Hello, We are attempting to use big_blast.pl and running into errors generating MSPcrunch output for import into ACT.
We're running big_blast.pl version: "# $Header: /nfs/disk222/yeastpub/Repository/zoo/general/big_blast.pl,v 1.23 2000/11/27 09:44:12 kmr Exp $" We're running blast+ as follows: /v/apps/ncbi-blast-2.2.26+/bin/blastn -query ../../human_screen/nohost_2.fa -db ../../../../Ichthyosporea/Ichthyosporea_874 -out Ichthyosporea_874.2.blast6.txt -outfmt 6 -dust yes We've installed the Pathogen Sequencing Unit's internal Perl module, which the script appears to find. When we run big_blast.pl we get the following error and 0 length output:" pened Ichthyosporea_874.1.blast6.txt.crunch for writing Couldn't read any blast results from Ichthyosporea_874.1.blast6.txt wrote Ichthyosporea_874.1.blast6.txt.crunch and Ichthyosporea_874.1.blast6.txt.tab" We've checked the manual which suggests outfmt 6 with blast+. The mailing list archives didn't have much coverage of blast+. Is there an updated option we need to pass to big_blast.pl or blast+? We've attached a sample of the output we are working with. We've also tried uncommenting the other blast parse from file line 326 to no avail, Perl can't find the blast parsing module used. We would appreciate any insight into how to generate blast+ output suitable for input into ACT. Thanks John
HWI-XXXX:359:C08U0ACXX:6:1101:10245:2034/1 gi|30421126|gb|AY267345.1| 100.00 44 0 0 7 50 369 326 1e-20 82.4 HWI-XXXX:359:C08U0ACXX:6:1101:11520:2249/1 gi|30421126|gb|AY267345.1| 94.00 50 3 0 1 50 872 921 5e-19 76.8 HWI-XXXX:359:C08U0ACXX:6:1101:14190:2151/1 gi|30421126|gb|AY267345.1| 97.06 34 1 0 17 50 1225 1258 2e-13 58.4 HWI-XXXX:359:C08U0ACXX:6:1101:15916:2193/1 gi|30421126|gb|AY267345.1| 100.00 32 0 0 1 32 563 532 5e-14 60.2 HWI-XXXX:359:C08U0ACXX:6:1101:13419:2341/1 gi|30421126|gb|AY267345.1| 92.86 42 3 0 1 42 1416 1375 1e-14 62.1 HWI-XXXX:359:C08U0ACXX:6:1101:19627:2320/1 gi|30421126|gb|AY267345.1| 97.06 34 1 0 2 35 404 371 2e-13 58.4 HWI-XXXX:359:C08U0ACXX:6:1101:1934:2617/1 gi|30421126|gb|AY267345.1| 100.00 42 0 0 1 42 930 889 1e-19 78.7 HWI-XXXX:359:C08U0ACXX:6:1101:6522:2679/1 gi|30421126|gb|AY267345.1| 100.00 43 0 0 1 43 931 889 4e-20 80.5 HWI-XXXX:359:C08U0ACXX:6:1101:15393:2560/1 gi|30421126|gb|AY267345.1| 97.06 34 1 0 4 37 734 701 2e-13 58.4 HWI-XXXX:359:C08U0ACXX:6:1101:11230:2848/1 gi|30421126|gb|AY267345.1| 97.06 34 1 0 1 34 1397 1430 2e-13 58.4
_______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
