[Wed Oct 22 12:19:12 2014] Beginning transcriptome assembly merge ------------------------------------------- [Wed Oct 22 12:19:12 2014] Preparing output location merged_asm_GM/ [Wed Oct 22 12:20:32 2014] Converting GTF files to SAM [12:20:32] Loading reference annotation. [12:20:52] Loading reference annotation. [12:21:12] Loading reference annotation. [12:21:32] Loading reference annotation. [12:21:52] Loading reference annotation. [12:22:13] Loading reference annotation. [12:22:33] Loading reference annotation. [12:22:53] Loading reference annotation. [Wed Oct 22 12:23:19 2014] Quantitating transcripts You are using Cufflinks v2.2.1, which is the most recent release. Command line: cufflinks -o merged_asm_GM/ -F 0.05 -g /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 merged_asm_GM/tmp/mergeSam_filesr4IAd [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). File merged_asm_GM/tmp/mergeSam_filesr4IAd doesn't appear to be a valid BAM file, trying SAM... [12:23:20] Loading reference annotation. [12:23:51] Inspecting reads and determining fragment length distribution. Processed 44804 loci. > Map Properties: > Normalized Map Mass: 1944014.00 > Raw Map Mass: 1944014.00 > Fragment Length Distribution: Truncated Gaussian (default) > Default Mean: 200 > Default Std Dev: 80 [12:24:22] Assembling transcripts and estimating abundances. Processed 44804 loci. [Wed Oct 22 12:34:15 2014] Comparing against reference file /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf You are using Cufflinks v2.2.1, which is the most recent release. Warning: couldn't find fasta record for 'HG1007_PATCH'! Warning: couldn't find fasta record for 'HG1032_PATCH'! Warning: couldn't find fasta record for 'HG104_HG975_PATCH'! Warning: couldn't find fasta record for 'HG1063_PATCH'! Warning: couldn't find fasta record for 'HG1074_PATCH'! Warning: couldn't find fasta record for 'HG1079_PATCH'! Warning: couldn't find fasta record for 'HG1082_HG167_PATCH'! Warning: couldn't find fasta record for 'HG1091_PATCH'! Warning: couldn't find fasta record for 'HG1133_PATCH'! Warning: couldn't find fasta record for 'HG1146_PATCH'! Warning: couldn't find fasta record for 'HG115_PATCH'! Warning: couldn't find fasta record for 'HG1208_PATCH'! Warning: couldn't find fasta record for 'HG1211_PATCH'! Warning: couldn't find fasta record for 'HG122_PATCH'! Warning: couldn't find fasta record for 'HG1257_PATCH'! Warning: couldn't find fasta record for 'HG1287_PATCH'! Warning: couldn't find fasta record for 'HG1292_PATCH'! Warning: couldn't find fasta record for 'HG1293_PATCH'! Warning: couldn't find fasta record for 'HG1304_PATCH'! Warning: couldn't find fasta record for 'HG1308_PATCH'! Warning: couldn't find fasta record for 'HG1322_PATCH'! Warning: couldn't find fasta record for 'HG1350_HG959_PATCH'! Warning: couldn't find fasta record for 'HG1423_PATCH'! Warning: couldn't find fasta record for 'HG1424_PATCH'! Warning: couldn't find fasta record for 'HG1425_PATCH'! Warning: couldn't find fasta record for 'HG1426_PATCH'! Warning: couldn't find fasta record for 'HG142_HG150_NOVEL_TEST'! Warning: couldn't find fasta record for 'HG1433_PATCH'! Warning: couldn't find fasta record for 'HG1434_PATCH'! Warning: couldn't find fasta record for 'HG1435_PATCH'! Warning: couldn't find fasta record for 'HG1436_HG1432_PATCH'! Warning: couldn't find fasta record for 'HG1437_PATCH'! Warning: couldn't find fasta record for 'HG1438_PATCH'! Warning: couldn't find fasta record for 'HG1439_PATCH'! Warning: couldn't find fasta record for 'HG1440_PATCH'! Warning: couldn't find fasta record for 'HG1441_PATCH'! Warning: couldn't find fasta record for 'HG1442_PATCH'! Warning: couldn't find fasta record for 'HG1443_HG1444_PATCH'! Warning: couldn't find fasta record for 'HG144_PATCH'! Warning: couldn't find fasta record for 'HG1453_PATCH'! Warning: couldn't find fasta record for 'HG1458_PATCH'! Warning: couldn't find fasta record for 'HG1459_PATCH'! Warning: couldn't find fasta record for 'HG1462_PATCH'! Warning: couldn't find fasta record for 'HG1463_PATCH'! Warning: couldn't find fasta record for 'HG1472_PATCH'! Warning: couldn't find fasta record for 'HG1479_PATCH'! Warning: couldn't find fasta record for 'HG1486_PATCH'! Warning: couldn't find fasta record for 'HG1487_PATCH'! Warning: couldn't find fasta record for 'HG1488_PATCH'! Warning: couldn't find fasta record for 'HG1490_PATCH'! Warning: couldn't find fasta record for 'HG1497_PATCH'! Warning: couldn't find fasta record for 'HG14_PATCH'! Warning: couldn't find fasta record for 'HG1500_PATCH'! Warning: couldn't find fasta record for 'HG1501_PATCH'! Warning: couldn't find fasta record for 'HG1502_PATCH'! Warning: couldn't find fasta record for 'HG151_NOVEL_TEST'! Warning: couldn't find fasta record for 'HG1591_PATCH'! Warning: couldn't find fasta record for 'HG1592_PATCH'! Warning: couldn't find fasta record for 'HG1595_PATCH'! Warning: couldn't find fasta record for 'HG1699_PATCH'! Warning: couldn't find fasta record for 'HG174_HG254_PATCH'! Warning: couldn't find fasta record for 'HG183_PATCH'! Warning: couldn't find fasta record for 'HG185_PATCH'! Warning: couldn't find fasta record for 'HG186_PATCH'! Warning: couldn't find fasta record for 'HG193_PATCH'! Warning: couldn't find fasta record for 'HG19_PATCH'! Warning: couldn't find fasta record for 'HG237_PATCH'! Warning: couldn't find fasta record for 'HG243_PATCH'! Warning: couldn't find fasta record for 'HG256_PATCH'! Warning: couldn't find fasta record for 'HG271_PATCH'! Warning: couldn't find fasta record for 'HG27_PATCH'! Warning: couldn't find fasta record for 'HG280_PATCH'! Warning: couldn't find fasta record for 'HG281_PATCH'! Warning: couldn't find fasta record for 'HG299_PATCH'! Warning: couldn't find fasta record for 'HG29_PATCH'! Warning: couldn't find fasta record for 'HG305_PATCH'! Warning: couldn't find fasta record for 'HG306_PATCH'! Warning: couldn't find fasta record for 'HG311_PATCH'! Warning: couldn't find fasta record for 'HG325_PATCH'! Warning: couldn't find fasta record for 'HG329_PATCH'! Warning: couldn't find fasta record for 'HG339_PATCH'! Warning: couldn't find fasta record for 'HG344_PATCH'! Warning: couldn't find fasta record for 'HG348_PATCH'! Warning: couldn't find fasta record for 'HG357_PATCH'! Warning: couldn't find fasta record for 'HG375_PATCH'! Warning: couldn't find fasta record for 'HG385_PATCH'! Warning: couldn't find fasta record for 'HG388_HG400_PATCH'! Warning: couldn't find fasta record for 'HG414_PATCH'! Warning: couldn't find fasta record for 'HG417_PATCH'! Warning: couldn't find fasta record for 'HG418_PATCH'! Warning: couldn't find fasta record for 'HG444_PATCH'! Warning: couldn't find fasta record for 'HG480_HG481_PATCH'! Warning: couldn't find fasta record for 'HG497_PATCH'! Warning: couldn't find fasta record for 'HG506_HG507_HG1000_PATCH'! Warning: couldn't find fasta record for 'HG50_PATCH'! Warning: couldn't find fasta record for 'HG531_PATCH'! Warning: couldn't find fasta record for 'HG536_PATCH'! Warning: couldn't find fasta record for 'HG544_PATCH'! Warning: couldn't find fasta record for 'HG686_PATCH'! Warning: couldn't find fasta record for 'HG706_PATCH'! Warning: couldn't find fasta record for 'HG729_PATCH'! Warning: couldn't find fasta record for 'HG730_PATCH'! Warning: couldn't find fasta record for 'HG736_PATCH'! Warning: couldn't find fasta record for 'HG745_PATCH'! Warning: couldn't find fasta record for 'HG747_PATCH'! Warning: couldn't find fasta record for 'HG748_PATCH'! Warning: couldn't find fasta record for 'HG75_PATCH'! Warning: couldn't find fasta record for 'HG79_PATCH'! Warning: couldn't find fasta record for 'HG7_PATCH'! Warning: couldn't find fasta record for 'HG858_PATCH'! Warning: couldn't find fasta record for 'HG865_PATCH'! Warning: couldn't find fasta record for 'HG871_PATCH'! Warning: couldn't find fasta record for 'HG873_PATCH'! Warning: couldn't find fasta record for 'HG883_PATCH'! Warning: couldn't find fasta record for 'HG905_PATCH'! Warning: couldn't find fasta record for 'HG944_PATCH'! Warning: couldn't find fasta record for 'HG946_PATCH'! Warning: couldn't find fasta record for 'HG953_PATCH'! Warning: couldn't find fasta record for 'HG957_PATCH'! Warning: couldn't find fasta record for 'HG962_PATCH'! Warning: couldn't find fasta record for 'HG971_PATCH'! Warning: couldn't find fasta record for 'HG979_PATCH'! Warning: couldn't find fasta record for 'HG987_PATCH'! Warning: couldn't find fasta record for 'HG989_PATCH'! Warning: couldn't find fasta record for 'HG990_PATCH'! Warning: couldn't find fasta record for 'HG991_PATCH'! Warning: couldn't find fasta record for 'HG996_PATCH'! Warning: couldn't find fasta record for 'HG998_1_PATCH'! Warning: couldn't find fasta record for 'HG998_2_PATCH'! Warning: couldn't find fasta record for 'HG999_1_PATCH'! Warning: couldn't find fasta record for 'HG999_2_PATCH'! Warning: couldn't find fasta record for 'HSCHR10_1_CTG2'! Warning: couldn't find fasta record for 'HSCHR10_1_CTG5'! Warning: couldn't find fasta record for 'HSCHR12_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR12_1_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR12_1_CTG5'! Warning: couldn't find fasta record for 'HSCHR12_2_CTG2'! Warning: couldn't find fasta record for 'HSCHR12_2_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR12_3_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR15_1_CTG4'! Warning: couldn't find fasta record for 'HSCHR15_1_CTG8'! Warning: couldn't find fasta record for 'HSCHR16_1_CTG3_1'! Warning: couldn't find fasta record for 'HSCHR16_2_CTG3_1'! Warning: couldn't find fasta record for 'HSCHR17_1'! Warning: couldn't find fasta record for 'HSCHR17_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR17_1_CTG4'! Warning: couldn't find fasta record for 'HSCHR17_2_CTG4'! Warning: couldn't find fasta record for 'HSCHR17_3_CTG4'! Warning: couldn't find fasta record for 'HSCHR17_4_CTG4'! Warning: couldn't find fasta record for 'HSCHR17_5_CTG4'! Warning: couldn't find fasta record for 'HSCHR17_6_CTG4'! Warning: couldn't find fasta record for 'HSCHR18_1_CTG1_1'! Warning: couldn't find fasta record for 'HSCHR18_1_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR18_2_CTG2'! Warning: couldn't find fasta record for 'HSCHR18_2_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR19LRC_COX1_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_COX2_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_LRC_I_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_LRC_J_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_LRC_S_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_LRC_T_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_PGF1_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_PGF2_CTG1'! Warning: couldn't find fasta record for 'HSCHR19_1_CTG3'! Warning: couldn't find fasta record for 'HSCHR19_1_CTG3_1'! Warning: couldn't find fasta record for 'HSCHR19_2_CTG3'! Warning: couldn't find fasta record for 'HSCHR19_3_CTG3'! Warning: couldn't find fasta record for 'HSCHR1_1_CTG31'! Warning: couldn't find fasta record for 'HSCHR1_2_CTG31'! Warning: couldn't find fasta record for 'HSCHR1_3_CTG31'! Warning: couldn't find fasta record for 'HSCHR20_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR21_2_CTG1_1'! Warning: couldn't find fasta record for 'HSCHR21_3_CTG1_1'! Warning: couldn't find fasta record for 'HSCHR21_4_CTG1_1'! Warning: couldn't find fasta record for 'HSCHR22_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR22_1_CTG2'! Warning: couldn't find fasta record for 'HSCHR22_2_CTG1'! Warning: couldn't find fasta record for 'HSCHR2_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR2_1_CTG12'! Warning: couldn't find fasta record for 'HSCHR2_2_CTG12'! Warning: couldn't find fasta record for 'HSCHR3_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR3_1_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR4_1'! Warning: couldn't find fasta record for 'HSCHR4_1_CTG12'! Warning: couldn't find fasta record for 'HSCHR4_1_CTG6'! Warning: couldn't find fasta record for 'HSCHR4_2_CTG9'! Warning: couldn't find fasta record for 'HSCHR5_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR5_1_CTG2'! Warning: couldn't find fasta record for 'HSCHR5_1_CTG5'! Warning: couldn't find fasta record for 'HSCHR5_2_CTG1'! Warning: couldn't find fasta record for 'HSCHR5_3_CTG1'! Warning: couldn't find fasta record for 'HSCHR6_1_CTG5'! Warning: couldn't find fasta record for 'HSCHR6_MHC_APD'! Warning: couldn't find fasta record for 'HSCHR6_MHC_COX'! Warning: couldn't find fasta record for 'HSCHR6_MHC_DBB'! Warning: couldn't find fasta record for 'HSCHR6_MHC_MANN'! Warning: couldn't find fasta record for 'HSCHR6_MHC_MCF'! Warning: couldn't find fasta record for 'HSCHR6_MHC_QBL'! Warning: couldn't find fasta record for 'HSCHR6_MHC_SSTO'! Warning: couldn't find fasta record for 'HSCHR7_1_CTG6'! Warning: couldn't find fasta record for 'HSCHR9_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR9_1_CTG35'! Warning: couldn't find fasta record for 'HSCHR9_2_CTG35'! Warning: couldn't find fasta record for 'HSCHR9_3_CTG35'! [Wed Oct 22 12:36:42 2014] Comparing against reference file /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf You are using Cufflinks v2.2.1, which is the most recent release. Warning: couldn't find fasta record for 'HG1007_PATCH'! Warning: couldn't find fasta record for 'HG1032_PATCH'! Warning: couldn't find fasta record for 'HG104_HG975_PATCH'! Warning: couldn't find fasta record for 'HG1063_PATCH'! Warning: couldn't find fasta record for 'HG1074_PATCH'! Warning: couldn't find fasta record for 'HG1079_PATCH'! Warning: couldn't find fasta record for 'HG1082_HG167_PATCH'! Warning: couldn't find fasta record for 'HG1091_PATCH'! Warning: couldn't find fasta record for 'HG1133_PATCH'! Warning: couldn't find fasta record for 'HG1146_PATCH'! Warning: couldn't find fasta record for 'HG115_PATCH'! Warning: couldn't find fasta record for 'HG1208_PATCH'! Warning: couldn't find fasta record for 'HG1211_PATCH'! Warning: couldn't find fasta record for 'HG122_PATCH'! Warning: couldn't find fasta record for 'HG1257_PATCH'! Warning: couldn't find fasta record for 'HG1287_PATCH'! Warning: couldn't find fasta record for 'HG1292_PATCH'! Warning: couldn't find fasta record for 'HG1293_PATCH'! Warning: couldn't find fasta record for 'HG1304_PATCH'! Warning: couldn't find fasta record for 'HG1308_PATCH'! Warning: couldn't find fasta record for 'HG1322_PATCH'! Warning: couldn't find fasta record for 'HG1350_HG959_PATCH'! Warning: couldn't find fasta record for 'HG1423_PATCH'! Warning: couldn't find fasta record for 'HG1424_PATCH'! Warning: couldn't find fasta record for 'HG1425_PATCH'! Warning: couldn't find fasta record for 'HG1426_PATCH'! Warning: couldn't find fasta record for 'HG142_HG150_NOVEL_TEST'! Warning: couldn't find fasta record for 'HG1433_PATCH'! Warning: couldn't find fasta record for 'HG1434_PATCH'! Warning: couldn't find fasta record for 'HG1435_PATCH'! Warning: couldn't find fasta record for 'HG1436_HG1432_PATCH'! Warning: couldn't find fasta record for 'HG1437_PATCH'! Warning: couldn't find fasta record for 'HG1438_PATCH'! Warning: couldn't find fasta record for 'HG1439_PATCH'! Warning: couldn't find fasta record for 'HG1440_PATCH'! Warning: couldn't find fasta record for 'HG1441_PATCH'! Warning: couldn't find fasta record for 'HG1442_PATCH'! Warning: couldn't find fasta record for 'HG1443_HG1444_PATCH'! Warning: couldn't find fasta record for 'HG144_PATCH'! Warning: couldn't find fasta record for 'HG1453_PATCH'! Warning: couldn't find fasta record for 'HG1458_PATCH'! Warning: couldn't find fasta record for 'HG1459_PATCH'! Warning: couldn't find fasta record for 'HG1462_PATCH'! Warning: couldn't find fasta record for 'HG1463_PATCH'! Warning: couldn't find fasta record for 'HG1472_PATCH'! Warning: couldn't find fasta record for 'HG1479_PATCH'! Warning: couldn't find fasta record for 'HG1486_PATCH'! Warning: couldn't find fasta record for 'HG1487_PATCH'! Warning: couldn't find fasta record for 'HG1488_PATCH'! Warning: couldn't find fasta record for 'HG1490_PATCH'! Warning: couldn't find fasta record for 'HG1497_PATCH'! Warning: couldn't find fasta record for 'HG14_PATCH'! Warning: couldn't find fasta record for 'HG1500_PATCH'! Warning: couldn't find fasta record for 'HG1501_PATCH'! Warning: couldn't find fasta record for 'HG1502_PATCH'! Warning: couldn't find fasta record for 'HG151_NOVEL_TEST'! Warning: couldn't find fasta record for 'HG1591_PATCH'! Warning: couldn't find fasta record for 'HG1592_PATCH'! Warning: couldn't find fasta record for 'HG1595_PATCH'! Warning: couldn't find fasta record for 'HG1699_PATCH'! Warning: couldn't find fasta record for 'HG174_HG254_PATCH'! Warning: couldn't find fasta record for 'HG183_PATCH'! Warning: couldn't find fasta record for 'HG185_PATCH'! Warning: couldn't find fasta record for 'HG186_PATCH'! Warning: couldn't find fasta record for 'HG193_PATCH'! Warning: couldn't find fasta record for 'HG19_PATCH'! Warning: couldn't find fasta record for 'HG237_PATCH'! Warning: couldn't find fasta record for 'HG243_PATCH'! Warning: couldn't find fasta record for 'HG256_PATCH'! Warning: couldn't find fasta record for 'HG271_PATCH'! Warning: couldn't find fasta record for 'HG27_PATCH'! Warning: couldn't find fasta record for 'HG280_PATCH'! Warning: couldn't find fasta record for 'HG281_PATCH'! Warning: couldn't find fasta record for 'HG299_PATCH'! Warning: couldn't find fasta record for 'HG29_PATCH'! Warning: couldn't find fasta record for 'HG305_PATCH'! Warning: couldn't find fasta record for 'HG306_PATCH'! Warning: couldn't find fasta record for 'HG311_PATCH'! Warning: couldn't find fasta record for 'HG325_PATCH'! Warning: couldn't