Fri Oct 14 15:11:54 2005 /xraid/bioware/linux/seqinfo/bin/assemble_cdna invoked from /xraid/habitat/estcdna/APfosmids Project name is set to: APfosmids Using chromat directory: chromat_dir Using phd directory: phd_dir Phred param file environment variable: /xraid/bioware/linux/Phred/phredpar/020425/phredpar.dat No new reads detected, running phred on all read files phred -id chromat_dir -pd phd_dir -trim_alt "" -trim_phd -trim_cutoff .075 chromat_dir/1AP4320C4A01.b1 chromat_dir/1AP4320C4A01.g1 chromat_dir/1AP4320C4A02.b1 chromat_dir/1AP4320C4A02.g1 chromat_dir/1AP4320C4A03.b1 chromat_dir/1AP4320C4A03.g1 chromat_dir/1AP4320C4A04.b1 chromat_dir/1AP4320C4A04.g1 chromat_dir/1AP4320C4A05.b1 chromat_dir/1AP4320C4A05.g1 chromat_dir/1AP4320C4A06.b1 chromat_dir/1AP4320C4A06.g1 chromat_dir/1AP4320C4A07.b1 chromat_dir/1AP4320C4A07.g1 chromat_dir/1AP4320C4A08.b1 chromat_dir/1AP4320C4A08.g1 chromat_dir/1AP4320C4A09.b1 chromat_dir/1AP4320C4A09.g1 chromat_dir/1AP4320C4A10.b1 chromat_dir/1AP4320C4A10.g1 chromat_dir/1AP4320C4A11.b1 chromat_dir/1AP4320C4A11.g1 chromat_dir/1AP4320C4A12.b1 chromat_dir/1AP4320C4A12.g1 chromat_dir/1AP4320C4B01.b1 chromat_dir/1AP4320C4B01.g1 chromat_dir/1AP4320C4B02.b1 chromat_dir/1AP4320C4B02.g1 chromat_dir/1AP4320C4B03.b1 chromat_dir/1AP4320C4B03.g1 chromat_dir/1AP4320C4B04.b1 chromat_dir/1AP4320C4B04.g1 chromat_dir/1AP4320C4B05.b1 chromat_dir/1AP4320C4B05.g1 chromat_dir/1AP4320C4B06.b1 chromat_dir/1AP4320C4B06.g1 chromat_dir/1AP4320C4B07.b1 chromat_dir/1AP4320C4B07.g1 chromat_dir/1AP4320C4B08.b1 chromat_dir/1AP4320C4B08.g1 chromat_dir/1AP4320C4B09.b1 chromat_dir/1AP4320C4B09.g1 chromat_dir/1AP4320C4B10.b1 chromat_dir/1AP4320C4B10.g1 chromat_dir/1AP4320C4B11.b1 chromat_dir/1AP4320C4B11.g1 chromat_dir/1AP4320C4B12.b1 chromat_dir/1AP4320C4B12.g1 chromat_dir/1AP4320C4C01.b1 chromat_dir/1AP4320C4C01.g1 chromat_dir/1AP4320C4C02.b1 chromat_dir/1AP4320C4C02.g1 chromat_dir/1AP4320C4C03.b1 chromat_dir/1AP4320C4C03.g1 chromat_dir/1AP4320C4C04.b1 chromat_dir/1AP4320C4C04.g1 chromat_dir/1AP4320C4C05.b1 chromat_dir/1AP4320C4C05.g1 chromat_dir/1AP4320C4C06.b1 chromat_dir/1AP4320C4C06.g1 chromat_dir/1AP4320C4C07.b1 chromat_dir/1AP4320C4C07.g1 chromat_dir/1AP4320C4C08.b1 chromat_dir/1AP4320C4C08.g1 chromat_dir/1AP4320C4C09.b1 chromat_dir/1AP4320C4C09.g1 chromat_dir/1AP4320C4C10.b1 chromat_dir/1AP4320C4C10.g1 chromat_dir/1AP4320C4C11.b1 chromat_dir/1AP4320C4C11.g1 chromat_dir/1AP4320C4C12.b1 chromat_dir/1AP4320C4C12.g1 chromat_dir/1AP4320C4D01.b1 chromat_dir/1AP4320C4D01.g1 chromat_dir/1AP4320C4D02.b1 chromat_dir/1AP4320C4D02.g1 chromat_dir/1AP4320C4D03.b1 chromat_dir/1AP4320C4D03.g1 chromat_dir/1AP4320C4D04.b1 chromat_dir/1AP4320C4D04.g1 chromat_dir/1AP4320C4D05.b1 chromat_dir/1AP4320C4D05.g1 chromat_dir/1AP4320C4D06.b1 chromat_dir/1AP4320C4D06.g1 chromat_dir/1AP4320C4D07.b1 chromat_dir/1AP4320C4D07.g1 chromat_dir/1AP4320C4D08.b1 chromat_dir/1AP4320C4D08.g1 chromat_dir/1AP4320C4D09.b1 chromat_dir/1AP4320C4D09.g1 chromat_dir/1AP4320C4D10.b1 chromat_dir/1AP4320C4D10.g1 chromat_dir/1AP4320C4D11.b1 chromat_dir/1AP4320C4D11.g1 chromat_dir/1AP4320C4D12.b1 chromat_dir/1AP4320C4D12.g1 chromat_dir/1AP4320C4E01.b1 chromat_dir/1AP4320C4E01.g1 chromat_dir/1AP4320C4E02.b1 chromat_dir/1AP4320C4E02.g1 chromat_dir/1AP4320C4E03.b1 