Job ID = 10536501 sra ファイルのダウンロード中... Completed: 1449823K bytes transferred in 44 seconds (265201K 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 40388974 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671196/SRR6696948.sra Written 40388974 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: 00:28:20 40388974 reads; of these: 40388974 (100.00%) were paired; of these: 5000415 (12.38%) aligned concordantly 0 times 31394659 (77.73%) aligned concordantly exactly 1 time 3993900 (9.89%) aligned concordantly >1 times ---- 5000415 pairs aligned concordantly 0 times; of these: 119930 (2.40%) aligned discordantly 1 time ---- 4880485 pairs aligned 0 times concordantly or discordantly; of these: 9760970 mates make up the pairs; of these: 9552472 (97.86%) aligned 0 times 142866 (1.46%) aligned exactly 1 time 65632 (0.67%) aligned >1 times 88.17% overall alignment rate Time searching: 00:28:20 Overall time: 00:28:20 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] 14187315 / 35460752 = 0.4001 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 10:36:37: # Command line: callpeak -t SRX3671196.bam -f BAM -g 12100000 -n SRX3671196.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671196.20 # format = BAM # ChIP-seq file = ['SRX3671196.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 10:36:37: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:36:37: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:36:37: # Command line: callpeak -t SRX3671196.bam -f BAM -g 12100000 -n SRX3671196.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671196.10 # format = BAM # ChIP-seq file = ['SRX3671196.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 10:36:37: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:36:37: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:36:37: # Command line: callpeak -t SRX3671196.bam -f BAM -g 12100000 -n SRX3671196.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671196.05 # format = BAM # ChIP-seq file = ['SRX3671196.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 10:36:37: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:36:37: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:36:43: 1000000 INFO @ Thu, 05 Apr 2018 10:36:43: 1000000 INFO @ Thu, 05 Apr 2018 10:36:43: 1000000 INFO @ Thu, 05 Apr 2018 10:36:49: 2000000 INFO @ Thu, 05 Apr 2018 10:36:49: 2000000 INFO @ Thu, 05 Apr 2018 10:36:49: 2000000 INFO @ Thu, 05 Apr 2018 10:36:55: 3000000 INFO @ Thu, 05 Apr 2018 10:36:55: 3000000 INFO @ Thu, 05 Apr 2018 10:36:56: 3000000 INFO @ Thu, 05 Apr 2018 10:37:00: 4000000 INFO @ Thu, 05 Apr 2018 10:37:01: 4000000 INFO @ Thu, 05 Apr 2018 10:37:01: 4000000 INFO @ Thu, 05 Apr 2018 10:37:06: 5000000 INFO @ Thu, 05 Apr 2018 10:37:07: 5000000 INFO @ Thu, 05 Apr 2018 10:37:07: 5000000 INFO @ Thu, 05 Apr 2018 10:37:12: 6000000 INFO @ Thu, 05 Apr 2018 10:37:13: 6000000 INFO @ Thu, 05 Apr 2018 10:37:13: 6000000 INFO @ Thu, 05 Apr 2018 10:37:18: 7000000 INFO @ Thu, 05 Apr 2018 10:37:18: 7000000 INFO @ Thu, 05 Apr 2018 10:37:19: 7000000 INFO @ Thu, 05 Apr 2018 10:37:24: 8000000 INFO @ Thu, 05 Apr 2018 10:37:24: 8000000 INFO @ Thu, 05 Apr 2018 10:37:25: 8000000 INFO @ Thu, 05 Apr 2018 10:37:29: 9000000 INFO @ Thu, 05 Apr 2018 10:37:30: 9000000 INFO @ Thu, 05 Apr 2018 10:37:31: 9000000 INFO @ Thu, 05 Apr 2018 10:37:35: 10000000 INFO @ Thu, 05 Apr 2018 10:37:35: 10000000 INFO @ Thu, 05 Apr 2018 10:37:37: 10000000 INFO @ Thu, 05 Apr 2018 10:37:41: 11000000 INFO @ Thu, 05 Apr 2018 10:37:41: 11000000 INFO @ Thu, 05 Apr 2018 10:37:43: 11000000 INFO @ Thu, 05 