Job ID = 11244889 sra ファイルのダウンロード中... Completed: 897757K bytes transferred in 12 seconds (566821K bits/sec), in 1 file. Completed: 943018K bytes transferred in 13 seconds (567037K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 17790829 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065335/SRR7145389.sra Written 17790829 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065335/SRR7145389.sra Read 18677968 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065335/SRR7145390.sra Written 18677968 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4065335/SRR7145390.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:30:13 36468797 reads; of these: 36468797 (100.00%) were paired; of these: 1906122 (5.23%) aligned concordantly 0 times 25044431 (68.67%) aligned concordantly exactly 1 time 9518244 (26.10%) aligned concordantly >1 times ---- 1906122 pairs aligned concordantly 0 times; of these: 677153 (35.53%) aligned discordantly 1 time ---- 1228969 pairs aligned 0 times concordantly or discordantly; of these: 2457938 mates make up the pairs; of these: 1366744 (55.61%) aligned 0 times 338531 (13.77%) aligned exactly 1 time 752663 (30.62%) aligned >1 times 98.13% overall alignment rate Time searching: 00:30:13 Overall time: 00:30:13 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 32 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] 4947675 / 35142615 = 0.1408 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Tue, 09 Oct 2018 23:26:47: # Command line: callpeak -t SRX4065335.bam -f BAM -g 12100000 -n SRX4065335.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4065335.05 # format = BAM # ChIP-seq file = ['SRX4065335.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 @ Tue, 09 Oct 2018 23:26:47: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:26:47: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:26:47: # Command line: callpeak -t SRX4065335.bam -f BAM -g 12100000 -n SRX4065335.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4065335.10 # format = BAM # ChIP-seq file = ['SRX4065335.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 @ Tue, 09 Oct 2018 23:26:47: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:26:47: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:26:47: # Command line: callpeak -t SRX4065335.bam -f BAM -g 12100000 -n SRX4065335.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4065335.20 # format = BAM # ChIP-seq file = ['SRX4065335.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 @ Tue, 09 Oct 2018 23:26:47: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:26:47: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:26:53: 1000000 INFO @ Tue, 09 Oct 2018 23:26:53: 1000000 INFO @ Tue, 09 Oct 2018 23:26:53: 1000000 INFO @ Tue, 09 Oct 2018 23:26:58: 2000000 INFO @ Tue, 09 Oct 2018 23:26:58: 2000000 INFO @ Tue, 09 Oct 2018 23:26:58: 2000000 INFO @ Tue, 09 Oct 2018 23:27:03: 3000000 INFO @ Tue, 09 Oct 2018 23:27:04: 3000000 INFO @ Tue, 09 Oct 2018 23:27:04: 3000000 INFO @ Tue, 09 Oct 2018 23:27:09: 4000000 INFO @ Tue, 09 Oct 2018 23:27:10: 4000000 INFO @ Tue, 09 Oct 2018 23:27:10: 4000000 INFO @ Tue, 09 Oct 2018 23:27:14: 5000000 INFO @ Tue, 09 Oct 2018 23:27:15: 5000000 INFO @ Tue, 09 Oct 2018 23:27:15: 5000000 INFO @ Tue, 09 Oct 2018 23:27:19: 6000000 INFO @ Tue, 09 Oct 2018 23:27:21: 6000000 INFO @ Tue, 09 Oct 2018 23:27:21: 6000000 INFO @ Tue, 09 Oct 2018 23:27:25: 7000000 INFO @ Tue, 09 Oct 2018 23:27:27: 7000000 INFO @ Tue, 09 Oct 2018 23:27:27: 7000000 INFO @ Tue, 09 Oct 2018 23:27:30: 8000000 INFO @ Tue, 09 Oct 2018 23:27:32: 8000000 INFO @ Tue, 09 Oct 2018 23:27:32: 8000000 INFO @ Tue, 09 Oct 2018 23:27:36: 9000000 INFO @ Tue, 09 Oct 2018 23:27:38: 9000000 INFO @ Tue, 09 Oct 2018 23:27:38: 9000000 INFO @ Tue, 09 Oct 2018 23:27:41: 10000000 INFO @ Tue, 09 Oct 2018 23:27:43: 10000000 INFO @ Tue, 09 Oct 2018 23:27:43: 10000000 INFO @ Tue, 09 Oct 2018 23:27:46: 11000000 INFO @ Tue, 09 Oct 2018 23:27:49: 11000000 INFO @ Tue, 09 Oct 2018 23:27:49: 11000000 INFO @ Tue, 09 Oct 2018 23:27:52: 12000000 INFO @ Tue, 09 Oct 2018 23:27:55: 12000000 INFO @ Tue, 09 Oct 2018 23:27:55: 12000000 INFO @ Tue, 09 Oct 2018 23:27:57: 13000000 INFO @ Tue, 09 Oct 2018 23:28:00: 13000000 INFO @ Tue, 09 Oct 2018 23:28:00: 13000000 INFO @ Tue, 09 Oct 2018 23:28:02: 14000000 INFO @ Tue, 09 Oct 2018 23:28:06: 14000000 INFO @ Tue, 09 Oct 2018 23:28:06: 14000000 INFO @ Tue, 09 Oct 2018 23:28:08: 15000000 INFO @ Tue, 09 Oct 2018 23:28:12: 15000000 INFO @ Tue, 09 Oct 2018 23:28:12: 15000000 INFO @ Tue, 09 Oct 2018 23:28:13: 16000000 INFO @ Tue, 09 Oct 2018 23:28:17: 16000000 INFO @ Tue, 09 Oct 2018 23:28:17: 16000000 INFO @ Tue, 09 Oct 2018 23:28:18: 17000000 INFO @ Tue, 09 Oct 2018 23:28:23: 17000000 INFO @ Tue, 09 Oct 2018 23:28:23: 17000000 INFO @ Tue, 09 Oct 2018 23:28:24: 18000000 INFO @ Tue, 09 Oct 2018 23:28:28: 18000000 INFO @ Tue, 09 Oct 2018 23:28:28: 18000000 INFO @ Tue, 09 Oct 2018 23:28:29: 19000000 INFO @ Tue, 09 Oct 2018 23:28:34: 19000000 INFO @ Tue, 09 Oct 2018 23:28:34: 19000000 INFO @ Tue, 09 Oct 2018 23:28:34: 20000000 INFO @ Tue, 09 Oct 2018 23:28:39: 20000000 INFO @ Tue, 09 Oct 2018 23:28:40: 20000000 INFO @ Tue, 09 Oct 2018 23:28:40: 21000000 INFO @ Tue, 09 Oct 2018 23:28:45: 21000000 INFO @ Tue, 09 Oct 2018 23:28:45: 22000000 INFO @ Tue, 09 Oct 2018 23:28:45: 21000000 INFO @ Tue, 09 Oct 2018 23:28:50: 23000000 INFO @ Tue, 09 Oct 2018 23:28:51: 22000000 INFO @ Tue, 09 Oct 2018 23:28:51: 22000000 INFO @ Tue, 09 Oct 2018 23:28:56: 24000000 INFO @ Tue, 09 Oct 2018 23:28:57: 23000000 INFO @ Tue, 09 Oct 2018 23:28:57: 23000000 INFO @ Tue, 09 Oct 2018 23:29:01: 25000000 INFO @ Tue, 09 Oct 2018 23:29:02: 24000000 INFO @ Tue, 09 Oct 2018 23:29:03: 24000000 INFO @ Tue, 09 Oct 2018 23:29:06: 26000000 INFO @ Tue, 09 Oct 2018 23:29:08: 25000000 INFO @ Tue, 09 Oct 2018 23:29:09: 25000000 INFO @ Tue, 09 Oct 2018 23:29:12: 27000000 INFO @ Tue, 09 Oct 2018 23:29:14: 26000000 INFO @ Tue, 09 Oct 2018 23:29:15: 26000000 INFO @ Tue, 09 Oct 2018 23:29:17: 28000000 INFO @ Tue, 09 Oct 2018 23:29:20: 27000000 INFO @ Tue, 09 Oct 2018 23:29:21: 27000000 INFO @ Tue, 09 Oct 2018 23:29:22: 29000000 INFO @ Tue, 09 Oct 2018 23:29:26: 28000000 INFO @ Tue, 09 Oct 2018 23:29:27: 28000000 INFO @ Tue, 09 Oct 2018 23:29:28: 30000000 INFO @ Tue, 09 Oct 2018 23:29:32: 29000000 INFO @ Tue, 09 Oct 2018 23:29:33: 31000000 INFO @ Tue, 09 Oct 2018 23:29:33: 29000000 INFO @ Tue, 09 Oct 2018 23:29:37: 30000000 INFO @ Tue, 09 Oct 2018 23:29:38: 32000000 INFO @ Tue, 09 Oct 2018 23:29:39: 30000000 INFO @ Tue, 09 Oct 2018 23:29:43: 31000000 INFO @ Tue, 09 Oct 2018 23:29:44: 33000000 INFO @ Tue, 09 Oct 2018 23:29:45: 31000000 INFO @ Tue, 09 Oct 2018 23:29:49: 34000000 INFO @ Tue, 09 Oct 2018 23:29:49: 32000000 INFO @ Tue, 09 Oct 2018 23:29:51: 32000000 INFO @ Tue, 09 Oct 2018 23:29:54: 35000000 INFO @ Tue, 