chromat_dir/1AP4320C4E03.g1 chromat_dir/1AP4320C4E04.b1 chromat_dir/1AP4320C4E04.g1 chromat_dir/1AP4320C4E05.b1 chromat_dir/1AP4320C4E05.g1 chromat_dir/1AP4320C4E06.b1 chromat_dir/1AP4320C4E06.g1 chromat_dir/1AP4320C4E07.b1 chromat_dir/1AP4320C4E07.g1 chromat_dir/1AP4320C4E08.b1 chromat_dir/1AP4320C4E08.g1 chromat_dir/1AP4320C4E09.b1 chromat_dir/1AP4320C4E09.g1 chromat_dir/1AP4320C4E10.b1 chromat_dir/1AP4320C4E10.g1 chromat_dir/1AP4320C4E11.b1 chromat_dir/1AP4320C4E11.g1 chromat_dir/1AP4320C4E12.b1 chromat_dir/1AP4320C4E12.g1 chromat_dir/1AP4320C4F01.b1 chromat_dir/1AP4320C4F01.g1 chromat_dir/1AP4320C4F02.b1 chromat_dir/1AP4320C4F02.g1 chromat_dir/1AP4320C4F03.b1 chromat_dir/1AP4320C4F03.g1 chromat_dir/1AP4320C4F04.b1 chromat_dir/1AP4320C4F04.g1 chromat_dir/1AP4320C4F05.b1 chromat_dir/1AP4320C4F05.g1 chromat_dir/1AP4320C4F06.b1 chromat_dir/1AP4320C4F06.g1 chromat_dir/1AP4320C4F07.b1 chromat_dir/1AP4320C4F07.g1 chromat_dir/1AP4320C4F08.b1 chromat_dir/1AP4320C4F08.g1 chromat_dir/1AP4320C4F09.b1 chromat_dir/1AP4320C4F09.g1 chromat_dir/1AP4320C4F10.b1 chromat_dir/1AP4320C4F10.g1 chromat_dir/1AP4320C4F11.b1 chromat_dir/1AP4320C4F11.g1 chromat_dir/1AP4320C4F12.b1 chromat_dir/1AP4320C4F12.g1 chromat_dir/1AP4320C4G01.b1 chromat_dir/1AP4320C4G01.g1 chromat_dir/1AP4320C4G02.b1 chromat_dir/1AP4320C4G02.g1 chromat_dir/1AP4320C4G03.b1 chromat_dir/1AP4320C4G03.g1 chromat_dir/1AP4320C4G04.b1 chromat_dir/1AP4320C4G04.g1 chromat_dir/1AP4320C4G05.b1 chromat_dir/1AP4320C4G05.g1 chromat_dir/1AP4320C4G06.b1 chromat_dir/1AP4320C4G06.g1 chromat_dir/1AP4320C4G07.b1 chromat_dir/1AP4320C4G07.g1 chromat_dir/1AP4320C4G08.b1 chromat_dir/1AP4320C4G08.g1 chromat_dir/1AP4320C4G09.b1 chromat_dir/1AP4320C4G09.g1 chromat_dir/1AP4320C4G10.b1 chromat_dir/1AP4320C4G10.g1 chromat_dir/1AP4320C4G11.b1 chromat_dir/1AP4320C4G11.g1 chromat_dir/1AP4320C4G12.b1 chromat_dir/1AP4320C4G12.g1 chromat_dir/1AP4320C4H01.b1 chromat_dir/1AP4320C4H01.g1 chromat_dir/1AP4320C4H02.b1 chromat_dir/1AP4320C4H02.g1 chromat_dir/1AP4320C4H03.b1 chromat_dir/1AP4320C4H03.g1 chromat_dir/1AP4320C4H04.b1 chromat_dir/1AP4320C4H04.g1 chromat_dir/1AP4320C4H05.b1 chromat_dir/1AP4320C4H05.g1 chromat_dir/1AP4320C4H06.b1 chromat_dir/1AP4320C4H06.g1 chromat_dir/1AP4320C4H07.b1 chromat_dir/1AP4320C4H07.g1 chromat_dir/1AP4320C4H08.b1 chromat_dir/1AP4320C4H08.g1 chromat_dir/1AP4320C4H09.b1 chromat_dir/1AP4320C4H09.g1 chromat_dir/1AP4320C4H10.b1 chromat_dir/1AP4320C4H10.g1 chromat_dir/1AP4320C4H11.b1 chromat_dir/1AP4320C4H11.g1 chromat_dir/1AP4320C4H12.b1 chromat_dir/1AP4320C4H12.g1 chromat_dir/3AP4320C4A01.b1 chromat_dir/3AP4320C4A01.g1 chromat_dir/3AP4320C4A02.b1 chromat_dir/3AP4320C4A02.g1 chromat_dir/3AP4320C4A03.b1 chromat_dir/3AP4320C4A03.g1 chromat_dir/3AP4320C4A04.b1 chromat_dir/3AP4320C4A04.g1 chromat_dir/3AP4320C4A05.b1 chromat_dir/3AP4320C4A05.g1 chromat_dir/3AP4320C4A06.b1 chromat_dir/3AP4320C4A06.g1 chromat_dir/3AP4320C4A07.b1 chromat_dir/3AP4320C4A07.g1 chromat_dir/3AP4320C4A08.b1 chromat_dir/3AP4320C4A08.g1 chromat_dir/3AP4320C4A09.b1 chromat_dir/3AP4320C4A09.g1 chromat_dir/3AP4320C4A10.b1 chromat_dir/3AP4320C4A10.g1 chromat_dir/3AP4320C4A11.b1 chromat_dir/3AP4320C4A11.g1 chromat_dir/3AP4320C4A12.b1 chromat_dir/3AP4320C4A12.g1 chromat_dir/3AP4320C4B01.b1 