Job ID = 10536505 sra ファイルのダウンロード中... Completed: 1106798K bytes transferred in 29 seconds (306483K 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... Written 28243828 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671200/SRR6696952.sra Written 28243828 spots total 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 rm: cannot remove `[DSE]RR*.fastq': 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: 00:18:50 28243828 reads; of these: 28243828 (100.00%) were paired; of these: 6082283 (21.53%) aligned concordantly 0 times 19340657 (68.48%) aligned concordantly exactly 1 time 2820888 (9.99%) aligned concordantly >1 times ---- 6082283 pairs aligned concordantly 0 times; of these: 93096 (1.53%) aligned discordantly 1 time ---- 5989187 pairs aligned 0 times concordantly or discordantly; of these: 11978374 mates make up the pairs; of these: 11796111 (98.48%) aligned 0 times 115078 (0.96%) aligned exactly 1 time 67185 (0.56%) aligned >1 times 79.12% overall alignment rate Time searching: 00:18:50 Overall time: 00:18:50 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] 5930576 / 22222226 = 0.2669 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 @ Thu, 05 Apr 2018 10:28:15: # Command line: callpeak -t SRX3671200.bam -f BAM -g 12100000 -n SRX3671200.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671200.10 # format = BAM # ChIP-seq file = ['SRX3671200.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 @ Thu, 05 Apr 2018 10:28:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:28:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:28:15: # Command line: callpeak -t SRX3671200.bam -f BAM -g 12100000 -n SRX3671200.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671200.20 # format = BAM # ChIP-seq file = ['SRX3671200.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 @ Thu, 05 Apr 2018 10:28:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:28:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:28:15: # Command line: callpeak -t SRX3671200.bam -f BAM -g 12100000 -n SRX3671200.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671200.05 # format = BAM # ChIP-seq file = ['SRX3671200.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 @ Thu, 05 Apr 2018 10:28:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:28:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:28:20: 1000000 INFO @ Thu, 05 Apr 2018 10:28:21: 1000000 INFO @ Thu, 05 Apr 2018 10:28:21: 1000000 INFO @ Thu, 05 Apr 2018 10:28:26: 2000000 INFO @ Thu, 05 Apr 2018 10:28:26: 2000000 INFO @ Thu, 05 Apr 2018 10:28:26: 2000000 INFO @ Thu, 05 Apr 2018 10:28:31: 3000000 INFO @ Thu, 05 Apr 2018 10:28:31: 3000000 INFO @ Thu, 05 Apr 2018 10:28:32: 3000000 INFO @ Thu, 05 Apr 2018 10:28:36: 4000000 INFO @ Thu, 05 Apr 2018 10:28:37: 4000000 INFO @ Thu, 05 Apr 2018 10:28:38: 4000000 INFO @ Thu, 05 Apr 2018 10:28:42: 5000000 INFO @ Thu, 05 Apr 2018 10:28:42: 5000000 INFO @ Thu, 05 Apr 2018 10:28:43: 5000000 INFO @ Thu, 05 Apr 2018 10:28:47: 6000000 INFO @ Thu, 05 Apr 2018 10:28:47: 6000000 INFO @ Thu, 05 Apr 2018 10:28:49: 6000000 INFO @ Thu, 05 Apr 2018 10:28:52: 7000000 INFO @ Thu, 05 Apr 2018 10:28:52: 7000000 INFO @ Thu, 05 Apr 2018 10:28:54: 7000000 INFO @ Thu, 05 Apr 2018 10:28:57: 8000000 INFO @ Thu, 05 Apr 2018 10:28:58: 8000000 INFO @ Thu, 05 Apr 2018 10:29:00: 8000000 INFO @ Thu, 05 Apr 2018 10:29:02: 9000000 INFO @ Thu, 05 Apr 2018 10:29:04: 9000000 INFO @ Thu, 05 Apr 2018 10:29:06: 9000000 INFO @ Thu, 05 Apr 2018 10:29:07: 10000000 INFO @ Thu, 05 Apr 2018 10:29:10: 10000000 INFO @ Thu, 05 Apr 2018 10:29:12: 10000000 INFO @ Thu, 05 Apr 2018 10:29:12: 11000000 INFO @ Thu, 05 Apr 2018 10:29:15: 11000000 INFO @ Thu, 05 Apr 2018 10:29:17: 11000000 INFO @ Thu, 05 Apr 2018 10:29:17: 12000000 INFO @ Thu, 05 Apr 2018 10:29:21: 12000000 INFO @ Thu, 05 Apr 2018 10:29:23: 13000000 INFO @ Thu, 05 Apr 2018 10:29:23: 12000000 INFO @ Thu, 05 Apr 2018 10:29:27: 13000000 INFO @ Thu, 05 Apr 2018 10:29:28: 14000000 INFO @ Thu, 05 Apr 2018 10:29:29: 13000000 INFO @ Thu, 05 Apr 2018 10:29:32: 14000000 INFO @ Thu, 05 Apr 2018 10:29:33: 15000000 INFO @ Thu, 05 Apr 2018 10:29:35: 14000000 INFO @ Thu, 05 Apr 2018 10:29:38: 16000000 INFO @ Thu, 05 Apr 2018 10:29:38: 15000000 INFO @ Thu, 05 Apr 2018 10:29:40: 15000000 INFO @ Thu, 05 Apr 2018 10:29:43: 17000000 INFO @ Thu, 05 Apr 2018 10:29:44: 16000000 INFO @ Thu, 05 Apr 2018 10:29:46: 16000000 INFO @ Thu, 05 Apr 2018 10:29:48: 18000000 INFO @ Thu, 05 Apr 2018 10:29:49: 17000000 INFO @ Thu, 05 Apr 2018 10:29:52: 17000000 INFO @ Thu, 05 Apr 2018 10:29:53: 19000000 INFO @ Thu, 05 Apr 2018 10:29:55: 18000000 INFO @ Thu, 05 Apr 2018 10:29:57: 18000000 INFO @ Thu, 05 Apr 2018 10:29:58: 20000000 INFO @ Thu, 05 Apr 2018 10:30:00: 19000000 INFO @ Thu, 05 Apr 2018 10:30:03: 21000000 INFO @ Thu, 05 Apr 2018 