Job ID = 10608974 sra ファイルのダウンロード中... Completed: 2135239K bytes transferred in 207 seconds (84476K 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 16876343 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2741981/SRR5453815.sra Written 16876343 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: 00:20:36 16876343 reads; of these: 16876343 (100.00%) were paired; of these: 1065504 (6.31%) aligned concordantly 0 times 14361274 (85.10%) aligned concordantly exactly 1 time 1449565 (8.59%) aligned concordantly >1 times ---- 1065504 pairs aligned concordantly 0 times; of these: 432453 (40.59%) aligned discordantly 1 time ---- 633051 pairs aligned 0 times concordantly or discordantly; of these: 1266102 mates make up the pairs; of these: 790226 (62.41%) aligned 0 times 352332 (27.83%) aligned exactly 1 time 123544 (9.76%) aligned >1 times 97.66% overall alignment rate Time searching: 00:20:36 Overall time: 00:20:36 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] 357391 / 16226659 = 0.0220 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 23:32:07: # Command line: callpeak -t SRX2741981.bam -f BAM -g 12100000 -n SRX2741981.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2741981.10 # format = BAM # ChIP-seq file = ['SRX2741981.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 23:32:07: #1 read tag files... INFO @ Thu, 03 May 2018 23:32:07: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:32:07: # Command line: callpeak -t SRX2741981.bam -f BAM -g 12100000 -n SRX2741981.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2741981.05 # format = BAM # ChIP-seq file = ['SRX2741981.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 23:32:07: #1 read tag files... INFO @ Thu, 03 May 2018 23:32:07: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:32:07: # Command line: callpeak -t SRX2741981.bam -f BAM -g 12100000 -n SRX2741981.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2741981.20 # format = BAM # ChIP-seq file = ['SRX2741981.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 23:32:07: #1 read tag files... INFO @ Thu, 03 May 2018 23:32:07: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:32:14: 1000000 INFO @ Thu, 03 May 2018 23:32:14: 1000000 INFO @ Thu, 03 May 2018 23:32:14: 1000000 INFO @ Thu, 03 May 2018 23:32:21: 2000000 INFO @ Thu, 03 May 2018 23:32:21: 2000000 INFO @ Thu, 03 May 2018 23:32:21: 2000000 INFO @ Thu, 03 May 2018 23:32:28: 3000000 INFO @ Thu, 03 May 2018 23:32:28: 3000000 INFO @ Thu, 03 May 2018 23:32:29: 3000000 INFO @ Thu, 03 May 2018 23:32:35: 4000000 INFO @ Thu, 03 May 2018 23:32:36: 4000000 INFO @ Thu, 03 May 2018 23:32:36: 4000000 INFO @ Thu, 03 May 2018 23:32:42: 5000000 INFO @ Thu, 03 May 2018 23:32:43: 5000000 INFO @ Thu, 03 May 2018 23:32:43: 5000000 INFO @ Thu, 03 May 2018 23:32:49: 6000000 INFO @ Thu, 03 May 2018 23:32:50: 6000000 INFO @ Thu, 03 May 2018 23:32:50: 6000000 INFO @ Thu, 03 May 2018 23:32:56: 7000000 INFO @ Thu, 03 May 2018 23:32:57: 7000000 INFO @ Thu, 03 May 2018 23:32:57: 7000000 INFO @ Thu, 03 May 2018 23:33:03: 8000000 INFO @ Thu, 03 May 2018 23:33:04: 8000000 INFO @ Thu, 03 May 2018 23:33:04: 8000000 INFO @ Thu, 03 May 2018 23:33:09: 9000000 INFO @ Thu, 03 May 2018 23:33:11: 9000000 INFO @ Thu, 03 May 2018 23:33:11: 9000000 INFO @ Thu, 03 May 2018 23:33:16: 10000000 INFO @ Thu, 03 May 2018 23:33:18: 10000000 INFO @ Thu, 03 May 2018 23:33:18: 10000000 INFO @ Thu, 03 May 2018 23:33:23: 11000000 INFO @ Thu, 03 May 2018 23:33:25: 11000000 INFO @ Thu, 03 May 2018 23:33:25: 11000000 INFO @ Thu, 03 May 2018 23:33:30: 12000000 INFO @ Thu, 03 May 2018 23:33:32: 12000000 INFO @ Thu, 03 May 2018 23:33:33: 12000000 INFO @ Thu, 03 May 2018 23:33:37: 13000000 INFO @ Thu, 03 May 2018 23:33:39: 13000000 INFO @ Thu, 03 May 2018 23:33:40: 13000000 INFO @ Thu, 03 May 2018 23:33:44: 14000000 INFO @ Thu, 03 May 2018 23:33:47: 14000000 INFO @ Thu, 03 May 2018 23:33:47: 14000000 INFO @ Thu, 03 May 2018 23:33:51: 15000000 INFO @ Thu, 03 May 2018 23:33:54: 15000000 INFO @ Thu, 03 May 2018 23:33:54: 15000000 INFO @ Thu, 03 May 2018 23:33:58: 16000000 INFO @ Thu, 03 May 2018 23:34:02: 16000000 INFO @ Thu, 03 May 2018 23:34:02: 16000000 INFO @ Thu, 03 May 2018 23:34:05: 17000000 INFO @ Thu, 03 May 2018 23:34:09: 17000000 INFO @ Thu, 03 May 2018 23:34:09: 17000000 INFO @ Thu, 03 May 2018 23:34:12: 18000000 INFO @ Thu, 03 May 2018 23:34:16: 18000000 INFO @ Thu, 03 May 2018 23:34:17: 18000000 INFO @ Thu, 03 May 2018 23:34:19: 19000000 INFO @ Thu, 03 May 2018 23:34:24: 19000000 INFO @ Thu, 03 May 2018 23:34:24: 19000000 INFO @ Thu, 03 May 2018 23:34:26: 20000000 INFO @ Thu, 03 May 2018 23:34:31: 20000000 INFO @ Thu, 03 May 2018 23:34:32: 20000000 INFO @ Thu, 03 May 2018 23:34:32: 21000000 