Job ID = 10536509 sra ファイルのダウンロード中... Completed: 1225999K bytes transferred in 27 seconds (371715K 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 34224269 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671203/SRR6696955.sra Written 34224269 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: 00:25:43 34224269 reads; of these: 34224269 (100.00%) were paired; of these: 3858427 (11.27%) aligned concordantly 0 times 26573510 (77.65%) aligned concordantly exactly 1 time 3792332 (11.08%) aligned concordantly >1 times ---- 3858427 pairs aligned concordantly 0 times; of these: 137430 (3.56%) aligned discordantly 1 time ---- 3720997 pairs aligned 0 times concordantly or discordantly; of these: 7441994 mates make up the pairs; of these: 7241038 (97.30%) aligned 0 times 121858 (1.64%) aligned exactly 1 time 79098 (1.06%) aligned >1 times 89.42% overall alignment rate Time searching: 00:25:43 Overall time: 00:25:43 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 28 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] 10349424 / 30455698 = 0.3398 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 10:35:10: # Command line: callpeak -t SRX3671203.bam -f BAM -g 12100000 -n SRX3671203.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671203.20 # format = BAM # ChIP-seq file = ['SRX3671203.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 10:35:10: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:35:10: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:35:10: # Command line: callpeak -t SRX3671203.bam -f BAM -g 12100000 -n SRX3671203.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671203.10 # format = BAM # ChIP-seq file = ['SRX3671203.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 10:35:10: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:35:10: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:35:10: # Command line: callpeak -t SRX3671203.bam -f BAM -g 12100000 -n SRX3671203.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671203.05 # format = BAM # ChIP-seq file = ['SRX3671203.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 10:35:10: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:35:10: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:35:17: 1000000 INFO @ Thu, 05 Apr 2018 10:35:18: 1000000 INFO @ Thu, 05 Apr 2018 10:35:18: 1000000 INFO @ Thu, 05 Apr 2018 10:35:23: 2000000 INFO @ Thu, 05 Apr 2018 10:35:25: 2000000 INFO @ Thu, 05 Apr 2018 10:35:25: 2000000 INFO @ Thu, 05 Apr 2018 10:35:29: 3000000 INFO @ Thu, 05 Apr 2018 10:35:33: 3000000 INFO @ Thu, 05 Apr 2018 10:35:33: 3000000 INFO @ Thu, 05 Apr 2018 10:35:35: 4000000 INFO @ Thu, 05 Apr 2018 10:35:40: 4000000 INFO @ Thu, 05 Apr 2018 10:35:40: 4000000 INFO @ Thu, 05 Apr 2018 10:35:41: 5000000 INFO @ Thu, 05 Apr 2018 10:35:47: 5000000 INFO @ Thu, 05 Apr 2018 10:35:47: 5000000 INFO @ Thu, 05 Apr 2018 10:35:47: 6000000 INFO @ Thu, 05 Apr 2018 10:35:54: 7000000 INFO @ Thu, 05 Apr 2018 10:35:55: 6000000 INFO @ Thu, 05 Apr 2018 10:35:55: 6000000 INFO @ Thu, 05 Apr 2018 10:36:00: 8000000 INFO @ Thu, 05 Apr 2018 10:36:02: 7000000 INFO @ Thu, 05 Apr 2018 10:36:02: 7000000 INFO @ Thu, 05 Apr 2018 10:36:06: 9000000 INFO @ Thu, 05 Apr 2018 10:36:09: 8000000 INFO @ Thu, 05 Apr 2018 10:36:09: 8000000 INFO @ Thu, 05 Apr 2018 10:36:12: 10000000 INFO @ Thu, 05 Apr 2018 10:36:17: 9000000 INFO @ Thu, 05 Apr 2018 10:36:17: 9000000 INFO @ Thu, 05 Apr 2018 10:36:18: 11000000 INFO @ Thu, 05 Apr 2018 10:36:24: 10000000 INFO @ Thu, 05 Apr 2018 10:36:24: 10000000 INFO @ Thu, 