Job ID = 2011845 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 24,337,769 reads read : 48,675,538 reads written : 48,675,229 reads 0-length : 309 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Warning: skipping mate #1 of read 'SRR8313292.234966 234966 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.234966 234966 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.937597 937597 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.937597 937597 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.3370579 3370579 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.3370579 3370579 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.3379139 3379139 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.3379139 3379139 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.4783661 4783661 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.4783661 4783661 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.6521068 6521068 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.6521068 6521068 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.7070772 7070772 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.7070772 7070772 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.7846906 7846906 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.7846906 7846906 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.8320912 8320912 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.8320912 8320912 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.8529753 8529753 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.8529753 8529753 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.9108676 9108676 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.9108676 9108676 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.10124457 10124457 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.10124457 10124457 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.10677106 10677106 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.10677106 10677106 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.11646877 11646877 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.11646877 11646877 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.12971148 12971148 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.12971148 12971148 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.13197679 13197679 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.13197679 13197679 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.16134778 16134778 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.16134778 16134778 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.16472332 16472332 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.16472332 16472332 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.17095127 17095127 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.17095127 17095127 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.17364616 17364616 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.17364616 17364616 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.18059412 18059412 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.18059412 18059412 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.18104206 18104206 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.18104206 18104206 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.18402553 18402553 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.18402553 18402553 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313292.23804210 23804210 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313292.23804210 23804210 length=1' because it was < 2 characters long Error, fewer reads in file specified with -1 than in file specified with -2 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 7330666 / 23186472 = 0.3162 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 03:51:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 06 Jul 2019 03:51:15: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:51:15: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:51:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 06 Jul 2019 03:51:16: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:51:16: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:51:25: 1000000 INFO @ Sat, 06 Jul 2019 03:51:25: 1000000 INFO @ Sat, 06 Jul 2019 03:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 06 Jul 2019 03:51:31: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:51:31: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:51:35: 2000000 INFO @ Sat, 06 Jul 2019 03:51:35: 2000000 INFO @ Sat, 06 Jul 2019 03:51:39: 1000000 INFO @ Sat, 06 Jul 2019 03:51:44: 3000000 INFO @ Sat, 06 Jul 2019 03:51:44: 3000000 INFO @ Sat, 06 Jul 2019 03:51:47: 2000000 INFO @ Sat, 06 Jul 2019 03:51:53: 4000000 INFO @ Sat, 06 Jul 2019 03:51:54: 4000000 INFO @ Sat, 06 Jul 2019 03:51:55: 3000000 INFO @ Sat, 06 Jul 2019 03:52:02: 4000000 INFO @ Sat, 06 Jul 2019 03:52:03: 5000000 INFO @ Sat, 06 Jul 2019 03:52:03: 5000000 INFO @ Sat, 06 Jul 2019 03:52:10: 5000000 INFO @ Sat, 06 Jul 2019 03:52:11: 6000000 INFO @ Sat, 06 Jul 2019 03:52:12: 6000000 INFO @ Sat, 06 Jul 2019 03:52:17: 6000000 INFO @ Sat, 06 Jul 2019 03:52:18: 7000000 INFO @ Sat, 06 Jul 2019 03:52:22: 7000000 INFO @ Sat, 06 Jul 2019 03:52:24: 8000000 INFO @ Sat, 06 Jul 2019 03:52:25: 7000000 INFO @ Sat, 06 Jul 2019 03:52:31: 8000000 INFO @ Sat, 06 Jul 2019 03:52:31: 9000000 INFO @ Sat, 06 Jul 2019 03:52:32: 8000000 INFO @ Sat, 06 Jul 2019 03:52:38: 