Job ID = 10608971 sra ファイルのダウンロード中... Completed: 2530653K bytes transferred in 311 seconds (66618K 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 20089435 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2741970/SRR5453804.sra Written 20089435 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: 00:23:52 20089435 reads; of these: 20089435 (100.00%) were paired; of these: 2553576 (12.71%) aligned concordantly 0 times 16023375 (79.76%) aligned concordantly exactly 1 time 1512484 (7.53%) aligned concordantly >1 times ---- 2553576 pairs aligned concordantly 0 times; of these: 816194 (31.96%) aligned discordantly 1 time ---- 1737382 pairs aligned 0 times concordantly or discordantly; of these: 3474764 mates make up the pairs; of these: 2553004 (73.47%) aligned 0 times 684653 (19.70%) aligned exactly 1 time 237107 (6.82%) aligned >1 times 93.65% overall alignment rate Time searching: 00:23:52 Overall time: 00:23:52 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 16 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] 1086653 / 18267682 = 0.0595 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, 03 May 2018 23:38:52: # Command line: callpeak -t SRX2741970.bam -f BAM -g 12100000 -n SRX2741970.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2741970.10 # format = BAM # ChIP-seq file = ['SRX2741970.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, 03 May 2018 23:38:52: # Command line: callpeak -t SRX2741970.bam -f BAM -g 12100000 -n SRX2741970.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2741970.05 # format = BAM # ChIP-seq file = ['SRX2741970.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, 03 May 2018 23:38:52: # Command line: callpeak -t SRX2741970.bam -f BAM -g 12100000 -n SRX2741970.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2741970.20 # format = BAM # ChIP-seq file = ['SRX2741970.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, 03 May 2018 23:38:52: #1 read tag files... INFO @ Thu, 03 May 2018 23:38:52: #1 read tag files... INFO @ Thu, 03 May 2018 23:38:52: #1 read tag files... INFO @ Thu, 03 May 2018 23:38:52: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:38:52: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:38:52: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:39:01: 1000000 INFO @ Thu, 03 May 2018 23:39:01: 1000000 INFO @ Thu, 03 May 2018 23:39:01: 1000000 INFO @ Thu, 03 May 2018 23:39:09: 2000000 INFO @ Thu, 03 May 2018 23:39:09: 2000000 INFO @ Thu, 03 May 2018 23:39:09: 2000000 INFO @ Thu, 03 May 2018 23:39:17: 3000000 INFO @ Thu, 03 May 2018 23:39:17: 3000000 INFO @ Thu, 03 May 2018 23:39:18: 3000000 INFO @ Thu, 03 May 2018 23:39:26: 4000000 INFO @ Thu, 03 May 2018 23:39:26: 4000000 INFO @ Thu, 03 May 2018 23:39:27: 4000000 INFO @ Thu, 03 May 2018 23:39:34: 5000000 INFO @ Thu, 03 May 2018 23:39:34: 5000000 INFO @ Thu, 03 May 2018 23:39:35: 5000000 INFO @ Thu, 03 May 2018 23:39:42: 6000000 INFO @ Thu, 03 May 2018 23:39:42: 6000000 INFO @ Thu, 03 May 2018 23:39:43: 6000000 INFO @ Thu, 03 May 2018 23:39:51: 7000000 INFO @ Thu, 03 May 2018 23:39:51: 7000000 INFO @ Thu, 03 May 2018 23:39:52: 7000000 INFO @ Thu, 03 May 2018 23:39:59: 8000000 INFO @ Thu, 03 May 2018 23:39:59: 8000000 INFO @ Thu, 03 May 2018 23:40:00: 8000000 INFO @ Thu, 03 May 2018 23:40:08: 9000000 INFO @ Thu, 03 May 2018 23:40:08: 9000000 INFO @ Thu, 03 May 2018 23:40:09: 9000000 INFO @ Thu, 03 May 2018 23:40:16: 10000000 INFO @ Thu, 03 May 2018 23:40:17: 10000000 INFO @ Thu, 03 May 2018 23:40:18: 10000000 INFO @ Thu, 03 May 2018 23:40:23: 11000000 INFO @ Thu, 03 May 2018 23:40:26: 11000000 INFO @ Thu, 03 May 2018 23:40:26: 11000000 INFO @ Thu, 03 May 2018 23:40:31: 12000000 INFO @ Thu, 03 May 2018 23:40:34: 12000000 INFO @ Thu, 03 May 2018 23:40:35: 12000000 INFO @ Thu, 03 May 2018 23:40:40: 13000000 INFO @ Thu, 03 May 2018 23:40:43: 13000000 INFO @ Thu, 03 May 2018 23:40:44: 13000000 INFO @ Thu, 03 May 2018 23:40:48: 14000000 INFO @ Thu, 03 May 2018 23:40:52: 14000000 INFO @ Thu, 03 May 2018 23:40:53: 14000000 INFO @ Thu, 03 May 2018 23:40:56: 15000000 INFO @ Thu, 03 May 2018 23:41:01: 15000000 INFO @ Thu, 03 May 2018 23:41:02: 15000000 INFO @ Thu, 03 May 2018 23:41:04: 16000000 INFO @ Thu, 03 May 2018 23:41:10: 16000000 INFO @ Thu, 03 May 2018 23:41:10: 16000000 INFO @ Thu, 03 May 2018 23:41:12: 17000000 INFO @ Thu, 03 May 2018 23:41:19: 17000000 INFO @ Thu, 03 May 2018 23:41:19: 17000000 INFO @ Thu, 03 May 2018 23:41:21: 18000000 INFO @ Thu, 03 May 2018 23:41:28: 18000000 INFO @ Thu, 03 May 2018 23:41:28: 18000000 INFO @ Thu, 03 May 2018 23:41:29: 19000000 INFO @ Thu, 03 May 2018 23:41:36: 19000000 INFO @ Thu, 03 May 2018 23:41:37: 19000000 INFO @ Thu, 03 May 2018 23:41:38: 20000000 INFO @ Thu, 03 May 2018 23:41:44: 20000000 INFO @ Thu, 03 May 2018 23:41:46: 20000000 INFO @ Thu, 03 May 2018 23:41:47: 21000000 INFO @ Thu, 03 May 2018 23:41:53: 21000000 INFO @ Thu, 03 May 2018 23:41:54: 21000000 INFO @ Thu, 03 May 2018 23:41:56: 22000000 INFO @ Thu, 03 May 2018 23:42:01: 22000000 INFO @ Thu, 03 May 2018 23:42:03: 22000000 INFO @ Thu, 03 May 2018 23:42:04: 23000000 INFO @ Thu, 03 May 2018 23:42:10: 23000000 INFO @ Thu, 03 May 2018 23:42:12: 23000000 INFO @ Thu, 03 May 2018 23:42:13: 24000000 INFO @ Thu, 03 May 2018 23:42:18: 24000000 INFO @ Thu, 03 May 2018 23:42:21: 24000000 INFO @ Thu, 03 May 2018 23:42:22: 25000000 INFO @ Thu, 03 May 2018 23:42:26: 25000000 INFO @ Thu, 03 May 2018 23:42:30: 25000000 INFO @ Thu, 03 May 2018 23:42:31: 26000000 INFO @ Thu, 03 May 2018 23:42:35: 26000000 INFO @ Thu, 03 May 2018 23:42:39: 26000000 INFO @ Thu, 03 May 2018 23:42:40: 27000000 INFO @ Thu, 03 May 2018 23:42:43: 27000000 INFO @ Thu, 03 May 2018 23:42:48: 27000000 INFO @ Thu, 03 May 2018 23:42:49: 28000000 INFO @ Thu, 03 May 2018 23:42:52: 28000000 INFO @ Thu, 03 May 2018 23:42:57: 28000000 INFO @ Thu, 03 May 2018 23:42:57: 29000000 INFO @ Thu, 03 May 2018 23:43:00: 29000000 INFO @ Thu, 03 May 2018 23:43:05: 29000000 INFO @ Thu, 03 May 2018 23:43:06: 30000000 INFO @ Thu, 03 May 2018 23:43:08: 30000000 INFO @ Thu, 03 May 2018 23:43:14: 30000000 INFO @ Thu, 03 May 2018 23:43:15: 31000000 INFO @ Thu, 03 May 2018 23:43:17: 31000000 INFO @ Thu, 03 May 2018 23:43:23: 31000000 INFO @ Thu, 03 May 2018 23:43:23: 32000000 INFO @ Thu, 03 May 2018 23:43:25: 32000000 INFO @ Thu, 03 May 2018 23:43:32: 32000000 INFO @ Thu, 03 May 2018 23:43:32: 33000000 INFO @ Thu, 03 May 2018 23:43:33: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 03 May 2018 23:43:41: 33000000 INFO @ Thu, 03 May 2018 23:43:41: 34000000 INFO @ Thu, 03 May 2018 23:43:42: 34000000 INFO @ Thu, 03 May 2018 23:43:49: 34000000 INFO @ Thu, 03 May 2018 23:43:49: 35000000 INFO @ Thu, 03 May 2018 23:43:50: 35000000 INFO @ Thu, 03 May 2018 23:43:53: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:43:53: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:43:53: #1 total tags in treatment: 16485477 INFO @ Thu, 03 May 2018 23:43:53: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:43:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:43:54: #1 tags after filtering in treatment: 10702250 INFO @ Thu, 03 May 2018 23:43:54: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 03 May 2018 23:43:54: #1 finished! INFO @ Thu, 03 May 2018 23:43:54: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:43:54: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:43:54: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:43:54: #1 total tags in treatment: 16485477 INFO @ Thu, 03 May 2018 23:43:54: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:43:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:43:55: #1 tags after filtering in treatment: 10702250 INFO @ Thu, 03 May 2018 23:43:55: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 03 May 2018 23:43:55: #1 finished! INFO @ Thu, 03 May 2018 23:43:55: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:43:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:43:55: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:43:55: 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, 03 May 2018 23:43:55: Process for pairing-model is terminated! cat: SRX2741970.05_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 `SRX2741970.05_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 `SRX2741970.05_*.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 `SRX2741970.05_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 @ Thu, 03 May 2018 23:43:55: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:43:55: 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, 03 May 2018 23:43:55: Process for pairing-model is terminated! cat: SRX2741970.10_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 `SRX2741970.10_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 `SRX2741970.10_*.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 `SRX2741970.10_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, 03 May 2018 23:43:58: 35000000 INFO @ Thu, 03 May 2018 23:44:01: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:44:01: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:44:01: #1 total tags in treatment: 16485477 INFO @ Thu, 03 May 2018 23:44:01: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:44:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Thu, 03 May 2018 23:44:02: #1 tags after filtering in treatment: 10702250 INFO @ Thu, 03 May 2018 23:44:02: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 03 May 2018 23:44:02: #1 finished! INFO @ Thu, 03 May 2018 23:44:02: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:44:02: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:44:02: 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, 03 May 2018 23:44:02: Process for pairing-model is terminated! cat: SRX2741970.20_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 `SRX2741970.20_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 `SRX2741970.20_*.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 `SRX2741970.20_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