find fasta record for 'HG329_PATCH'! Warning: couldn't find fasta record for 'HG339_PATCH'! Warning: couldn't find fasta record for 'HG344_PATCH'! Warning: couldn't find fasta record for 'HG348_PATCH'! Warning: couldn't find fasta record for 'HG357_PATCH'! Warning: couldn't find fasta record for 'HG375_PATCH'! Warning: couldn't find fasta record for 'HG385_PATCH'! Warning: couldn't find fasta record for 'HG388_HG400_PATCH'! Warning: couldn't find fasta record for 'HG414_PATCH'! Warning: couldn't find fasta record for 'HG417_PATCH'! Warning: couldn't find fasta record for 'HG418_PATCH'! Warning: couldn't find fasta record for 'HG444_PATCH'! Warning: couldn't find fasta record for 'HG480_HG481_PATCH'! Warning: couldn't find fasta record for 'HG497_PATCH'! Warning: couldn't find fasta record for 'HG506_HG507_HG1000_PATCH'! Warning: couldn't find fasta record for 'HG50_PATCH'! Warning: couldn't find fasta record for 'HG531_PATCH'! Warning: couldn't find fasta record for 'HG536_PATCH'! Warning: couldn't find fasta record for 'HG544_PATCH'! Warning: couldn't find fasta record for 'HG686_PATCH'! Warning: couldn't find fasta record for 'HG706_PATCH'! Warning: couldn't find fasta record for 'HG729_PATCH'! Warning: couldn't find fasta record for 'HG730_PATCH'! Warning: couldn't find fasta record for 'HG736_PATCH'! Warning: couldn't find fasta record for 'HG745_PATCH'! Warning: couldn't find fasta record for 'HG747_PATCH'! Warning: couldn't find fasta record for 'HG748_PATCH'! Warning: couldn't find fasta record for 'HG75_PATCH'! Warning: couldn't find fasta record for 'HG79_PATCH'! Warning: couldn't find fasta record for 'HG7_PATCH'! Warning: couldn't find fasta record for 'HG858_PATCH'! Warning: couldn't find fasta record for 'HG865_PATCH'! Warning: couldn't find fasta record for 'HG871_PATCH'! Warning: couldn't find fasta record for 'HG873_PATCH'! Warning: couldn't find fasta record for 'HG883_PATCH'! Warning: couldn't find fasta record for 'HG905_PATCH'! Warning: couldn't find fasta record for 'HG944_PATCH'! Warning: couldn't find fasta record for 'HG946_PATCH'! Warning: couldn't find fasta record for 'HG953_PATCH'! Warning: couldn't find fasta record for 'HG957_PATCH'! Warning: couldn't find fasta record for 'HG962_PATCH'! Warning: couldn't find fasta record for 'HG971_PATCH'! Warning: couldn't find fasta record for 'HG979_PATCH'! Warning: couldn't find fasta record for 'HG987_PATCH'! Warning: couldn't find fasta record for 'HG989_PATCH'! Warning: couldn't find fasta record for 'HG990_PATCH'! Warning: couldn't find fasta record for 'HG991_PATCH'! Warning: couldn't find fasta record for 'HG996_PATCH'! Warning: couldn't find fasta record for 'HG998_1_PATCH'! Warning: couldn't find fasta record for 'HG998_2_PATCH'! Warning: couldn't find fasta record for 'HG999_1_PATCH'! Warning: couldn't find fasta record for 'HG999_2_PATCH'! Warning: couldn't find fasta record for 'HSCHR10_1_CTG2'! Warning: couldn't find fasta record for 'HSCHR10_1_CTG5'! Warning: couldn't find fasta record for 'HSCHR12_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR12_1_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR12_1_CTG5'! Warning: couldn't find fasta record for 'HSCHR12_2_CTG2'! Warning: couldn't find fasta record for 'HSCHR12_2_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR12_3_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR15_1_CTG4'! Warning: couldn't find fasta record for 'HSCHR15_1_CTG8'! Warning: couldn't find fasta record for 'HSCHR16_1_CTG3_1'! Warning: couldn't find fasta record for 'HSCHR16_2_CTG3_1'! Warning: couldn't find fasta record for 'HSCHR17_1'! Warning: couldn't find fasta record for 'HSCHR17_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR17_1_CTG4'! Warning: couldn't find fasta record for 'HSCHR17_2_CTG4'! Warning: couldn't find fasta record for 'HSCHR17_3_CTG4'! Warning: couldn't find fasta record for 'HSCHR17_4_CTG4'! Warning: couldn't find fasta record for 'HSCHR17_5_CTG4'! Warning: couldn't find fasta record for 'HSCHR17_6_CTG4'! Warning: couldn't find fasta record for 'HSCHR18_1_CTG1_1'! Warning: couldn't find fasta record for 'HSCHR18_1_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR18_2_CTG2'! Warning: couldn't find fasta record for 'HSCHR18_2_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR19LRC_COX1_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_COX2_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_LRC_I_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_LRC_J_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_LRC_S_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_LRC_T_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_PGF1_CTG1'! Warning: couldn't find fasta record for 'HSCHR19LRC_PGF2_CTG1'! Warning: couldn't find fasta record for 'HSCHR19_1_CTG3'! Warning: couldn't find fasta record for 'HSCHR19_1_CTG3_1'! Warning: couldn't find fasta record for 'HSCHR19_2_CTG3'! Warning: couldn't find fasta record for 'HSCHR19_3_CTG3'! Warning: couldn't find fasta record for 'HSCHR1_1_CTG31'! Warning: couldn't find fasta record for 'HSCHR1_2_CTG31'! Warning: couldn't find fasta record for 'HSCHR1_3_CTG31'! Warning: couldn't find fasta record for 'HSCHR20_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR21_2_CTG1_1'! Warning: couldn't find fasta record for 'HSCHR21_3_CTG1_1'! Warning: couldn't find fasta record for 'HSCHR21_4_CTG1_1'! Warning: couldn't find fasta record for 'HSCHR22_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR22_1_CTG2'! Warning: couldn't find fasta record for 'HSCHR22_2_CTG1'! Warning: couldn't find fasta record for 'HSCHR2_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR2_1_CTG12'! Warning: couldn't find fasta record for 'HSCHR2_2_CTG12'! Warning: couldn't find fasta record for 'HSCHR3_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR3_1_CTG2_1'! Warning: couldn't find fasta record for 'HSCHR4_1'! Warning: couldn't find fasta record for 'HSCHR4_1_CTG12'! Warning: couldn't find fasta record for 'HSCHR4_1_CTG6'! Warning: couldn't find fasta record for 'HSCHR4_2_CTG9'! Warning: couldn't find fasta record for 'HSCHR5_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR5_1_CTG2'! Warning: couldn't find fasta record for 'HSCHR5_1_CTG5'! Warning: couldn't find fasta record for 'HSCHR5_2_CTG1'! Warning: couldn't find fasta record for 'HSCHR5_3_CTG1'! Warning: couldn't find fasta record for 'HSCHR6_1_CTG5'! Warning: couldn't find fasta record for 'HSCHR6_MHC_APD'! Warning: couldn't find fasta record for 'HSCHR6_MHC_COX'! Warning: couldn't find fasta record for 'HSCHR6_MHC_DBB'! Warning: couldn't find fasta record for 'HSCHR6_MHC_MANN'! Warning: couldn't find fasta record for 'HSCHR6_MHC_MCF'! Warning: couldn't find fasta record for 'HSCHR6_MHC_QBL'! Warning: couldn't find fasta record for 'HSCHR6_MHC_SSTO'! Warning: couldn't find fasta record for 'HSCHR7_1_CTG6'! Warning: couldn't find fasta record for 'HSCHR9_1_CTG1'! Warning: couldn't find fasta record for 'HSCHR9_1_CTG35'! Warning: couldn't find fasta record for 'HSCHR9_2_CTG35'! Warning: couldn't find fasta record for 'HSCHR9_3_CTG35'!