05 Apr 2018 10:36:24: 12000000 INFO @ Thu, 05 Apr 2018 10:36:31: 13000000 INFO @ Thu, 05 Apr 2018 10:36:32: 11000000 INFO @ Thu, 05 Apr 2018 10:36:32: 11000000 INFO @ Thu, 05 Apr 2018 10:36:37: 14000000 INFO @ Thu, 05 Apr 2018 10:36:39: 12000000 INFO @ Thu, 05 Apr 2018 10:36:39: 12000000 INFO @ Thu, 05 Apr 2018 10:36:43: 15000000 INFO @ Thu, 05 Apr 2018 10:36:46: 13000000 INFO @ Thu, 05 Apr 2018 10:36:46: 13000000 INFO @ Thu, 05 Apr 2018 10:36:49: 16000000 INFO @ Thu, 05 Apr 2018 10:36:53: 14000000 INFO @ Thu, 05 Apr 2018 10:36:53: 14000000 INFO @ Thu, 05 Apr 2018 10:36:55: 17000000 INFO @ Thu, 05 Apr 2018 10:37:01: 15000000 INFO @ Thu, 05 Apr 2018 10:37:01: 15000000 INFO @ Thu, 05 Apr 2018 10:37:01: 18000000 INFO @ Thu, 05 Apr 2018 10:37:07: 19000000 INFO @ Thu, 05 Apr 2018 10:37:08: 16000000 INFO @ Thu, 05 Apr 2018 10:37:08: 16000000 INFO @ Thu, 05 Apr 2018 10:37:13: 20000000 INFO @ Thu, 05 Apr 2018 10:37:15: 17000000 INFO @ Thu, 05 Apr 2018 10:37:15: 17000000 INFO @ Thu, 05 Apr 2018 10:37:20: 21000000 INFO @ Thu, 05 Apr 2018 10:37:23: 18000000 INFO @ Thu, 05 Apr 2018 10:37:23: 18000000 INFO @ Thu, 05 Apr 2018 10:37:27: 22000000 INFO @ Thu, 05 Apr 2018 10:37:29: 19000000 INFO @ Thu, 05 Apr 2018 10:37:30: 19000000 INFO @ Thu, 05 Apr 2018 10:37:34: 23000000 INFO @ Thu, 05 Apr 2018 10:37:36: 20000000 INFO @ Thu, 05 Apr 2018 10:37:37: 20000000 INFO @ Thu, 05 Apr 2018 10:37:41: 24000000 INFO @ Thu, 05 Apr 2018 10:37:43: 21000000 INFO @ Thu, 05 Apr 2018 10:37:44: 21000000 INFO @ Thu, 05 Apr 2018 10:37:48: 25000000 INFO @ Thu, 05 Apr 2018 10:37:50: 22000000 INFO @ Thu, 05 Apr 2018 10:37:51: 22000000 INFO @ Thu, 05 Apr 2018 10:37:55: 26000000 INFO @ Thu, 05 Apr 2018 10:37:57: 23000000 INFO @ Thu, 05 Apr 2018 10:37:58: 23000000 INFO @ Thu, 05 Apr 2018 10:38:03: 27000000 INFO @ Thu, 05 Apr 2018 10:38:04: 24000000 INFO @ Thu, 05 Apr 2018 10:38:05: 24000000 INFO @ Thu, 05 Apr 2018 10:38:10: 28000000 INFO @ Thu, 05 Apr 2018 10:38:11: 25000000 INFO @ Thu, 05 Apr 2018 10:38:13: 25000000 INFO @ Thu, 05 Apr 2018 10:38:17: 29000000 INFO @ Thu, 05 Apr 2018 10:38:18: 26000000 INFO @ Thu, 05 Apr 2018 10:38:20: 26000000 INFO @ Thu, 05 Apr 2018 10:38:24: 30000000 INFO @ Thu, 05 Apr 2018 10:38:24: 27000000 INFO @ Thu, 05 Apr 2018 10:38:27: 27000000 INFO @ Thu, 05 Apr 2018 10:38:31: 28000000 INFO @ Thu, 05 Apr 2018 10:38:31: 31000000 INFO @ Thu, 05 Apr 2018 10:38:34: 28000000 INFO @ Thu, 05 Apr 2018 10:38:38: 29000000 INFO @ Thu, 05 Apr 2018 10:38:39: 32000000 INFO @ Thu, 05 Apr 2018 10:38:41: 29000000 INFO @ Thu, 05 Apr 2018 10:38:45: 30000000 INFO @ Thu, 05 Apr 2018 10:38:46: 33000000 INFO @ Thu, 05 Apr 2018 10:38:48: 30000000 INFO @ Thu, 05 Apr 2018 10:38:52: 31000000 INFO @ Thu, 05 Apr 2018 10:38:53: 34000000 INFO @ Thu, 05 Apr 2018 10:38:56: 31000000 INFO @ Thu, 05 Apr 2018 10:38:59: 32000000 INFO @ Thu, 05 Apr 2018 10:39:00: 35000000 INFO @ Thu, 05 Apr 2018 10:39:03: 32000000 INFO @ Thu, 05 Apr 2018 10:39:06: 33000000 INFO @ Thu, 05 Apr 2018 10:39:07: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 10:39:10: 33000000 INFO @ Thu, 05 Apr 2018 10:39:13: 34000000 INFO @ Thu, 05 Apr 2018 10:39:14: 37000000 INFO @ Thu, 05 Apr 2018 10:39:17: 34000000 INFO @ Thu, 05 Apr 2018 10:39:19: 35000000 INFO @ Thu, 05 Apr 2018 10:39:22: 38000000 INFO @ Thu, 05 Apr 2018 10:39:24: 35000000 INFO @ Thu, 05 Apr 2018 10:39:26: 36000000 BigWig に変換しました。 