09 Oct 2018 23:29:55: 33000000 INFO @ Tue, 09 Oct 2018 23:29:58: 33000000 INFO @ Tue, 09 Oct 2018 23:29:59: 36000000 INFO @ Tue, 09 Oct 2018 23:30:01: 34000000 INFO @ Tue, 09 Oct 2018 23:30:04: 34000000 INFO @ Tue, 09 Oct 2018 23:30:05: 37000000 INFO @ Tue, 09 Oct 2018 23:30:07: 35000000 INFO @ Tue, 09 Oct 2018 23:30:10: 35000000 INFO @ Tue, 09 Oct 2018 23:30:10: 38000000 INFO @ Tue, 09 Oct 2018 23:30:12: 36000000 INFO @ Tue, 09 Oct 2018 23:30:15: 39000000 INFO @ Tue, 09 Oct 2018 23:30:15: 36000000 INFO @ Tue, 09 Oct 2018 23:30:18: 37000000 INFO @ Tue, 09 Oct 2018 23:30:20: 40000000 INFO @ Tue, 09 Oct 2018 23:30:21: 37000000 INFO @ Tue, 09 Oct 2018 23:30:24: 38000000 INFO @ Tue, 09 Oct 2018 23:30:26: 41000000 INFO @ Tue, 09 Oct 2018 23:30:27: 38000000 INFO @ Tue, 09 Oct 2018 23:30:29: 39000000 INFO @ Tue, 09 Oct 2018 23:30:31: 42000000 INFO @ Tue, 09 Oct 2018 23:30:33: 39000000 INFO @ Tue, 09 Oct 2018 23:30:35: 40000000 INFO @ Tue, 09 Oct 2018 23:30:36: 43000000 INFO @ Tue, 09 Oct 2018 23:30:39: 40000000 INFO @ Tue, 09 Oct 2018 23:30:41: 41000000 INFO @ Tue, 09 Oct 2018 23:30:41: 44000000 INFO @ Tue, 09 Oct 2018 23:30:45: 41000000 INFO @ Tue, 09 Oct 2018 23:30:46: 42000000 INFO @ Tue, 09 Oct 2018 23:30:47: 45000000 INFO @ Tue, 09 Oct 2018 23:30:50: 42000000 INFO @ Tue, 09 Oct 2018 23:30:52: 43000000 INFO @ Tue, 09 Oct 2018 23:30:52: 46000000 INFO @ Tue, 09 Oct 2018 23:30:56: 43000000 INFO @ Tue, 09 Oct 2018 23:30:57: 44000000 INFO @ Tue, 09 Oct 2018 23:30:58: 47000000 INFO @ Tue, 09 Oct 2018 23:31:02: 44000000 INFO @ Tue, 09 Oct 2018 23:31:03: 45000000 INFO @ Tue, 09 Oct 2018 23:31:03: 48000000 INFO @ Tue, 09 Oct 2018 23:31:07: 45000000 INFO @ Tue, 09 Oct 2018 23:31:08: 46000000 INFO @ Tue, 09 Oct 2018 23:31:09: 49000000 INFO @ Tue, 09 Oct 2018 23:31:13: 46000000 INFO @ Tue, 09 Oct 2018 23:31:13: 47000000 INFO @ Tue, 09 Oct 2018 23:31:14: 50000000 INFO @ Tue, 09 Oct 2018 23:31:18: 47000000 INFO @ Tue, 09 Oct 2018 23:31:19: 48000000 INFO @ Tue, 09 Oct 2018 23:31:20: 51000000 INFO @ Tue, 09 Oct 2018 23:31:24: 48000000 INFO @ Tue, 09 Oct 2018 23:31:24: 49000000 INFO @ Tue, 09 Oct 2018 23:31:25: 52000000 INFO @ Tue, 09 Oct 2018 23:31:30: 49000000 INFO @ Tue, 09 Oct 2018 23:31:30: 50000000 INFO @ Tue, 09 Oct 2018 23:31:31: 53000000 INFO @ Tue, 09 Oct 2018 23:31:35: 50000000 INFO @ Tue, 09 Oct 2018 23:31:35: 51000000 INFO @ Tue, 09 Oct 2018 23:31:36: 54000000 INFO @ Tue, 09 Oct 2018 23:31:41: 52000000 INFO @ Tue, 09 Oct 2018 23:31:41: 51000000 INFO @ Tue, 09 Oct 2018 23:31:42: 55000000 INFO @ Tue, 09 Oct 2018 23:31:46: 53000000 INFO @ Tue, 09 Oct 2018 23:31:46: 52000000 INFO @ Tue, 09 Oct 2018 23:31:47: 56000000 INFO @ Tue, 09 Oct 2018 23:31:51: 54000000 INFO @ Tue, 09 Oct 2018 23:31:52: 53000000 INFO @ Tue, 09 Oct 2018 23:31:53: 57000000 INFO @ Tue, 09 Oct 2018 23:31:57: 55000000 INFO @ Tue, 09 Oct 2018 23:31:57: 54000000 INFO @ Tue, 09 Oct 2018 23:31:58: 58000000 INFO @ Tue, 09 Oct 2018 23:32:03: 56000000 INFO @ Tue, 09 Oct 2018 23:32:03: 55000000 INFO @ Tue, 09 Oct 2018 23:32:04: 59000000 INFO @ Tue, 09 Oct 2018 23:32:08: 57000000 INFO @ Tue, 09 Oct 2018 23:32:09: 56000000 INFO @ Tue, 09 Oct 2018 23:32:09: 60000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 09 Oct 2018 23:32:14: 58000000 INFO @ Tue, 09 Oct 2018 23:32:14: 57000000 INFO @ Tue, 09 Oct 2018 23:32:15: 61000000 INFO @ Tue, 09 Oct 2018 23:32:19: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:32:19: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:32:19: #1 total tags in treatment: 29620729 INFO @ Tue, 09 Oct 2018 23:32:19: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:32:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:32:19: 59000000 INFO @ Tue, 09 Oct 2018 23:32:20: #1 tags after filtering in treatment: 12136234 INFO @ Tue, 09 Oct 2018 23:32:20: #1 Redundant rate of treatment: 0.59 INFO @ Tue, 09 Oct 2018 23:32:20: #1 finished! INFO @ Tue, 09 Oct 2018 23:32:20: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:32:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:32:20: 58000000 INFO @ Tue, 09 Oct 2018 23:32:20: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:32:20: 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 @ Tue, 09 Oct 2018 23:32:20: Process for pairing-model is terminated! cat: SRX4065335.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4065335.10_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4065335.10_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4065335.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:32:25: 60000000 INFO @ Tue, 09 Oct 2018 23:32:25: 59000000 INFO @ Tue, 09 Oct 2018 23:32:30: 61000000 INFO @ Tue, 09 Oct 2018 23:32:30: 60000000 BigWig に変換しました。 INFO @ Tue, 09 Oct 2018 23:32:35: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:32:35: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:32:35: #1 total tags in treatment: 29620729 INFO @ Tue, 09 Oct 2018 23:32:35: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:32:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:32:35: #1 tags after filtering in treatment: 12136234 INFO @ Tue, 09 Oct 2018 23:32:35: #1 Redundant rate of treatment: 0.59 INFO @ Tue, 09 Oct 2018 23:32:35: #1 finished! INFO @ Tue, 09 Oct 2018 23:32:35: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:32:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:32:36: 61000000 INFO @ Tue, 09 Oct 2018 23:32:36: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:32:36: 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 @ Tue, 09 Oct 2018 23:32:36: Process for pairing-model is terminated! cat: SRX4065335.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4065335.05_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4065335.05_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4065335.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:32:40: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 23:32:40: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 23:32:40: #1 total tags in treatment: 29620729 INFO @ Tue, 09 Oct 2018 23:32:40: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:32:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:32:40: #1 tags after filtering in treatment: 12136234 INFO @ Tue, 09 Oct 2018 23:32:40: #1 Redundant rate of treatment: 0.59 INFO @ Tue, 09 Oct 2018 23:32:40: #1 finished! INFO @ Tue, 09 Oct 2018 23:32:40: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:32:41: #2 number of paired peaks: 0 WARNING @ Tue, 09 Oct 2018 23:32:41: 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 @ Tue, 09 Oct 2018 23:32:41: Process for pairing-model is terminated! cat: SRX4065335.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4065335.20_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4065335.20_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX4065335.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling