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  • 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

  • #2
    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

    Comment

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