10:30:03: 19000000 INFO @ Thu, 05 Apr 2018 10:30:06: 20000000 INFO @ Thu, 05 Apr 2018 10:30:08: 22000000 INFO @ Thu, 05 Apr 2018 10:30:09: 20000000 INFO @ Thu, 05 Apr 2018 10:30:12: 21000000 INFO @ Thu, 05 Apr 2018 10:30:13: 23000000 INFO @ Thu, 05 Apr 2018 10:30:15: 21000000 INFO @ Thu, 05 Apr 2018 10:30:17: 22000000 INFO @ Thu, 05 Apr 2018 10:30:18: 24000000 INFO @ Thu, 05 Apr 2018 10:30:20: 22000000 INFO @ Thu, 05 Apr 2018 10:30:23: 23000000 INFO @ Thu, 05 Apr 2018 10:30:23: 25000000 INFO @ Thu, 05 Apr 2018 10:30:26: 23000000 INFO @ Thu, 05 Apr 2018 10:30:28: 26000000 INFO @ Thu, 05 Apr 2018 10:30:29: 24000000 INFO @ Thu, 05 Apr 2018 10:30:32: 24000000 INFO @ Thu, 05 Apr 2018 10:30:33: 27000000 INFO @ Thu, 05 Apr 2018 10:30:34: 25000000 INFO @ Thu, 05 Apr 2018 10:30:37: 25000000 INFO @ Thu, 05 Apr 2018 10:30:38: 28000000 INFO @ Thu, 05 Apr 2018 10:30:40: 26000000 INFO @ Thu, 05 Apr 2018 10:30:43: 26000000 INFO @ Thu, 05 Apr 2018 10:30:44: 29000000 INFO @ Thu, 05 Apr 2018 10:30:46: 27000000 INFO @ Thu, 05 Apr 2018 10:30:49: 30000000 INFO @ Thu, 05 Apr 2018 10:30:49: 27000000 INFO @ Thu, 05 Apr 2018 10:30:51: 28000000 INFO @ Thu, 05 Apr 2018 10:30:54: 31000000 INFO @ Thu, 05 Apr 2018 10:30:55: 28000000 INFO @ Thu, 05 Apr 2018 10:30:57: 29000000 INFO @ Thu, 05 Apr 2018 10:30:59: 32000000 INFO @ Thu, 05 Apr 2018 10:31:00: 29000000 INFO @ Thu, 05 Apr 2018 10:31:03: 30000000 INFO @ Thu, 05 Apr 2018 10:31:03: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:31:03: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:31:03: #1 total tags in treatment: 16250239 INFO @ Thu, 05 Apr 2018 10:31:03: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:31:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:31:04: #1 tags after filtering in treatment: 6475018 INFO @ Thu, 05 Apr 2018 10:31:04: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:31:04: #1 finished! INFO @ Thu, 05 Apr 2018 10:31:04: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:31:04: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:31:04: 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 @ Thu, 05 Apr 2018 10:31:04: Process for pairing-model is terminated! cat: SRX3671200.20_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 `SRX3671200.20_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 `SRX3671200.20_*.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 `SRX3671200.20_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 INFO @ Thu, 05 Apr 2018 10:31:06: 30000000 INFO @ Thu, 05 Apr 2018 10:31:08: 31000000 INFO @ Thu, 05 Apr 2018 10:31:12: 31000000 INFO @ Thu, 05 Apr 2018 10:31:14: 32000000 INFO @ Thu, 05 Apr 2018 10:31:17: 32000000 INFO @ Thu, 05 Apr 2018 10:31:19: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:31:19: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:31:19: #1 total tags in treatment: 16250239 INFO @ Thu, 05 Apr 2018 10:31:19: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:31:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:31:19: #1 tags after filtering in treatment: 6475018 INFO @ Thu, 05 Apr 2018 10:31:19: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:31:19: #1 finished! INFO @ Thu, 05 Apr 2018 10:31:19: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:31:20: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:31:20: 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 @ Thu, 05 Apr 2018 10:31:20: Process for pairing-model is terminated! cat: SRX3671200.10_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 `SRX3671200.10_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 `SRX3671200.10_*.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 `SRX3671200.10_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 @ Thu, 05 Apr 2018 10:31:22: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:31:22: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:31:22: #1 total tags in treatment: 16250239 INFO @ Thu, 05 Apr 2018 10:31:22: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:31:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:31:22: #1 tags after filtering in treatment: 6475018 INFO @ Thu, 05 Apr 2018 10:31:22: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:31:22: #1 finished! INFO @ Thu, 05 Apr 2018 10:31:22: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:31:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:31:23: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:31:23: 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 @ Thu, 05 Apr 2018 10:31:23: Process for pairing-model is terminated! cat: SRX3671200.05_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 `SRX3671200.05_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 `SRX3671200.05_*.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 `SRX3671200.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。