INFO @ Thu, 05 Apr 2018 10:39:31: 39000000 INFO @ Thu, 05 Apr 2018 10:39:32: 36000000 INFO @ Thu, 05 Apr 2018 10:39:32: 37000000 INFO @ Thu, 05 Apr 2018 10:39:39: 40000000 INFO @ Thu, 05 Apr 2018 10:39:39: 38000000 INFO @ Thu, 05 Apr 2018 10:39:39: 37000000 INFO @ Thu, 05 Apr 2018 10:39:43: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:39:43: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:39:43: #1 total tags in treatment: 20050911 INFO @ Thu, 05 Apr 2018 10:39:43: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:39:43: #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 10:39:44: #1 tags after filtering in treatment: 7055548 INFO @ Thu, 05 Apr 2018 10:39:44: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:39:44: #1 finished! INFO @ Thu, 05 Apr 2018 10:39:44: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:39:44: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:39:44: 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 10:39:44: Process for pairing-model is terminated! cat: SRX3671203.05_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 `SRX3671203.05_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 `SRX3671203.05_*.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 `SRX3671203.05_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, 05 Apr 2018 10:39:45: 39000000 INFO @ Thu, 05 Apr 2018 10:39:47: 38000000 INFO @ Thu, 05 Apr 2018 10:39:52: 40000000 INFO @ Thu, 05 Apr 2018 10:39:54: 39000000 INFO @ Thu, 05 Apr 2018 10:39:55: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:39:55: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:39:55: #1 total tags in treatment: 20050911 INFO @ Thu, 05 Apr 2018 10:39:55: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:39:55: #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 10:39:56: #1 tags after filtering in treatment: 7055548 INFO @ Thu, 05 Apr 2018 10:39:56: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:39:56: #1 finished! INFO @ Thu, 05 Apr 2018 10:39:56: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:39:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:39:56: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:39:56: 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 10:39:56: Process for pairing-model is terminated! cat: SRX3671203.10_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 `SRX3671203.10_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 `SRX3671203.10_*.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 `SRX3671203.10_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 10:40:00: 40000000 INFO @ Thu, 05 Apr 2018 10:40:04: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:40:04: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:40:04: #1 total tags in treatment: 20050911 INFO @ Thu, 05 Apr 2018 10:40:04: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:40:04: #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 10:40:04: #1 tags after filtering in treatment: 7055548 INFO @ Thu, 05 Apr 2018 10:40:04: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:40:04: #1 finished! INFO @ Thu, 05 Apr 2018 10:40:04: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:40:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:40:05: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:40:05: 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 10:40:05: Process for pairing-model is terminated! cat: SRX3671203.20_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 `SRX3671203.20_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 `SRX3671203.20_*.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 `SRX3671203.20_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