chromat_dir/3AP4320C4B01.g1 chromat_dir/3AP4320C4B02.b1 chromat_dir/3AP4320C4B02.g1 chromat_dir/3AP4320C4B03.b1 chromat_dir/3AP4320C4B03.g1 chromat_dir/3AP4320C4B04.b1 chromat_dir/3AP4320C4B04.g1 chromat_dir/3AP4320C4B05.b1 chromat_dir/3AP4320C4B05.g1 chromat_dir/3AP4320C4B06.b1 chromat_dir/3AP4320C4B06.g1 chromat_dir/3AP4320C4B07.b1 chromat_dir/3AP4320C4B07.g1 chromat_dir/3AP4320C4B08.b1 chromat_dir/3AP4320C4B08.g1 chromat_dir/3AP4320C4B09.b1 chromat_dir/3AP4320C4B09.g1 chromat_dir/3AP4320C4B10.b1 chromat_dir/3AP4320C4B10.g1 chromat_dir/3AP4320C4B11.b1 chromat_dir/3AP4320C4B11.g1 chromat_dir/3AP4320C4B12.b1 chromat_dir/3AP4320C4B12.g1 chromat_dir/3AP4320C4C01.b1 chromat_dir/3AP4320C4C01.g1 chromat_dir/3AP4320C4C02.b1 chromat_dir/3AP4320C4C02.g1 chromat_dir/3AP4320C4C03.b1 chromat_dir/3AP4320C4C03.g1 chromat_dir/3AP4320C4C04.b1 chromat_dir/3AP4320C4C04.g1 chromat_dir/3AP4320C4C05.b1 chromat_dir/3AP4320C4C05.g1 chromat_dir/3AP4320C4C06.b1 chromat_dir/3AP4320C4C06.g1 chromat_dir/3AP4320C4C07.b1 chromat_dir/3AP4320C4C07.g1 chromat_dir/3AP4320C4C08.b1 chromat_dir/3AP4320C4C08.g1 chromat_dir/3AP4320C4C09.b1 chromat_dir/3AP4320C4C09.g1 chromat_dir/3AP4320C4C10.b1 chromat_dir/3AP4320C4C10.g1 chromat_dir/3AP4320C4C11.b1 chromat_dir/3AP4320C4C11.g1 chromat_dir/3AP4320C4C12.b1 chromat_dir/3AP4320C4C12.g1 chromat_dir/3AP4320C4D01.b1 chromat_dir/3AP4320C4D01.g1 chromat_dir/3AP4320C4D02.b1 chromat_dir/3AP4320C4D02.g1 chromat_dir/3AP4320C4D03.b1 chromat_dir/3AP4320C4D03.g1 chromat_dir/3AP4320C4D04.b1 chromat_dir/3AP4320C4D04.g1 chromat_dir/3AP4320C4D05.b1 chromat_dir/3AP4320C4D05.g1 chromat_dir/3AP4320C4D06.b1 chromat_dir/3AP4320C4D06.g1 chromat_dir/3AP4320C4D07.b1 chromat_dir/3AP4320C4D07.g1 chromat_dir/3AP4320C4D08.b1 chromat_dir/3AP4320C4D08.g1 chromat_dir/3AP4320C4D09.b1 chromat_dir/3AP4320C4D09.g1 chromat_dir/3AP4320C4D10.b1 chromat_dir/3AP4320C4D10.g1 chromat_dir/3AP4320C4D11.b1 chromat_dir/3AP4320C4D11.g1 chromat_dir/3AP4320C4D12.b1 chromat_dir/3AP4320C4D12.g1 chromat_dir/3AP4320C4E01.b1 chromat_dir/3AP4320C4E01.g1 chromat_dir/3AP4320C4E02.b1 chromat_dir/3AP4320C4E02.g1 chromat_dir/3AP4320C4E03.b1 chromat_dir/3AP4320C4E03.g1 chromat_dir/3AP4320C4E04.b1 chromat_dir/3AP4320C4E04.g1 chromat_dir/3AP4320C4E05.b1 chromat_dir/3AP4320C4E05.g1 chromat_dir/3AP4320C4E06.b1 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chromat_dir/4AP4320C5B11.g1 chromat_dir/4AP4320C5B12.b1 chromat_dir/4AP4320C5B12.g1 chromat_dir/4AP4320C5C11.b1 chromat_dir/4AP4320C5C11.g1 chromat_dir/4AP4320C5C12.b1 chromat_dir/4AP4320C5C12.g1 chromat_dir/4AP4320C5D11.b1 chromat_dir/4AP4320C5D11.g1 chromat_dir/4AP4320C5D12.b1 chromat_dir/4AP4320C5D12.g1 chromat_dir/4AP4320C5E11.b1 chromat_dir/4AP4320C5E11.g1 chromat_dir/4AP4320C5E12.b1 chromat_dir/4AP4320C5E12.g1 chromat_dir/4AP4320C5F11.b1 chromat_dir/4AP4320C5F11.g1 chromat_dir/4AP4320C5F12.b1 chromat_dir/4AP4320C5F12.g1 chromat_dir/4AP4320C5G11.b1 chromat_dir/4AP4320C5G11.g1 chromat_dir/4AP4320C5G12.b1 chromat_dir/4AP4320C5G12.g1 chromat_dir/4AP4320C5H11.b1 chromat_dir/4AP4320C5H11.g1 chromat_dir/4AP4320C5H12.b1 chromat_dir/4AP4320C5H12.g1 chromat_dir/4AP4320C5A11.b1 phd2fasta -id phd_dir -os edit_dir/APfosmids.fasta -oq edit_dir/APfosmids.fasta.screen.qual lucy -v /xraid/bioware/linux/seqinfo/vectors/pSMARTcDNAlinker_vector.fa /xraid/bioware/linux/seqinfo/vectors/pSMARTcDNAlinker_splice.fa -o lucy.fasta lucy.qual -t 90 -i edit_dir/APfosmids.fasta edit_dir/APfosmids.fasta.screen.qual 2>&1 > lucy.log Less Useful Chunks Yank (lucy) 1.19s, by Hui-Hsien Chou and Michael Holmes, with help from Granger, Anna, John and Terry Shea. Phase 1: Checking the number of input sequences... 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 756 input sequences found. Phase 2: Reading sequence name, length and position data... 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 0 empty sequences discarded. Phase 3: Reading quality values and checking good sequence regions... 0 lucy: ==> dropping 1AP4320C4A02.b1 lucy: ==> dropping 1AP4320C4A05.b1 lucy: ==> dropping 1AP4320C4B02.b1 lucy: ==> dropping 1AP4320C4B03.b1 50 lucy: ==> dropping 1AP4320C4C09.b1 lucy: ==> dropping 1AP4320C4C09.g1 lucy: ==> dropping 1AP4320C4C10.b1 lucy: ==> dropping 1AP4320C4D11.g1 lucy: ==> dropping 1AP4320C4D12.g1 lucy: ==> dropping 1AP4320C4E02.b1 lucy: ==> dropping 1AP4320C4E04.b1 100 lucy: ==> dropping 1AP4320C4F01.g1 lucy: ==> dropping 1AP4320C4F04.b1 lucy: ==> dropping 1AP4320C4F07.g1 lucy: ==> dropping 1AP4320C4F10.b1 lucy: ==> dropping 1AP4320C4G01.g1 lucy: ==> dropping 1AP4320C4G02.g1 lucy: ==> dropping 1AP4320C4G11.b1 150 lucy: ==> dropping 1AP4320C4H10.g1 lucy: ==> dropping 1AP4320C4H12.b1 200 lucy: ==> dropping 2AP3320C5D02.g1 lucy: ==> dropping 2AP3320C5D04.g1 lucy: ==> dropping 2AP3320C5D05.g1 lucy: ==> dropping 2AP3320C5D09.g1 lucy: ==> dropping 2AP3320C5G05.g1 250 lucy: ==> dropping 2AP3320C5G09.g1 lucy: ==> dropping 2AP3320C5G11.b1 lucy: ==> dropping 2AP3320C5H03.g1 lucy: ==> dropping 2AP3320C5H04.b1 lucy: ==> dropping 2AP3320C5H11.g1 lucy: ==> dropping 3AP4320C4A02.b1 lucy: ==> dropping 3AP4320C4A05.b1 lucy: ==> dropping 3AP4320C4A07.b1 lucy: ==> dropping 3AP4320C4A08.b1 lucy: ==> dropping 3AP4320C4A09.b1 300 lucy: ==> dropping 3AP4320C4B08.b1 lucy: ==> dropping 3AP4320C4B08.g1 lucy: ==> dropping 3AP4320C4C05.b1 lucy: ==> dropping 3AP4320C4C05.g1 lucy: ==> dropping 3AP4320C4C08.g1 lucy: ==> dropping 3AP4320C4C10.g1 350 lucy: ==> dropping 3AP4320C4G06.g1 lucy: ==> dropping 3AP4320C4G08.b1 lucy: ==> dropping 3AP4320C4G08.g1 lucy: ==> dropping 3AP4320C4G12.g1 lucy: ==> dropping 3AP4320C4H03.g1 lucy: ==> dropping 3AP4320C4H07.g1 lucy: ==> dropping 3AP4320C4H08.g1 lucy: ==> dropping 3AP4320C4H10.b1 lucy: ==> dropping 3AP4320C4H10.g1 400 lucy: ==> dropping 4AP4320C05A11.g1 lucy: ==> dropping 4AP4320C05B12.g1 lucy: ==> dropping 4AP4320C05C12.g1 lucy: ==> dropping 4AP4320C5A11.g1 lucy: ==> dropping 4AP4320C5B12.g1 lucy: ==> dropping 4AP4320C5C12.g1 450 lucy: ==> dropping 5AP3320C3A12.b1 lucy: ==> dropping 5AP3320C3C12.b1 lucy: ==> dropping 5AP3320C3C12.g1 500 lucy: ==> dropping 5AP3320C3D11.g1 lucy: ==> dropping 5AP3320C3E03.b1 lucy: ==> dropping 5AP3320C3F02.b1 lucy: ==> dropping 5AP3320C3F04.b1 550 lucy: ==> dropping 5AP3320C3G08.g1 lucy: ==> dropping 5AP3320C3G12.g1 lucy: ==> dropping 5AP3320C3H02.g1 lucy: ==> dropping 5AP3320C3H08.b1 600 lucy: ==> dropping 6AP4320C2A07.b1 lucy: ==> dropping 6AP4320C2B02.b1 650 lucy: ==> dropping 6AP4320C2C06.b1 lucy: ==> dropping 6AP4320C2C06.g1 lucy: ==> dropping 6AP4320C2D08.b1 lucy: ==> dropping 6AP4320C2D08.g1 lucy: ==> dropping 6AP4320C2E11.b1 lucy: ==> dropping 6AP4320C2F01.b1 700 lucy: ==> dropping 6AP4320C2F02.g1 lucy: ==> dropping 6AP4320C2G12.b1 lucy: ==> dropping 6AP4320C2H05.g1 750 lucy: ==> dropping 6AP4320C2H10.b1 lucy: ==> dropping 6AP4320C2H10.g1 lucy: ==> dropping 6AP4320C2H11.b1 756 quality sequences read; 81 low quality sequences dropped. Phase 4: 2nd sequences comparsion skipped... no 2nd sequence file provided. Phase 5: Locating splice sites...Number of splice sequences: 4 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 1 short or no insert sequences discarded. Phase 6: Kicking out vector sequences... 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 23 vector sequences discarded. Phase 7: Producing output sequence and quality files... 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 651 good sequences written in lucy.fasta and lucy.qual. trimest -sequence=lucy.fasta -outseq=trimest.fasta -minlength 14 -mismatches 1000 -fiveprime -noreverse 2>&1 Trim poly-A tails off EST sequences zapping.awk trimest.fasta > lucy.trim cross_match lucy.trim -screen /xraid/bioware/linux/seqinfo/vectors/pSMARTcDNAlinker_vector.fa cross_match lucy.trim -screen /xraid/bioware/linux/seqinfo/vectors/pSMARTcDNAlinker_vector.fa cross_match version 0.990329 Reading parameters ... cross_match lucy.trim -screen /xraid/bioware/linux/seqinfo/vectors/pSMARTcDNAlinker_vector.fa cross_match version 0.990329 0.504 Mbytes allocated -- total 0.504 Mbytes Run date:time 051014:151544 Done Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks Run date:time 051014:151544 Query file(s): lucy.trim Subject file(s): /xraid/bioware/linux/seqinfo/vectors/pSMARTcDNAlinker_vector.fa Presumed sequence type: DNA Pairwise comparison algorithm: banded Smith-Waterman Score matrix (set by value of penalty: -2) A C G T N X A 1 -2 -2 -2 0 -3 C -2 1 -2 -2 0 -3 G -2 -2 1 -2 0 -3 T -2 -2 -2 1 0 -3 N 0 0 0 0 0 0 X -3 -3 -3 -3 0 -3 Gap penalties: gap_init: -4, gap_ext: -3, ins_gap_ext: -3, del_gap_ext: -3, Using complexity-adjusted scores. Assumed background frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000 minmatch: 14, maxmatch: 14, max_group_size: 20, minscore: 30, bandwidth: 14, indexwordsize: 10 vector_bound: 0 word_raw: 0 masklevel: 80Reading query file into memory ...1.008 Mbytes allocated -- total 1.512 Mbytes Done Total space allocated: 1.512 Mbytes; currently free: 0.622 Mbytes in 3 blocks Sequence file: lucy.trim 651 entries Residue counts: a 92532 c 107746 g 102541 n 8 t 94601 Total 397428Complementing ... Done Total space allocated: 1.512 Mbytes; currently free: 0.622 Mbytes in 3 blocks Allocating align_entries ... Done Total space allocated: 1.512 Mbytes; currently free: 0.151 Mbytes in 3 blocks Reading quality files ... NO QUALITY FILE lucy.trim.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done Total space allocated: 1.512 Mbytes; currently free: 0.151 Mbytes in 3 blocks NO QUALITY FILE lucy.trim.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15.4.536 Mbytes allocated -- total 6.048 Mbytes Finding words ... 0 795009 10 249043 20 772 30 377 40 408 50 344 60 236 70 357 80 315 90 348 100 457 110 208 120 238 130 213 140 198 150 33 160 2 170 3 180 9 190 1 200 3 210 1 220 1 min no. words: 0 at 0 max no. words: 216 at 755968 avg no. words: 0.03.528 Mbytes allocated -- total 9.576 Mbytes 1.008 Mbytes allocated -- total 10.584 Mbytes Done Total space allocated: 10.584 Mbytes; currently free: 1.084 Mbytes in 6 blocks 794856 words; after pruning: 777730 Sorting words ... Done 14 323663 Finding subject matches ... Done Total space allocated: 10.584 Mbytes; currently free: 0.924 Mbytes in 7 blocks # pass words: 349, #fail words: 12 Quickalign: 110 successes, 0 failures 233 SWAT alignments performed. 110 pairs have score >= 30 Making reversed pairs ... Done Total space allocated: 10.584 Mbytes; currently free: 9.010 Mbytes in 8 blocks Printing matches ... Maximal single base matches (low complexity regions): 372 0.52 0.00 0.00 1AP4320C4C11.b1 146 529 (0) pSMART-cDNA 1248 1631 (253) 85 0.00 0.00 1.10 1AP4320C4D09.g1 22 112 (477) C pSMART-cDNA (1515) 369 280 315 0.31 0.00 0.00 1AP4320C4G10.b1 149 473 (0) pSMART-cDNA 1248 1572 (312) 105 0.00 0.00 0.00 1AP4320C4H10.b1 151 257 (445) pSMART-cDNA 280 386 (1498) 287 0.33 0.00 0.33 2AP3320C5A02.b1 300 600 (0) pSMART-cDNA 1248 1547 (337) 267 0.71 0.00 0.35 2AP3320C5A03.b1 302 584 (1) pSMART-cDNA 1248 1529 (355) 233 0.41 0.00 0.41 2AP3320C5A04.b1 345 589 (0) pSMART-cDNA 1248 1491 (393) 447 1.08 0.00 0.00 2AP3320C5A09.b1 56 520 (0) pSMART-cDNA 1248 1712 (172) 370 1.99 0.00 0.25 2AP3320C5B01.b1 58 460 (0) pSMART-cDNA 1248 1649 (235) 217 0.45 0.00 0.00 2AP3320C5B04.b1 374 597 (0) pSMART-cDNA 1248 1471 (413) 323 2.79 0.00 0.00 2AP3320C5B08.b1 8 366 (0) pSMART-cDNA 1248 1606 (278) 261 1.09 0.00 0.00 2AP3320C5B09.b1 280 553 (0) pSMART-cDNA 1248 1521 (363) 287 0.67 0.00 0.00 2AP3320C5B12.b1 283 581 (0) pSMART-cDNA 1248 1546 (338) 477 0.59 0.00 0.79 2AP3320C5C02.b1 142 650 (0) pSMART-cDNA 1248 1752 (132) 420 0.23 0.00 0.00 2AP3320C5C03.b1 145 571 (0) pSMART-cDNA 1248 1674 (210) 237 0.41 0.00 0.00 2AP3320C5C06.b1 224 467 (0) pSMART-cDNA 1248 1491 (393) 350 0.28 0.00 0.00 2AP3320C5C11.b1 150 508 (0) pSMART-cDNA 1248 1606 (278) 198 1.43 0.00 0.00 2AP3320C5D01.b1 320 529 (0) pSMART-cDNA 1248 1457 (427) 347 0.56 0.00 0.00 2AP3320C5D02.b1 224 583 (0) pSMART-cDNA 1248 1607 (277) 142 0.68 0.00 0.00 2AP3320C5D03.b1 431 577 (0) pSMART-cDNA 1248 1394 (490) 171 1.59 0.00 0.53 2AP3320C5D05.b1 313 501 (0) pSMART-cDNA 1248 1435 (449) 177 0.00 0.00 0.54 2AP3320C5D06.b1 329 514 (0) pSMART-cDNA 1248 1432 (452) 336 1.13 0.00 0.00 2AP3320C5D08.b1 148 501 (0) pSMART-cDNA 1248 1601 (283) 180 4.17 0.00 0.46 2AP3320C5D11.b1 299 514 (0) pSMART-cDNA 1248 1462 (422) 266 0.72 0.00 0.00 2AP3320C5E04.b1 273 548 (0) pSMART-cDNA 1248 1523 (361) 209 0.45 0.00 0.45 2AP3320C5E05.b1 294 514 (0) pSMART-cDNA 1248 1467 (417) 366 1.29 0.00 0.00 2AP3320C5E06.b1 223 609 (0) pSMART-cDNA 1248 1634 (250) 174 1.61 0.00 0.00 2AP3320C5E12.b1 364 549 (0) pSMART-cDNA 1248 1433 (451) 351 0.82 0.00 0.00 2AP3320C5F06.b1 82 447 (0) pSMART-cDNA 1248 1613 (271) 288 0.97 0.00 0.32 2AP3320C5F09.b1 100 407 (0) pSMART-cDNA 1248 1554 (330) 240 0.80 0.00 0.00 2AP3320C5G03.b1 354 603 (0) pSMART-cDNA 1248 1497 (387) 179 1.06 0.00 0.00 2AP3320C5H03.b1 274 462 (0) pSMART-cDNA 1248 1436 (448) 273 2.88 0.00 0.32 2AP3320C5H05.b1 49 360 (0) pSMART-cDNA 1253 1563 (321) 207 1.36 0.00 0.00 2AP3320C5H06.b1 245 464 (0) pSMART-cDNA 1248 1467 (417) 438 1.72 0.00 0.00 3AP4320C4A06.b1 54 518 (0) pSMART-cDNA 1248 1712 (172) 263 0.37 0.00 0.00 3AP4320C4A11.b1 418 688 (0) pSMART-cDNA 1248 1518 (366) 259 0.74 0.00 0.00 3AP4320C4A12.b1 420 688 (0) pSMART-cDNA 1248 1516 (368) 346 0.28 0.00 0.00 3AP4320C4B02.b1 226 580 (0) pSMART-cDNA 1248 1602 (282) 303 1.23 0.00 0.31 3AP4320C4B04.b1 268 593 (0) pSMART-cDNA 1248 1572 (312) 262 0.74 0.00 0.00 3AP4320C4B05.b1 342 613 (0) pSMART-cDNA 1248 1519 (365) 389 0.75 0.00 0.00 3AP4320C4C01.b1 180 581 (0) pSMART-cDNA 1248 1649 (235) 408 0.70 0.00 0.23 3AP4320C4C11.b1 60 485 (0) pSMART-cDNA 1252 1676 (208) 240 0.80 0.00 0.00 3AP4320C4D01.b1 419 667 (2) pSMART-cDNA 1248 1496 (388) 70 0.00 0.00 0.00 3AP4320C4D02.g1 499 571 (0) C pSMART-cDNA (1498) 386 314 141 0.69 0.00 0.00 3AP4320C4D05.b1 407 551 (0) pSMART-cDNA 1248 1392 (492) 156 0.62 0.00 0.00 3AP4320C4D11.b1 419 580 (0) pSMART-cDNA 1248 1409 (475) 486 0.78 0.00 0.39 3AP4320C4E03.b1 101 611 (0) pSMART-cDNA 1248 1756 (128) 317 0.31 0.00 0.00 3AP4320C4E04.b1 289 614 (0) pSMART-cDNA 1248 1573 (311) 242 2.28 0.00 0.00 3AP4320C4E09.b1 268 530 (0) pSMART-cDNA 1248 1510 (374) 139 0.70 0.00 0.00 3AP4320C4E10.b1 510 652 (0) pSMART-cDNA 1248 1390 (494) 344 0.84 0.00 0.00 3AP4320C4F08.b1 154 512 (0) pSMART-cDNA 1248 1606 (278) 357 1.31 0.00 0.26 3AP4320C4F10.b1 47 428 (0) pSMART-cDNA 1251 1631 (253) 450 0.86 0.00 0.00 3AP4320C4F11.b1 83 547 (0) pSMART-cDNA 1248 1712 (172) 162 0.60 0.00 0.00 3AP4320C4F12.b1 394 560 (0) pSMART-cDNA 1248 1414 (470) 471 0.41 0.00 0.21 3AP4320C4G02.b1 97 581 (0) pSMART-cDNA 1248 1731 (153) 572 0.67 0.00 0.34 3AP4320C4G03.b1 89 684 (0) pSMART-cDNA 1248 1841 (43) 216 0.88 0.00 0.00 3AP4320C4H01.b1 419 644 (0) pSMART-cDNA 1248 1473 (411) 342 0.28 0.00 0.00 3AP4320C4H03.b1 271 621 (0) pSMART-cDNA 1248 1598 (286) 314 0.30 0.00 0.30 3AP4320C4H05.b1 204 531 (0) pSMART-cDNA 1248 1574 (310) 54 0.00 0.00 0.00 4AP4320C05E11.b1 371 424 (0) pSMART-cDNA 1248 1301 (583) 146 0.62 0.00 1.24 4AP4320C05F11.b1 372 532 (0) pSMART-cDNA 1248 1406 (478) 210 0.91 0.00 0.00 4AP4320C05G11.b1 420 639 (0) pSMART-cDNA 1248 1467 (417) 199 1.86 0.00 0.00 4AP4320C05G12.b1 143 357 (0) pSMART-cDNA 1248 1462 (422) 235 0.82 0.00 0.00 4AP4320C05H11.b1 430 673 (0) pSMART-cDNA 1248 1491 (393) 54 0.00 0.00 0.00 4AP4320C5E11.b1 371 424 (0) pSMART-cDNA 1248 1301 (583) 146 0.62 0.00 1.24 4AP4320C5F11.b1 372 532 (0) pSMART-cDNA 1248 1406 (478) 210 0.91 0.00 0.00 4AP4320C5G11.b1 420 639 (0) pSMART-cDNA 1248 1467 (417) 199 1.86 0.00 0.00 4AP4320C5G12.b1 143 357 (0) pSMART-cDNA 1248 1462 (422) 235 0.82 0.00 0.00 4AP4320C5H11.b1 430 673 (0) pSMART-cDNA 1248 1491 (393) 423 0.23 0.00 0.00 5AP3320C3A01.b1 201 630 (0) pSMART-cDNA 1248 1677 (207) 265 0.37 0.00 0.00 5AP3320C3A02.b1 325 596 (0) pSMART-cDNA 1248 1519 (365) 263 0.73 0.00 0.00 5AP3320C3B07.b1 394 666 (0) pSMART-cDNA 1248 1520 (364) 476 1.19 0.00 0.40 5AP3320C3B08.b1 80 585 (0) pSMART-cDNA 1248 1751 (133) 474 0.41 0.00 0.00 5AP3320C3B09.b1 102 585 (0) pSMART-cDNA 1248 1731 (153) 335 0.57 0.00 0.00 5AP3320C3C03.b1 328 675 (0) pSMART-cDNA 1248 1595 (289) 353 0.55 0.00 0.00 5AP3320C3C05.b1 290 654 (0) pSMART-cDNA 1248 1612 (272) 540 0.18 0.00 0.18 5AP3320C3D01.b1 148 698 (0) pSMART-cDNA 1248 1797 (87) 321 0.60 0.00 0.00 5AP3320C3D07.b1 103 435 (0) pSMART-cDNA 1248 1580 (304) 213 0.90 0.00 0.00 5AP3320C3D12.b1 452 674 (0) pSMART-cDNA 1248 1470 (414) 151 2.42 0.00 0.00 5AP3320C3E06.b1 184 348 (0) pSMART-cDNA 1248 1412 (472) 254 1.83 0.00 0.00 5AP3320C3F03.b1 366 638 (0) pSMART-cDNA 1248 1520 (364) 43 0.00 0.00 0.00 5AP3320C3F08.b1 667 711 (0) pSMART-cDNA 1248 1292 (592) 372 0.52 0.00 0.00 5AP3320C3G03.b1 193 576 (0) pSMART-cDNA 1248 1631 (253) 42 0.00 0.00 0.00 5AP3320C3G08.b1 1 45 (624) pSMART-cDNA 344 388 (1496) 69 0.00 0.00 0.00 5AP3320C3G10.g1 573 644 (2) C p Done Total space allocated: 10.584 Mbytes; currently free: 8.948 Mbytes in 9 blocks SMART-cDNA (1498) 386 315 468 0.83 0.00 0.00 5AP3320C3H02.b1 149 631 (0) pSMART-cDNA 1248 1730 (154) 287 4.48 0.00 0.00 5AP3320C3H03.b1 1 335 (0) pSMART-cDNA 1296 1630 (254) 279 0.35 0.00 0.00 5AP3320C3H10.b1 452 738 (0) pSMART-cDNA 1248 1534 (350) 201 0.48 0.00 0.00 6AP4320C2A01.b1 431 638 (0) pSMART-cDNA 1248 1455 (429) 423 0.23 0.00 0.00 6AP4320C2A02.b1 173 602 (0) pSMART-cDNA 1248 1677 (207) 261 0.74 0.00 0.00 6AP4320C2A06.b1 320 590 (0) pSMART-cDNA 1248 1518 (366) 159 0.61 0.00 0.00 6AP4320C2A12.b1 417 581 (0) pSMART-cDNA 1248 1412 (472) 303 1.21 0.00 0.60 6AP4320C2B05.b1 230 560 (0) pSMART-cDNA 1248 1576 (308) 375 0.52 0.00 0.00 6AP4320C2B06.b1 273 659 (0) pSMART-cDNA 1248 1634 (250) 175 1.60 0.00 0.00 6AP4320C2C01.b1 406 592 (0) pSMART-cDNA 1248 1434 (450) 459 1.04 0.21 0.00 6AP4320C2C09.b1 71 552 (0) pSMART-cDNA 1253 1735 (149) 181 4.27 0.00 0.00 6AP4320C2C11.b1 321 531 (0) pSMART-cDNA 1248 1458 (426) 177 0.53 0.00 0.53 6AP4320C2D01.b1 320 508 (0) pSMART-cDNA 1248 1435 (449) 171 2.15 0.00 0.00 6AP4320C2D11.b1 271 456 (0) pSMART-cDNA 1248 1433 (451) 214 0.89 0.00 0.00 6AP4320C2E04.b1 450 673 (0) pSMART-cDNA 1248 1471 (413) 89 3.06 0.00 0.00 6AP4320C2E10.b1 464 561 (0) pSMART-cDNA 1248 1345 (539) 44 1.96 1.96 0.00 6AP4320C2E10.g1 24 74 (541) pSMART-cDNA 1692 1743 (141) 376 1.50 0.00 0.00 6AP4320C2F02.b1 202 600 (0) pSMART-cDNA 1248 1646 (238) 304 1.22 0.00 0.31 6AP4320C2F09.b1 272 598 (0) pSMART-cDNA 1248 1573 (311) 340 0.57 0.00 0.00 6AP4320C2F11.b1 164 515 (0) pSMART-cDNA 1248 1599 (285) 179 0.54 0.00 0.00 6AP4320C2G03.b1 419 604 (0) pSMART-cDNA 1248 1433 (451) 189 1.45 0.00 0.48 6AP4320C2G05.b1 430 636 (0) pSMART-cDNA 1248 1453 (431) 242 2.62 0.00 0.00 6AP4320C2G09.b1 183 449 (0) pSMART-cDNA 1248 1514 (370) 337 0.84 0.00 0.28 6AP4320C2G10.b1 231 587 (0) pSMART-cDNA 1248 1603 (281) 329 0.86 0.00 0.29 6AP4320C2H05.b1 99 447 (0) pSMART-cDNA 1248 1595 (289) 110 matching entries (first file). Discrepancy summary: Qual algn cum rcum (%) unalgn X N sub del ins total (%) cum rcum (%) Checking pairs ... Screened sequences written to lucy.trim.screen Done Total space allocated: 10.584 Mbytes; currently free: 8.948 Mbytes in 8 blocks Total space allocated: 10.584 Mbytes; currently free: 8.948 Mbytes in 8 blocks Total # pairs: 1000, size: 0.044 Mbytes Total # segment blocks: 1, size: 0.060 Mbytes Total # diffs: 847, in 110 lists, size: 0.001 Mbytes mv lucy.trim.screen lucy.trim tr "[a-z]" "[A-Z]" < lucy.trim | stripx.pl > lucy.trim.stripx trimseq -sequence=lucy.trim.stripx -outseq=lucy.trim2 -window 50 -percent 20 2>&1 Trim ambiguous bits off the ends of sequences daffy 200 lucy.trim2 > APfosmids.tgicl 2>&1