Job ID = 2640990 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,572,334 reads read : 27,144,668 reads written : 27,144,668 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 Multiseed full-index search: 00:17:30 13572334 reads; of these: 13572334 (100.00%) were paired; of these: 860510 (6.34%) aligned concordantly 0 times 11576693 (85.30%) aligned concordantly exactly 1 time 1135131 (8.36%) aligned concordantly >1 times ---- 860510 pairs aligned concordantly 0 times; of these: 107524 (12.50%) aligned discordantly 1 time ---- 752986 pairs aligned 0 times concordantly or discordantly; of these: 1505972 mates make up the pairs; of these: 1452206 (96.43%) aligned 0 times 28106 (1.87%) aligned exactly 1 time 25660 (1.70%) aligned >1 times 94.65% overall alignment rate Time searching: 00:17:30 Overall time: 00:17:30 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 12 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] 199878 / 12815621 = 0.0156 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.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, 24 Aug 2019 21:04:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:04:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:04:22: 1000000 INFO @ Sat, 24 Aug 2019 21:04:31: 2000000 INFO @ Sat, 24 Aug 2019 21:04:40: 3000000 INFO @ Sat, 24 Aug 2019 21:04:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.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, 24 Aug 2019 21:04:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:04:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:04:48: 4000000 INFO @ Sat, 24 Aug 2019 21:04:51: 1000000 INFO @ Sat, 24 Aug 2019 21:04:57: 5000000 INFO @ Sat, 24 Aug 2019 21:04:59: 2000000 INFO @ Sat, 24 Aug 2019 21:05:06: 6000000 INFO @ Sat, 24 Aug 2019 21:05:06: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:05:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.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, 24 Aug 2019 21:05:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:05:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:05:14: 4000000 INFO @ Sat, 24 Aug 2019 21:05:15: 7000000 INFO @ Sat, 24 Aug 2019 21:05:22: 5000000 INFO @ Sat, 24 Aug 2019 21:05:23: 8000000 INFO @ Sat, 24 Aug 2019 21:05:24: 1000000 INFO @ Sat, 24 Aug 2019 21:05:30: 6000000 INFO @ Sat, 24 Aug 2019 21:05:32: 9000000 INFO @ Sat, 24 Aug 2019 21:05:36: 2000000 INFO @ Sat, 24 Aug 2019 21:05:37: 7000000 INFO @ Sat, 24 Aug 2019 21:05:42: 10000000 INFO @ Sat, 24 Aug 2019 21:05:45: 8000000 INFO @ Sat, 24 Aug 2019 21:05:49: 3000000 INFO @ Sat, 24 Aug 2019 21:05:53: 9000000 INFO @ Sat, 24 Aug 2019 21:05:55: 11000000 INFO @ Sat, 24 Aug 2019 21:06:00: 10000000 INFO @ Sat, 24 Aug 2019 21:06:01: 4000000 INFO @ Sat, 24 Aug 2019 21:06:07: 12000000 INFO @ Sat, 24 Aug 2019 21:06:08: 11000000 INFO @ Sat, 24 Aug 2019 21:06:14: 5000000 INFO @ Sat, 24 Aug 2019 21:06:16: 12000000 INFO @ Sat, 24 Aug 2019 21:06:20: 13000000 INFO @ Sat, 24 Aug 2019 21:06:24: 13000000 INFO @ Sat, 24 Aug 2019 21:06:27: 6000000 INFO @ Sat, 24 Aug 2019 21:06:31: 14000000 INFO @ Sat, 24 Aug 2019 21:06:32: 14000000 INFO @ Sat, 24 Aug 2019 21:06:39: 15000000 INFO @ Sat, 24 Aug 2019 21:06:39: 7000000 INFO @ Sat, 24 Aug 2019 21:06:45: 15000000 INFO @ Sat, 24 Aug 2019 21:06:47: 16000000 INFO @ Sat, 24 Aug 2019 21:06:52: 8000000 INFO @ Sat, 24 Aug 2019 21:06:54: 17000000 INFO @ Sat, 24 Aug 2019 21:06:57: 16000000 INFO @ Sat, 24 Aug 2019 21:07:02: 18000000 INFO @ Sat, 24 Aug 2019 21:07:04: 9000000 INFO @ Sat, 24 Aug 2019 21:07:10: 17000000 INFO @ Sat, 24 Aug 2019 21:07:10: 19000000 INFO @ Sat, 24 Aug 2019 21:07:16: 10000000 INFO @ Sat, 24 Aug 2019 21:07:17: 20000000 INFO @ Sat, 24 Aug 2019 21:07:22: 18000000 INFO @ Sat, 24 Aug 2019 21:07:25: 21000000 INFO @ Sat, 24 Aug 2019 21:07:29: 11000000 INFO @ Sat, 24 Aug 2019 21:07:33: 22000000 INFO @ Sat, 24 Aug 2019 21:07:34: 19000000 INFO @ Sat, 24 Aug 2019 21:07:40: 23000000 INFO @ Sat, 24 Aug 2019 21:07:41: 12000000 INFO @ Sat, 24 Aug 2019 21:07:46: 20000000 INFO @ Sat, 24 Aug 2019 21:07:48: 24000000 INFO @ Sat, 24 Aug 2019 21:07:53: 13000000 INFO @ Sat, 24 Aug 2019 21:07:56: 25000000 INFO @ Sat, 24 Aug 2019 21:07:58: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:07:58: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:07:58: #1 total tags in treatment: 12512935 INFO @ Sat, 24 Aug 2019 21:07:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:07:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:07:58: 21000000 INFO @ Sat, 24 Aug 2019 21:07:58: #1 tags after filtering in treatment: 9037065 INFO @ Sat, 24 Aug 2019 21:07:58: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:07:58: #1 finished! INFO @ Sat, 24 Aug 2019 21:07:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:07:59: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:07:59: 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, 24 Aug 2019 21:07:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.10_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/SRX4936096/SRX4936096.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:08:05: 14000000 INFO @ Sat, 24 Aug 2019 21:08:09: 22000000 INFO @ Sat, 24 Aug 2019 21:08:16: 15000000 INFO @ Sat, 24 Aug 2019 21:08:21: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:08:28: 16000000 INFO @ Sat, 24 Aug 2019 21:08:32: 24000000 INFO @ Sat, 24 Aug 2019 21:08:40: 17000000 INFO @ Sat, 24 Aug 2019 21:08:44: 25000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:08:47: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:08:47: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:08:47: #1 total tags in treatment: 12512935 INFO @ Sat, 24 Aug 2019 21:08:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:08:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:08:47: #1 tags after filtering in treatment: 9037065 INFO @ Sat, 24 Aug 2019 21:08:47: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:08:47: #1 finished! INFO @ Sat, 24 Aug 2019 21:08:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:08:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:08:48: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:08:48: 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, 24 Aug 2019 21:08:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.05_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/SRX4936096/SRX4936096.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:08:51: 18000000 INFO @ Sat, 24 Aug 2019 21:09:01: 19000000 INFO @ Sat, 24 Aug 2019 21:09:10: 20000000 INFO @ Sat, 24 Aug 2019 21:09:20: 21000000 INFO @ Sat, 24 Aug 2019 21:09:30: 22000000 INFO @ Sat, 24 Aug 2019 21:09:40: 23000000 INFO @ Sat, 24 Aug 2019 21:09:49: 24000000 INFO @ Sat, 24 Aug 2019 21:09:59: 25000000 INFO @ Sat, 24 Aug 2019 21:10:02: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:10:02: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:10:02: #1 total tags in treatment: 12512935 INFO @ Sat, 24 Aug 2019 21:10:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:10:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:10:03: #1 tags after filtering in treatment: 9037065 INFO @ Sat, 24 Aug 2019 21:10:03: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:10:03: #1 finished! INFO @ Sat, 24 Aug 2019 21:10:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:10:03: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:10:03: 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, 24 Aug 2019 21:10:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.20_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/SRX4936096/SRX4936096.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936096/SRX4936096.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling