -s Blaster -c RecPil -m Map -f MCL
(Note the “Grp” was removed from the -c option due to the above error)

results in:

Code:
[19:43:52] [DmelChr4_TEdenovo]$ TEdenovo.py -P DmelChr4 -C TEdenovo.cfg -S 8 -s Blaster -c RecPil -m Map -f MCL

START TEdenovo.py (2016-05-29 19:44:04)
version 2.5
project name = DmelChr4
project directory = /home/srsantos/DmelChr4_TEdenovo
2016-05-29 19:44:04 - TEdenovo - INFO - beginning of step 8
2016-05-29 19:44:04 - TEdenovo - INFO - self-alignment with Blaster
2016-05-29 19:44:04 - TEdenovo - INFO - clustering with RecPil
2016-05-29 19:44:04 - TEdenovo - INFO - multiple alignment with Map
2016-05-29 19:44:04 - TEdenovo - INFO - clustering the filtered consensus with MCL
submitting job(s) with groupid 'DmelChr4_TEdenovo_S8_MCL' (2016-05-29 19:44:05)
waiting for 1 job(s) with groupid 'DmelChr4_TEdenovo_S8_MCL' (2016-05-29 19:44:05)
job 'Launch_MCL_1' in error, re-submitting (1)
job 'Launch_MCL_1' in error, re-submitting (2)
-----------------------------
[19:44:20] [DmelChr4_TEdenovo]$
Resulting directory structure of DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL/ is:

Code:
[19:46:06] [DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL]$ ll
total 48K
drwxr-xr-x.  3 srsantos adm 4.0K May 29 19:44 ./
drwxr-xr-x. 19 srsantos adm 4.0K May 29 19:44 ../
-rwxr-xr-x.  1 srsantos adm 5.2K May 29 19:44 ClusterLauncher_DmelChr4_TEdenovo_S8_MCL_Launch_MCL_1_2016-5-29_5402.py*
lrwxrwxrwx.  1 srsantos adm   87 May 29 19:44 DmelChr4_sim_denovoLibTEs_filtered.fa -> ../DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered/DmelChr4_sim_denovoLibTEs_filtered.fa
drwxr-xr-x.  3 srsantos adm 4.0K May 29 19:44 DmelChr4_TEdenovo_S8_MCL_Launch_MCL_1_20160529-194405/
-rw-------.  1 srsantos adm  798 May 29 19:44 Launch_MCL_1.e116
-rw-------.  1 srsantos adm  798 May 29 19:44 Launch_MCL_1.e117
-rw-------.  1 srsantos adm  798 May 29 19:44 Launch_MCL_1.e118
-rw-------.  1 srsantos adm  913 May 29 19:44 Launch_MCL_1.o116
-rw-------.  1 srsantos adm  913 May 29 19:44 Launch_MCL_1.o117
-rw-------.  1 srsantos adm  913 May 29 19:44 Launch_MCL_1.o118
lrwxrwxrwx.  1 srsantos adm   45 May 29 19:44 TEdenovo.cfg -> /home/srsantos/DmelChr4_TEdenovo/TEdenovo.cfg*
-----------------------------
[19:46:07] [DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL]$
Cat of Launch_MCL_1.e116:

Code:
[19:47:18] [DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL]$ cat Launch_MCL_1.e116
stty: standard input: Invalid argument
Traceback (most recent call last):
  File "/usr/local/genome/REPET_linux-x64-2.5/bin/PostAnalyzeTELib.py", line 377, in <module>
    iLaunch.run()
  File "/usr/local/genome/REPET_linux-x64-2.5/bin/PostAnalyzeTELib.py", line 257, in run
    iLaunchMCL.run()
  File "/usr/local/genome/REPET_linux-x64-2.5/commons/launcher/LaunchMCL.py", line 179, in run
    self._logAndRaise("ERROR when launching '%s'" % cmd)
  File "/usr/local/genome/REPET_linux-x64-2.5/commons/launcher/LaunchMCL.py", line 131, in _logAndRaise
    raise Exception(errorMsg)
Exception: ERROR when launching 'matcher -m DmelChr4_sim_denovoLibTEs_filtered.fa.shortH.align -q DmelChr4_sim_denovoLibTEs_filtered.fa.shortH -s DmelChr4_sim_denovoLibTEs_filtered2.fa -a >> blasterMatcher.log 2>&1'
-----------------------------
[19:47:24] [DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL]$
Cat of Launch_MCL_1.o116:

Code:
[19:47:24] [DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL]$ cat Launch_MCL_1.o116
('Linux', 'xxxxxxx.edu', '2.6.32-573.3.1.el6.x86_64', '#1 SMP Thu Aug 13 12:55:33 CDT 2015', 'x86_64')
beginTime=1464569045.520128
work in dir '/home/srsantos/DmelChr4_TEdenovo/DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL'
current status: waiting
updated status: running
2016-05-29 19:44:05 - LaunchMCL - INFO - START LaunchMCL
2016-05-29 19:44:05 - LaunchMCL - INFO - START Blaster-Matcher
2016-05-29 19:44:05 - LaunchMCL - ERROR - ERROR when launching 'matcher -m DmelChr4_sim_denovoLibTEs_filtered.fa.shortH.align -q DmelChr4_sim_denovoLibTEs_filtered.fa.shortH -s DmelChr4_sim_denovoLibTEs_filtered2.fa -a >> blasterMatcher.log 2>&1'
tmpDir is : /home/srsantos/DmelChr4_TEdenovo/DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL
cDir is : /home/srsantos/DmelChr4_TEdenovo/DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL
ERROR: job returned 256
current status: running
updated status: error
-----------------------------
[19:48:17] [DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL]$
Here, matcher is specifically identified as being the issue associated with the error and a -m option again appears.

Again, all other parts of the tutorial complete without issue and produce expected results. So TORQUE:

Code:
[19:55:06] [DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL]$ qsub --version
Version: 4.2.10
Commit: ddf5c4f40091b6157164a8846e5b60f42a5ae7f6
-----------------------------
[19:55:10] [DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL]$
and all the dependencies appear to be fine. This is on a RHEL 6.7 server that is up to date.

Any suggestions you can supply on whether this is a misconfiguration on my part or a bug would be greatly appreciated. Thank you in advance for any insight you can supply.

@halocaridina
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Old 10-26-2016, 08:22 AM   #2
Pantoffeltierchen
Junior Member
 
Location: Germany

Join Date: Oct 2016
Posts: 1
Default

Dear halocaridina,
I want to apologize in advance that this is not an answer. But I recently installed REPET v 2.5 and I'm experiencing the very same problems. Did you ever happen to find a solution for this problem?
Best regards,
Pantoffeltierchen
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