Apr 2018 10:37:47: 12000000 INFO @ Thu, 05 Apr 2018 10:37:47: 12000000 INFO @ Thu, 05 Apr 2018 10:37:49: 12000000 INFO @ Thu, 05 Apr 2018 10:37:52: 13000000 INFO @ Thu, 05 Apr 2018 10:37:53: 13000000 INFO @ Thu, 05 Apr 2018 10:37:55: 13000000 INFO @ Thu, 05 Apr 2018 10:37:58: 14000000 INFO @ Thu, 05 Apr 2018 10:37:59: 14000000 INFO @ Thu, 05 Apr 2018 10:38:01: 14000000 INFO @ Thu, 05 Apr 2018 10:38:03: 15000000 INFO @ Thu, 05 Apr 2018 10:38:05: 15000000 INFO @ Thu, 05 Apr 2018 10:38:07: 15000000 INFO @ Thu, 05 Apr 2018 10:38:09: 16000000 INFO @ Thu, 05 Apr 2018 10:38:10: 16000000 INFO @ Thu, 05 Apr 2018 10:38:13: 16000000 INFO @ Thu, 05 Apr 2018 10:38:14: 17000000 INFO @ Thu, 05 Apr 2018 10:38:16: 17000000 INFO @ Thu, 05 Apr 2018 10:38:19: 17000000 INFO @ Thu, 05 Apr 2018 10:38:20: 18000000 INFO @ Thu, 05 Apr 2018 10:38:22: 18000000 INFO @ Thu, 05 Apr 2018 10:38:25: 18000000 INFO @ Thu, 05 Apr 2018 10:38:25: 19000000 INFO @ Thu, 05 Apr 2018 10:38:28: 19000000 INFO @ Thu, 05 Apr 2018 10:38:31: 20000000 INFO @ Thu, 05 Apr 2018 10:38:31: 19000000 INFO @ Thu, 05 Apr 2018 10:38:33: 20000000 INFO @ Thu, 05 Apr 2018 10:38:36: 21000000 INFO @ Thu, 05 Apr 2018 10:38:37: 20000000 INFO @ Thu, 05 Apr 2018 10:38:39: 21000000 INFO @ Thu, 05 Apr 2018 10:38:42: 22000000 INFO @ Thu, 05 Apr 2018 10:38:43: 21000000 INFO @ Thu, 05 Apr 2018 10:38:45: 22000000 INFO @ Thu, 05 Apr 2018 10:38:47: 23000000 INFO @ Thu, 05 Apr 2018 10:38:49: 22000000 INFO @ Thu, 05 Apr 2018 10:38:51: 23000000 INFO @ Thu, 05 Apr 2018 10:38:53: 24000000 INFO @ Thu, 05 Apr 2018 10:38:55: 23000000 INFO @ Thu, 05 Apr 2018 10:38:56: 24000000 INFO @ Thu, 05 Apr 2018 10:38:58: 25000000 INFO @ Thu, 05 Apr 2018 10:39:01: 24000000 INFO @ Thu, 05 Apr 2018 10:39:02: 25000000 INFO @ Thu, 05 Apr 2018 10:39:04: 26000000 INFO @ Thu, 05 Apr 2018 10:39:07: 25000000 INFO @ Thu, 05 Apr 2018 10:39:08: 26000000 INFO @ Thu, 05 Apr 2018 10:39:09: 27000000 INFO @ Thu, 05 Apr 2018 10:39:13: 26000000 INFO @ Thu, 05 Apr 2018 10:39:14: 27000000 INFO @ Thu, 05 Apr 2018 10:39:15: 28000000 INFO @ Thu, 05 Apr 2018 10:39:19: 27000000 INFO @ Thu, 05 Apr 2018 10:39:19: 28000000 INFO @ Thu, 05 Apr 2018 10:39:20: 29000000 INFO @ Thu, 05 Apr 2018 10:39:24: 28000000 INFO @ Thu, 05 Apr 2018 10:39:25: 29000000 INFO @ Thu, 05 Apr 2018 10:39:26: 30000000 INFO @ Thu, 05 Apr 2018 10:39:30: 29000000 INFO @ Thu, 05 Apr 2018 10:39:31: 30000000 INFO @ Thu, 05 Apr 2018 10:39:31: 31000000 INFO @ Thu, 05 Apr 2018 10:39:36: 30000000 INFO @ Thu, 05 Apr 2018 10:39:37: 31000000 INFO @ Thu, 05 Apr 2018 10:39:37: 32000000 INFO @ Thu, 05 Apr 2018 10:39:42: 33000000 INFO @ Thu, 05 Apr 2018 10:39:42: 31000000 INFO @ Thu, 05 Apr 2018 10:39:42: 32000000 INFO @ Thu, 05 Apr 2018 10:39:48: 34000000 INFO @ Thu, 05 Apr 2018 10:39:48: 33000000 INFO @ Thu, 05 Apr 2018 10:39:48: 32000000 INFO @ Thu, 05 Apr 2018 10:39:53: 35000000 INFO @ Thu, 05 Apr 2018 10:39:54: 34000000 INFO @ Thu, 05 Apr 2018 10:39:54: 33000000 INFO @ Thu, 05 Apr 2018 10:39:59: 36000000 INFO @ Thu, 05 Apr 2018 10:40:00: 35000000 INFO @ Thu, 05 Apr 2018 10:40:00: 34000000 INFO @ Thu, 05 Apr 2018 10:40:04: 37000000 INFO @ Thu, 05 Apr 2018 10:40:05: 36000000 INFO @ Thu, 05 Apr 2018 10:40:06: 35000000 INFO @ Thu, 05 Apr 2018 10:40:10: 38000000 INFO @ Thu, 05 Apr 2018 10:40:11: 37000000 INFO @ Thu, 05 Apr 2018 10:40:12: 36000000 INFO @ Thu, 05 Apr 2018 10:40:15: 39000000 INFO @ Thu, 05 Apr 2018 10:40:17: 38000000 INFO @ Thu, 05 Apr 2018 10:40:18: 37000000 INFO @ Thu, 05 Apr 2018 10:40:21: 40000000 INFO @ Thu, 05 Apr 2018 10:40:23: 39000000 INFO @ Thu, 05 Apr 2018 10:40:24: 38000000 INFO @ Thu, 05 Apr 2018 10:40:26: 41000000 INFO @ Thu, 05 Apr 2018 10:40:29: 40000000 INFO @ Thu, 05 Apr 2018 10:40:30: 39000000 INFO @ Thu, 05 Apr 2018 10:40:32: 42000000 INFO @ Thu, 05 Apr 2018 10:40:35: 41000000 INFO @ Thu, 05 Apr 2018 10:40:36: 40000000 INFO @ Thu, 05 Apr 2018 10:40:37: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:40:37: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:40:37: #1 total tags in treatment: 21235256 INFO @ Thu, 05 Apr 2018 10:40:37: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:40:37: #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 10:40:37: #1 tags after filtering in treatment: 7426467 INFO @ Thu, 05 Apr 2018 10:40:37: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:40:37: #1 finished! INFO @ Thu, 05 Apr 2018 10:40:37: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:40:38: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:40:38: 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 10:40:38: Process for pairing-model is terminated! cat: SRX3671196.05_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 `SRX3671196.05_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 `SRX3671196.05_*.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 `SRX3671196.05_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 10:40:40: 42000000 INFO @ Thu, 05 Apr 2018 10:40:42: 41000000 INFO @ Thu, 05 Apr 2018 10:40:45: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:40:45: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:40:45: #1 total tags in treatment: 21235256 INFO @ Thu, 05 Apr 2018 10:40:45: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:40:45: #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 10:40:46: #1 tags after filtering in treatment: 7426467 INFO @ Thu, 05 Apr 2018 10:40:46: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:40:46: #1 finished! INFO @ Thu, 05 Apr 2018 10:40:46: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:40:46: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:40:46: 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 10:40:46: Process for pairing-model is terminated! cat: SRX3671196.10_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 `SRX3671196.10_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 `SRX3671196.10_*.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 `SRX3671196.10_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 10:40:47: 42000000 INFO @ Thu, 05 Apr 2018 10:40:52: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:40:52: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:40:52: #1 total tags in treatment: 21235256 INFO @ Thu, 05 Apr 2018 10:40:52: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:40:52: #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 10:40:53: #1 tags after filtering in treatment: 7426467 INFO @ Thu, 05 Apr 2018 10:40:53: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:40:53: #1 finished! INFO @ Thu, 05 Apr 2018 10:40:53: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:40:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:40:53: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:40:53: 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 10:40:53: Process for pairing-model is terminated! cat: SRX3671196.20_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 `SRX3671196.20_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 `SRX3671196.20_*.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 `SRX3671196.20_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。