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:
results in:
Resulting directory structure of DmelChr4_Blaster_Grouper/ is:
Cat of Matcher_1.o113:
Cat of Matcher_1.e113:
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):
The second error occurs at Step 8 of the TEdenovo_tuto.txt tutorial, specifically executing:
(Note the “Grp” was removed from the -c option due to the above error)
results in:
Resulting directory structure of DmelChr4_Blaster_RecPil_Map_TEclassif_Filtered_MCL/ is:
Cat of Launch_MCL_1.e116:
Cat of Launch_MCL_1.o116:
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:
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
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
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]$
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]$
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]$
Code:
[19:35:28] [DmelChr4_Blaster_Grouper]$ cat Matcher_1.e115 Died: Unknown qualifier -m ----------------------------- [19:36:00] [DmelChr4_Blaster_Grouper]$
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
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]$
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]$
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]$
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]$
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]$
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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