INFO @ Thu, 03 May 2018 23:34:39: 21000000 INFO @ Thu, 03 May 2018 23:34:39: 21000000 INFO @ Thu, 03 May 2018 23:34:39: 22000000 INFO @ Thu, 03 May 2018 23:34:46: 22000000 INFO @ Thu, 03 May 2018 23:34:46: 23000000 INFO @ Thu, 03 May 2018 23:34:46: 22000000 INFO @ Thu, 03 May 2018 23:34:53: 24000000 INFO @ Thu, 03 May 2018 23:34:53: 23000000 INFO @ Thu, 03 May 2018 23:34:53: 23000000 INFO @ Thu, 03 May 2018 23:35:00: 25000000 INFO @ Thu, 03 May 2018 23:35:00: 24000000 INFO @ Thu, 03 May 2018 23:35:01: 24000000 INFO @ Thu, 03 May 2018 23:35:06: 26000000 INFO @ Thu, 03 May 2018 23:35:08: 25000000 INFO @ Thu, 03 May 2018 23:35:08: 25000000 INFO @ Thu, 03 May 2018 23:35:13: 27000000 INFO @ Thu, 03 May 2018 23:35:15: 26000000 INFO @ Thu, 03 May 2018 23:35:15: 26000000 INFO @ Thu, 03 May 2018 23:35:20: 28000000 INFO @ Thu, 03 May 2018 23:35:22: 27000000 INFO @ Thu, 03 May 2018 23:35:22: 27000000 INFO @ Thu, 03 May 2018 23:35:27: 29000000 INFO @ Thu, 03 May 2018 23:35:29: 28000000 INFO @ Thu, 03 May 2018 23:35:29: 28000000 INFO @ Thu, 03 May 2018 23:35:33: 30000000 INFO @ Thu, 03 May 2018 23:35:36: 29000000 INFO @ Thu, 03 May 2018 23:35:36: 29000000 INFO @ Thu, 03 May 2018 23:35:41: 31000000 INFO @ Thu, 03 May 2018 23:35:43: 30000000 INFO @ Thu, 03 May 2018 23:35:44: 30000000 INFO @ Thu, 03 May 2018 23:35:48: 32000000 INFO @ Thu, 03 May 2018 23:35:50: 31000000 INFO @ Thu, 03 May 2018 23:35:50: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:35:50: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:35:50: #1 total tags in treatment: 15456554 INFO @ Thu, 03 May 2018 23:35:50: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:35:50: #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 23:35:51: #1 tags after filtering in treatment: 10489651 INFO @ Thu, 03 May 2018 23:35:51: #1 Redundant rate of treatment: 0.32 INFO @ Thu, 03 May 2018 23:35:51: #1 finished! INFO @ Thu, 03 May 2018 23:35:51: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:35:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:35:51: 31000000 INFO @ Thu, 03 May 2018 23:35:52: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:35:52: 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 23:35:52: Process for pairing-model is terminated! cat: SRX2741981.05_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 `SRX2741981.05_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 `SRX2741981.05_*.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 `SRX2741981.05_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 23:35:57: 32000000 INFO @ Thu, 03 May 2018 23:35:58: 32000000 INFO @ Thu, 03 May 2018 23:35:59: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:35:59: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:35:59: #1 total tags in treatment: 15456554 INFO @ Thu, 03 May 2018 23:35:59: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:35:59: #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 23:35:59: #1 tags after filtering in treatment: 10489651 INFO @ Thu, 03 May 2018 23:35:59: #1 Redundant rate of treatment: 0.32 INFO @ Thu, 03 May 2018 23:35:59: #1 finished! INFO @ Thu, 03 May 2018 23:35:59: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:35:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:36:00: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:36:00: 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 23:36:00: Process for pairing-model is terminated! cat: SRX2741981.10_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 `SRX2741981.10_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 `SRX2741981.10_*.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 `SRX2741981.10_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 23:36:00: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:36:00: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:36:00: #1 total tags in treatment: 15456554 INFO @ Thu, 03 May 2018 23:36:00: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:36:00: #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 23:36:00: #1 tags after filtering in treatment: 10489651 INFO @ Thu, 03 May 2018 23:36:00: #1 Redundant rate of treatment: 0.32 INFO @ Thu, 03 May 2018 23:36:00: #1 finished! INFO @ Thu, 03 May 2018 23:36:00: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:36:01: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:36:01: 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 23:36:01: Process for pairing-model is terminated! cat: SRX2741981.20_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 `SRX2741981.20_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 `SRX2741981.20_*.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 `SRX2741981.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。