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Re: [AMOS-help] bank-transact and asmQC errors
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From: Viola N. <vio...@ve...> - 2010-05-01 20:17:42
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Hi, I would just like to share that this does not seem to be a general problem of either ABySS or amos bank-transact - this same action, generating an afg file from ABySS and bank-transact to amos works for me: KAligner -v --seq -mk 41 s_2_sequence_read1+2.fa contigs.fa | abyss2afg contigs.fa - >out.afg bank-transact -c -b out.bnk -m out.afg I cannot come up with an interpretation for your error messages though. There seem to be different realizations of an .afg file (velvet caused me some trouble as well), but if you generated the afg file using abyss2afg then misconfiguration of the read 1/read2 input for example would have caused abyss2afg to fail already (as far as I could figure out it only works with interleaved paired read files). cheers Viola On 4/30/10, Anastasia Gioti <ana...@eb...> wrote: > Hello, > Had the same problem with velvet assemblies at the exact same level > and with the same message. Apparently, amos cannot bank-transact a > whole-genome assembly, at least that was the hint I got by the only > person who replied to me back then. Which is quite a pity because amos > has very nice utilities.... > On Apr 28, 2010, at 12:39 PM, <kri...@sy...> <kri...@sy... > > > wrote: > > > ** Apologies for the double-post. I forgot the subject line in the > > first message** > > > > Dear Fellow AMOS users, > > I am having trouble bringing and ABYSS assembly into AMOS for > > examination. The failure occurs during the bank-transact operation > > (call below): > > > > /usr/local/amos-2.0.8/bin/bank-transact -cb > > assembled_contigs_k34.bnk -m assembled_contigs_k34.afg > > > > The error seems to be coming from the asmQC command. > > > > Can anyone suggest a likely source of the problem? The error > > messages don't direct me toward a specific problem to examine. > > > > > > Error messages follow: > > --------------STDOUT/STDERR---------------------------- > > START DATE: Thu Apr 8 21:29:40 2010 > > Bank is: assembled_contigs_k34.bnk > > 0% 100% > > AFG .................................................. > > Messages read: 58058497 > > Objects added: 58058497 > > Objects deleted: 0 > > Objects replaced: 0 > > END DATE: Thu Apr 8 23:22:36 2010 > > The log file is: assembled_contigs_k34.bnk.runAmos.log > > Doing step 100: Creating FastA > > Command: /usr/local/amos-2.0.8/bin/bank2fasta -b > > assembled_contigs_k34.bnk > assembled_contigs_k34.fasta exited with > > status: 1 > > > > > > --------------From the *.runAmos.log > > file:------------------------------------- > > !!! 2010-04-08 16:13:40 Started by u537306@usrebiocns01 on Thu Apr > > 8 16:13:40 2010 > > > > !!! 2010-04-08 16:13:40 Doing step 100: Creating FastA > > !!! 2010-04-08 16:13:40 Running: /usr/local/amos-2.0.8/bin/ > > bank2fasta -b test2.bnk > test2.fasta > > !!! 2010-04-08 16:14:46 Done! Elapsed time:0d 0h 1m 6s > > > > !!! 2010-04-08 16:14:46 Doing step 300: Analyzing mate-pairs > > !!! 2010-04-08 16:14:46 Running: /usr/local/amos-2.0.8/bin/asmQC -b > > test2.bnk -scaff -recompute -update -numsd 2 > > No library account found in bank test2.bnk > > Invocation: /usr/local/amos-2.0.8/bin/asmQC -b test2.bnk -scaff - > > recompute -update -numsd 2 > > > > Will update libraries in bank > > Will not write features in bank > > Mates within 2 standard deviations from mean considered good > > Reporting regions with less than 0 good mate coverage > > Will recompute library sizes > > Libraries whose mean changes by less than 50 > > and whose std. dev. changes by less than 10 are considered to not > > have changed > > Minimum number of observations required to change library size: 100 > > Reporting regions with more than 2 short mate coverage > > Reporting regions with more than 2 long mate coverage > > Reporting regions with more than 3 coverage by mates oriented the > > same way > > Reporting regions with more than 3 coverage by outie mates > > Reporting regions with more than 3 coverage by outie mates > > Reporting regions with more than 3 coverage by linking mates > > Reporting regions with more than 3 coverage by singleton mates > > > > > > Reporting results by scaffold. In this mode linking clones connect > > different scaffolds. > > > > !!! 2010-04-08 16:14:46 Command: /usr/local/amos-2.0.8/bin/asmQC -b > > test2.bnk -scaff - > > recompute -update -numsd 2 exited with status: 1 > > !!! END - Elapsed time: 0d 0h 1m 6s > > > > Any suggestions greatly appreciated! > > > > -Kristen > > > > > > Kristen Dang > > Syngenta Biotechnology > > Research Triangle Park, NC 27709 > > > > > > > > -------------------------------------------------------------------------- > > This message may contain confidential information. If you are not > > the designated recipient, please notify the sender immediately, and > > delete the original and any copies. Any use of the message by you is > > prohibited. > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > > AMOS-help mailing list > > AMO...@li... > > https://lists.sourceforge.net/lists/listinfo/amos-help > > > Anastasia Gioti > Post-Doc, Evolutionary Biology Department > Uppsala University > Norbyvägen 18D, > SE-75236 UPPSALA > > ana...@eb... > Tel: +46-18-471-2837 > Fax:+46-18-471-6310 > > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > AMOS-help mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-help > |