Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
On Fri, Aug 22, 2014 at 9:39 AM, Marija Atanaskovic ma...@unimelb.edu.au wrote: Mira doesn’t work on Galaxy. This is the log message I receive. Tool: Assemble with MIRA v3.4 Name: MIRA log Created: Fri Aug 22 00:24:38 2014 (UTC) Filesize: 0 bytes Dbkey: ? Format: txt Galaxy Tool Version: 0.0.10 Tool Version: None Tool Standard Output: stdout Tool Standard Error: stderr Tool Exit Code: None API ID: d5f55b83db1f410a Full Path: /mnt/galaxy/files/000/dataset_326.dat ... What was the stdout and stderr information? Did you install this from the main tool shed?: https://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler Also I can’t install Mira 4. This is the message I receive. Any suggestions. Getting Internal Server Error is unhelpful - I can't really guess what might be going wrong here :( I have had problems with the MIRA dependencies when Bastien has renamed folders on sourceforge... are you using the Test Tool Shed here (since I have not yet released the MIRA 4 wrapper on the main ToolShed)?: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Regards, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
On Fri, Aug 22, 2014 at 8:18 PM, Marija Atanaskovic ma...@unimelb.edu.au wrote: Hi Peter, I don¹t know what the stdout and stderr information was. I click on it but nothing comes up. I installed from the main toolshed: http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler Yes, I did use the test toolshed for Mira 4. Regards, Marija If stdout and stderr are empty, this is consistent with MIRA never even starting (as suggested by the next bit of information below). On Fri, Aug 22, 2014 at 8:20 PM, Marija Atanaskovic ma...@unimelb.edu.au wrote: Hi Peter, This is the error in history under MIRA log: tool error An error occurred with this dataset:Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. Regards, Marija That suggests your Galaxy job runner is not properly configured, and MIRA itself was never started. Are you the site administrator? Are other Galaxy tools working? Are other Galaxy tools installed from the ToolShed working? On Fri, Aug 22, 2014 at 8:22 PM, Marija Atanaskovic ma...@unimelb.edu.au wrote: Hi Peter, One more thing. The data that I am trying to analyse are fastq files of Ion Torrent reads. I have used them with other assemblers e.g., velvet, CLC. Marija I have not personally used Ion Torrent, but that ought to be fine. Peter P.S. You forgot to CC the mailing list. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
On Fri, Aug 22, 2014 at 8:00 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Aug 22, 2014 at 9:39 AM, Marija Atanaskovic ma...@unimelb.edu.au wrote: Also I can’t install Mira 4. This is the message I receive. Any suggestions. Getting Internal Server Error is unhelpful - I can't really guess what might be going wrong here :( This is a guess, but it could be you need to set the https_proxy in the /etc/environment file - see this thread: http://dev.list.galaxyproject.org/Internal-Server-Error-when-trying-to-install-a-tool-from-the-Tool-shed-tt4665361.html Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
Hi Peter, Thanks for your response and for the advice from the other subscribers. I am not the site administrator, but I have passed on all the email correspondence to the administrators. I am a “wet-lab” scientist who wanted to use the programme for my work. That is why I use Galaxy as the script writing etc., is taken care of. Galaxy is a great resource for people like me. I’ll let you know what happens. Best regards, Marija On 23/08/2014 8:48 am, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Aug 22, 2014 at 8:18 PM, Marija Atanaskovic ma...@unimelb.edu.au wrote: Hi Peter, I don¹t know what the stdout and stderr information was. I click on it but nothing comes up. I installed from the main toolshed: http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler Yes, I did use the test toolshed for Mira 4. Regards, Marija If stdout and stderr are empty, this is consistent with MIRA never even starting (as suggested by the next bit of information below). On Fri, Aug 22, 2014 at 8:20 PM, Marija Atanaskovic ma...@unimelb.edu.au wrote: Hi Peter, This is the error in history under MIRA log: tool error An error occurred with this dataset:Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. Regards, Marija That suggests your Galaxy job runner is not properly configured, and MIRA itself was never started. Are you the site administrator? Are other Galaxy tools working? Are other Galaxy tools installed from the ToolShed working? On Fri, Aug 22, 2014 at 8:22 PM, Marija Atanaskovic ma...@unimelb.edu.au wrote: Hi Peter, One more thing. The data that I am trying to analyse are fastq files of Ion Torrent reads. I have used them with other assemblers e.g., velvet, CLC. Marija I have not personally used Ion Torrent, but that ought to be fine. Peter P.S. You forgot to CC the mailing list. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
On Thu, Apr 19, 2012 at 12:40 AM, JIE CHEN jiechenable1...@gmail.com wrote: The version I installed is : mira_3.4.0_prod_linux-gnu_x86_64_static OK, good. The other key question I asked was did you get anything in the MIRA log file (it should be in your history with text data even though it will be red as a failed job)? Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
Hi Peter, Thank you for your patience. I checked the error message in the history. They all give exactly the same error-- the one i gave in the first thread. I re thinks the procedure many times and it shouldn't have any problem. Don't know why. What i have done: 1. Installed the mira wrappers using the Galaxy web UI and checked that the mira.py and mira.xml is under one of the directoriesof the shed_tools directory. 2. installed the mira 3.4.0 binaries in my host Thanks a lot. Tyler On Thu, Apr 19, 2012 at 2:11 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Thu, Apr 19, 2012 at 12:40 AM, JIE CHEN jiechenable1...@gmail.com wrote: The version I installed is : mira_3.4.0_prod_linux-gnu_x86_64_static OK, good. The other key question I asked was did you get anything in the MIRA log file (it should be in your history with text data even though it will be red as a failed job)? Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
On Thu, Apr 19, 2012 at 6:35 PM, JIE CHEN jiechenable1...@gmail.com wrote: Hi Peter, Thank you for your patience. I checked the error message in the history. They all give exactly the same error-- the one i gave in the first thread. Are you saying this is the entire contents of the MIRA log entry in the history? Return error code 1 from command: mira --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat SOLEXA_SETTINGS -LR:lsd=1:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1 I'm pretty sure you are just telling me the error message. I would have expected more than that, e.g. a line MIRA took XXX minutes before that error message. To try to be even clearer: 1. Start your web browser and goto your Galaxy 2. Upload/import the files 3. Select the MIRA tool from left hand pane 4. Select input files and set parameters 5. Click Execute 6. Notice that six new history entries appear: MIRA contigs (FASTA), MIRA contigs (QUAL),MIRA contigs (CAF), MIRA contigs (ACE), MIRA coverage (Wiggle), MIRA log 7. Wait for MIRA to fail and the six new history entries to go red. 8. Click on the eye icon for the red history item MIRA log 9. Copy and paste the MIRA log contents to an email. Also, and perhaps equally useful, can you access this server at the command line and try the exact same failing command (from a temp directory - it may create lots of files and folders)? Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
Hi Peter, Here is the full log: This is MIRA V3.4.0 (production version). Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. To (un-)subscribe the MIRA mailing lists, see: http://www.chevreux.org/mira_mailinglists.html After subscribing, mail general questions to the MIRA talk mailing list: mira_t...@freelists.org To report bugs or ask for features, please use the new ticketing system at: http://sourceforge.net/apps/trac/mira-assembler/ This ensures that requests don't get lost. Compiled by: bach Sun Aug 21 17:50:30 CEST 2011 On: Linux arcadia 2.6.38-11-generic #48-Ubuntu SMP Fri Jul 29 19:02:55 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux Compiled in boundtracking mode. Compiled in bugtracking mode. Compiled with ENABLE64 activated. Runtime settings (sorry, for debug): Size of size_t : 8 Size of uint32 : 4 Size of uint32_t: 4 Size of uint64 : 8 Size of uint64_t: 8 Current system: Linux whsiao-ubuntu 2.6.32-40-generic #87-Ubuntu SMP Tue Mar 6 00:56:56 UTC 2012 x86_64 GNU/Linux Parsing parameters: --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1 Parameters parsed without error, perfect. -CL:pec and -CO:emeas1clpec are set, setting -CO:emea values to 1. -- Parameter settings seen for: Sanger data (also common parameters) Used parameter settings: General (-GE): Project name in (proin) : mira Project name out (proout) : mira Number of threads (not) : 2 Automatic memory management (amm) : yes Keep percent memory free (kpmf) : 15 Max. process size (mps) : 0 EST SNP pipeline step (esps): 0 Use template information (uti) : yes Template insert size minimum (tismin) : -1 Template insert size maximum (tismax) : -1 Template partner build direction (tpbd) : -1 Colour reads by hash frequency (crhf) : yes Load reads options (-LR): Load sequence data (lsd): yes File type (ft) : fastq External quality (eq) : from SCF (scf) Ext. qual. override (eqo) : no Discard reads on e.q. error (droeqe): no Solexa scores in qual file (ssiqf) : no FASTQ qual offset (fqqo): 0 Wants quality file (wqf): yes Read naming scheme (rns): [san] Sanger Institute (sanger) Merge with XML trace info (mxti): no Filecheck only (fo) : no Assembly options (-AS): Number of passes (nop) : 4 Skim each pass (sep): yes Maximum number of RMB break loops (rbl) : 2 Maximum contigs per pass (mcpp) : 0 Minimum read length (mrl) : 80 Minimum reads per contig (mrpc) : 2 Base default quality (bdq) : 10 Enforce presence of qualities (epoq): yes Automatic repeat detection (ard): yes Coverage threshold (ardct) : 2 Minimum length (ardml) : 400 Grace length (ardgl): 40 Use uniform read distribution (urd) : no Start in pass (urdsip): 3 Cutoff multiplier (urdcm) : 1.5 Keep long repeats separated (klrs) : no Spoiler detection (sd) : yes Last pass only (sdlpo) : yes Use genomic pathfinder (ugpf) : yes Use emergency search stop (uess): yes ESS partner depth (esspd) : 500 Use emergency blacklist (uebl) : yes Use max. contig build time (umcbt) : no Build time in seconds (bts) : 1 Strain and backbone options (-SB): Load straindata (lsd) : no Assign default strain (ads) : no Default strain name (dsn) : StrainX Load backbone (lb) : no Start backbone usage in pass (sbuip): 3 Backbone file type (bft): fasta
Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
On Thu, Apr 19, 2012 at 7:13 PM, JIE CHEN jiechenable1...@gmail.com wrote: Hi Peter, Here is the full log: Excellent :) The good news is MIRA seems to be installed and running fine - it just didn't like your test data, and I understand why: ... Sanger will load 1 reads. Longest Sanger: 36 Longest 454: 0 Longest IonTor: 0 Longest PacBio: 0 Longest Solexa: 0 Longest Solid: 0 Longest overall: 36 Total reads to load: 1 ... Sangertotal bases:36 used bases in used reads: 0 454 total bases:0 used bases in used reads: 0 IonTortotal bases:0 used bases in used reads: 0 PacBiototal bases:0 used bases in used reads: 0 Solexatotal bases:0 used bases in used reads: 0 Solid total bases:0 used bases in used reads: 0 .. Fatal error (may be due to problems of the input data or parameters): No read can be used for assembly. ... Then finally some information my wrapper script adds: MIRA took 0.00 minutes Return error code 1 from command: mira --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1 It appears you are trying to run MIRA with a single 36bp read, telling MIRA this is a Sanger read. That is very odd (not least because a 36bp read sounds more likely to be an early Solexa/Illumina read from the length). Has something gone wrong with loading the data into Galaxy? Or did you just want to try a trivial test case? If so, it was too simple and MIRA has stopped because it thinks it is bad input. The MIRA output log file (which is actually written to the stout if you run MIRA yourself at the command line) is quite verbose, but it is incredibly useful for diagnosing problems. That is why I collect it as one of the output files in Galaxy. You should be able to try some larger realistic examples, e.g. a virus or a bacterial genome depending on your server's capabilities. And if they fail, have a look through the log file for why MIRA said it failed. Also keep in mind that the Galaxy wrapper is deliberately a simplified front end - MIRA has dozens of command line options which are not available via my wrapper for simplicity. Regards, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
On Wed, Apr 18, 2012 at 11:21 PM, JIE CHEN jiechenable1...@gmail.com wrote: Dear all, I just installed Mira-Assembler via Galaxy tool sheds. As expected, it downloaded the wrappers into the shed-tools directory. Then I downloaded and installed Mira binaries on the system and add it to $PATH. Right now, mira can run successfully in the command line prompt. Which version of MIRA did you install? However when i run it in the Galaxy UI, i run into the below error: Return error code 1 from command: mira --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat SOLEXA_SETTINGS -LR:lsd=1:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1 Anyone know why? Thanks in advance. Did you get anything in the MIRA log file (it should be in your history with text data even though it will be red as a failed job)? Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY
The version I installed is : mira_3.4.0_prod_linux-gnu_x86_64_static On Wed, Apr 18, 2012 at 3:31 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, Apr 18, 2012 at 11:21 PM, JIE CHEN jiechenable1...@gmail.com wrote: Dear all, I just installed Mira-Assembler via Galaxy tool sheds. As expected, it downloaded the wrappers into the shed-tools directory. Then I downloaded and installed Mira binaries on the system and add it to $PATH. Right now, mira can run successfully in the command line prompt. Which version of MIRA did you install? However when i run it in the Galaxy UI, i run into the below error: Return error code 1 from command: mira --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat SOLEXA_SETTINGS -LR:lsd=1:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1 Anyone know why? Thanks in advance. Did you get anything in the MIRA log file (it should be in your history with text data even though it will be red as a failed job)? Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