10000000 INFO @ Sat, 06 Jul 2019 03:52:40: 9000000 INFO @ Sat, 06 Jul 2019 03:52:40: 9000000 INFO @ Sat, 06 Jul 2019 03:52:44: 11000000 INFO @ Sat, 06 Jul 2019 03:52:47: 10000000 INFO @ Sat, 06 Jul 2019 03:52:49: 10000000 INFO @ Sat, 06 Jul 2019 03:52:51: 12000000 INFO @ Sat, 06 Jul 2019 03:52:55: 11000000 INFO @ Sat, 06 Jul 2019 03:52:58: 11000000 INFO @ Sat, 06 Jul 2019 03:52:59: 13000000 INFO @ Sat, 06 Jul 2019 03:53:02: 12000000 INFO @ Sat, 06 Jul 2019 03:53:05: 14000000 INFO @ Sat, 06 Jul 2019 03:53:07: 12000000 INFO @ Sat, 06 Jul 2019 03:53:09: 13000000 INFO @ Sat, 06 Jul 2019 03:53:12: 15000000 INFO @ Sat, 06 Jul 2019 03:53:16: 13000000 INFO @ Sat, 06 Jul 2019 03:53:17: 14000000 INFO @ Sat, 06 Jul 2019 03:53:20: 16000000 INFO @ Sat, 06 Jul 2019 03:53:24: 15000000 INFO @ Sat, 06 Jul 2019 03:53:25: 14000000 INFO @ Sat, 06 Jul 2019 03:53:26: 17000000 INFO @ Sat, 06 Jul 2019 03:53:32: 16000000 INFO @ Sat, 06 Jul 2019 03:53:33: 18000000 INFO @ Sat, 06 Jul 2019 03:53:33: 15000000 INFO @ Sat, 06 Jul 2019 03:53:39: 17000000 INFO @ Sat, 06 Jul 2019 03:53:39: 19000000 INFO @ Sat, 06 Jul 2019 03:53:41: 16000000 INFO @ Sat, 06 Jul 2019 03:53:46: 20000000 INFO @ Sat, 06 Jul 2019 03:53:46: 18000000 INFO @ Sat, 06 Jul 2019 03:53:49: 17000000 INFO @ Sat, 06 Jul 2019 03:53:52: 21000000 INFO @ Sat, 06 Jul 2019 03:53:53: 19000000 INFO @ Sat, 06 Jul 2019 03:53:58: 18000000 INFO @ Sat, 06 Jul 2019 03:53:59: 22000000 INFO @ Sat, 06 Jul 2019 03:54:00: 20000000 INFO @ Sat, 06 Jul 2019 03:54:05: 23000000 INFO @ Sat, 06 Jul 2019 03:54:06: 19000000 INFO @ Sat, 06 Jul 2019 03:54:07: 21000000 INFO @ Sat, 06 Jul 2019 03:54:12: 24000000 INFO @ Sat, 06 Jul 2019 03:54:14: 22000000 INFO @ Sat, 06 Jul 2019 03:54:15: 20000000 INFO @ Sat, 06 Jul 2019 03:54:19: 25000000 INFO @ Sat, 06 Jul 2019 03:54:21: 23000000 INFO @ Sat, 06 Jul 2019 03:54:23: 21000000 INFO @ Sat, 06 Jul 2019 03:54:25: 26000000 INFO @ Sat, 06 Jul 2019 03:54:29: 24000000 INFO @ Sat, 06 Jul 2019 03:54:32: 22000000 INFO @ Sat, 06 Jul 2019 03:54:32: 27000000 INFO @ Sat, 06 Jul 2019 03:54:36: 25000000 INFO @ Sat, 06 Jul 2019 03:54:38: 28000000 INFO @ Sat, 06 Jul 2019 03:54:40: 23000000 INFO @ Sat, 06 Jul 2019 03:54:43: 26000000 INFO @ Sat, 06 Jul 2019 03:54:46: 29000000 INFO @ Sat, 06 Jul 2019 03:54:49: 24000000 INFO @ Sat, 06 Jul 2019 03:54:50: 27000000 INFO @ Sat, 06 Jul 2019 03:54:53: 30000000 INFO @ Sat, 06 Jul 2019 03:54:57: 28000000 INFO @ Sat, 06 Jul 2019 03:54:58: 25000000 INFO @ Sat, 06 Jul 2019 03:55:00: 31000000 INFO @ Sat, 06 Jul 2019 03:55:05: 29000000 INFO @ Sat, 06 Jul 2019 03:55:06: 26000000 INFO @ Sat, 06 Jul 2019 03:55:07: 32000000 INFO @ Sat, 06 Jul 2019 03:55:09: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:55:09: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:55:09: #1 total tags in treatment: 15816252 INFO @ Sat, 06 Jul 2019 03:55:09: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:55:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:55:09: #1 tags after filtering in treatment: 9697919 INFO @ Sat, 06 Jul 2019 03:55:09: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 06 Jul 2019 03:55:09: #1 finished! INFO @ Sat, 06 Jul 2019 03:55:09: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:55:10: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:55:10: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 06 Jul 2019 03:55:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:55:12: 30000000 INFO @ Sat, 06 Jul 2019 03:55:15: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:55:19: 31000000 INFO @ Sat, 06 Jul 2019 03:55:23: 28000000 INFO @ Sat, 06 Jul 2019 03:55:26: 32000000 INFO @ Sat, 06 Jul 2019 03:55:28: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:55:28: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:55:28: #1 total tags in treatment: 15816252 INFO @ Sat, 06 Jul 2019 03:55:28: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:55:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:55:28: #1 tags after filtering in treatment: 9697919 INFO @ Sat, 06 Jul 2019 03:55:28: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 06 Jul 2019 03:55:28: #1 finished! INFO @ Sat, 06 Jul 2019 03:55:28: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:55:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:55:29: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:55:29: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 06 Jul 2019 03:55:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:55:31: 29000000 INFO @ Sat, 06 Jul 2019 03:55:39: 30000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:55:48: 31000000 INFO @ Sat, 06 Jul 2019 03:55:56: 32000000 INFO @ Sat, 06 Jul 2019 03:55:58: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:55:58: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:55:58: #1 total tags in treatment: 15816252 INFO @ Sat, 06 Jul 2019 03:55:58: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:55:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:55:59: #1 tags after filtering in treatment: 9697919 INFO @ Sat, 06 Jul 2019 03:55:59: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 06 Jul 2019 03:55:59: #1 finished! INFO @ Sat, 06 Jul 2019 03:55:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:55:59: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:55:59: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 06 Jul 2019 03:55:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126600/SRX5126600.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling