Job ID = 10536508 sra ファイルのダウンロード中... Completed: 1297629K bytes transferred in 34 seconds (311395K 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 36382043 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671202/SRR6696954.sra Written 36382043 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: 00:25:48 36382043 reads; of these: 36382043 (100.00%) were paired; of these: 4698436 (12.91%) aligned concordantly 0 times 27890597 (76.66%) aligned concordantly exactly 1 time 3793010 (10.43%) aligned concordantly >1 times ---- 4698436 pairs aligned concordantly 0 times; of these: 161007 (3.43%) aligned discordantly 1 time ---- 4537429 pairs aligned 0 times concordantly or discordantly; of these: 9074858 mates make up the pairs; of these: 8865127 (97.69%) aligned 0 times 124656 (1.37%) aligned exactly 1 time 85075 (0.94%) aligned >1 times 87.82% overall alignment rate Time searching: 00:25:48 Overall time: 00:25:48 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] 11158581 / 31790836 = 0.3510 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 10:34:52: # Command line: callpeak -t SRX3671202.bam -f BAM -g 12100000 -n SRX3671202.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671202.20 # format = BAM # ChIP-seq file = ['SRX3671202.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 10:34:52: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:34:52: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:34:52: # Command line: callpeak -t SRX3671202.bam -f BAM -g 12100000 -n SRX3671202.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671202.10 # format = BAM # ChIP-seq file = ['SRX3671202.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 10:34:52: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:34:52: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:34:52: # Command line: callpeak -t SRX3671202.bam -f BAM -g 12100000 -n SRX3671202.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671202.05 # format = BAM # ChIP-seq file = ['SRX3671202.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 10:34:52: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:34:52: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:34:57: 1000000 INFO @ Thu, 05 Apr 2018 10:34:57: 1000000 INFO @ Thu, 05 Apr 2018 10:34:57: 1000000 INFO @ Thu, 05 Apr 2018 10:35:02: 2000000 INFO @ Thu, 05 Apr 2018 10:35:02: 2000000 INFO @ Thu, 05 Apr 2018 10:35:03: 2000000 INFO @ Thu, 05 Apr 2018 10:35:07: 3000000 INFO @ Thu, 05 Apr 2018 10:35:08: 3000000 INFO @ Thu, 05 Apr 2018 10:35:08: 3000000 INFO @ Thu, 05 Apr 2018 10:35:12: 4000000 INFO @ Thu, 05 Apr 2018 10:35:13: 4000000 INFO @ Thu, 05 Apr 2018 10:35:14: 4000000 INFO @ Thu, 05 Apr 2018 10:35:17: 5000000 INFO @ Thu, 05 Apr 2018 10:35:19: 5000000 INFO @ Thu, 05 Apr 2018 10:35:20: 5000000 INFO @ Thu, 05 Apr 2018 10:35:22: 6000000 INFO @ Thu, 05 Apr 2018 10:35:24: 6000000 INFO @ Thu, 05 Apr 2018 10:35:25: 6000000 INFO @ Thu, 05 Apr 2018 10:35:28: 7000000 INFO @ Thu, 05 Apr 2018 10:35:29: 7000000 INFO @ Thu, 05 Apr 2018 10:35:31: 7000000 INFO @ Thu, 05 Apr 2018 10:35:33: 8000000 INFO @ Thu, 05 Apr 2018 10:35:33: 8000000 INFO @ Thu, 05 Apr 2018 10:35:36: 8000000 INFO @ Thu, 05 Apr 2018 10:35:38: 9000000 INFO @ Thu, 05 Apr 2018 10:35:38: 9000000 INFO @ Thu, 05 Apr 2018 10:35:42: 9000000 INFO @ Thu, 05 Apr 2018 10:35:43: 10000000 INFO @ Thu, 05 Apr 2018 10:35:43: 10000000 INFO @ Thu, 05 Apr 2018 10:35:47: 10000000 INFO @ Thu, 05 Apr 2018 10:35:48: 11000000 INFO @ Thu, 05 Apr 2018 10:35:48: 11000000 INFO @ Thu, 05 Apr 2018 10:35:52: 11000000 INFO @ Thu, 05 Apr 2018 10:35:53: 12000000 INFO @ Thu, 05 Apr 2018 10:35:53: 12000000 INFO @ Thu, 05 Apr 2018 10:35:58: 12000000 INFO @ Thu, 05 Apr 2018 10:35:58: 13000000 INFO @ Thu, 05 Apr 2018 10:35:59: 13000000 INFO @ Thu, 05 Apr 2018 10:36:02: 14000000 INFO @ Thu, 05 Apr 2018 10:36:03: 13000000 INFO @ Thu, 05 Apr 2018 10:36:04: 14000000 INFO @ Thu, 05 Apr 2018 10:36:07: 15000000 INFO @ Thu, 05 Apr 2018 10:36:08: 14000000 INFO @ Thu, 05 Apr 2018 10:36:09: 15000000 INFO @ Thu, 05 Apr 2018 10:36:12: 16000000 INFO @ Thu, 05 Apr 2018 10:36:14: 15000000 INFO @ Thu, 05 Apr 2018 10:36:14: 16000000 INFO @ Thu, 05 Apr 2018 10:36:17: 17000000 INFO @ Thu, 05 Apr 2018 10:36:19: 16000000 INFO @ Thu, 05 Apr 2018 10:36:20: 17000000 INFO @ Thu, 05 Apr 2018 10:36:22: 18000000 INFO @ Thu, 05 Apr 2018 10:36:25: 17000000 INFO @ Thu, 05 Apr 2018 10:36:25: 18000000 INFO @ Thu, 05 Apr 2018 10:36:27: 19000000 INFO @ Thu, 05 Apr 2018 10:36:30: 19000000 INFO @ Thu, 05 Apr 2018 10:36:30: 18000000 INFO @ Thu, 05 Apr 2018 10:36:31: 20000000 INFO @ Thu, 05 Apr 2018 10:36:36: 20000000 INFO @ Thu, 05 Apr 2018 10:36:36: 19000000 INFO @ Thu, 05 Apr 2018 10:36:36: 21000000 INFO @ Thu, 05 Apr 2018 10:36:41: 22000000 INFO @ Thu, 05 Apr 2018 10:36:41: 21000000 INFO @ Thu, 05 Apr 2018 10:36:42: 20000000 INFO @ Thu, 05 Apr 2018 10:36:46: 23000000 INFO @ Thu, 05 Apr 2018 10:36:47: 22000000 INFO @ Thu, 05 Apr 2018 10:36:48: 21000000 INFO @ Thu, 05 Apr 2018 10:36:51: 24000000 INFO @ Thu, 05 Apr 2018 10:36:52: 23000000 INFO @ Thu, 05 Apr 2018 10:36:53: 22000000 INFO @ Thu, 05 Apr 2018 10:36:56: 25000000 INFO @ Thu, 05 Apr 2018 10:36:57: 24000000 INFO @ Thu, 05 Apr 2018 10:36:58: 23000000 INFO @ Thu, 05 Apr 2018 10:37:00: 26000000 INFO @ Thu, 05 Apr 2018 10:37:02: 25000000 INFO @ Thu, 05 Apr 2018 10:37:04: 24000000 INFO @ Thu, 05 Apr 2018 10:37:05: 27000000 INFO @ Thu, 05 Apr 2018 10:37:07: 26000000 INFO @ Thu, 05 Apr 2018 10:37:09: 25000000 INFO @ Thu, 05 Apr 2018 10:37:10: 28000000 INFO @ Thu, 05 Apr 2018 10:37:12: 27000000 INFO @ Thu, 05 Apr 2018 10:37:15: 26000000 INFO @ Thu, 05 Apr 2018 10:37:15: 29000000 INFO @ Thu, 05 Apr 2018 10:37:18: 28000000 INFO @ Thu, 05 Apr 2018 10:37:20: 30000000 INFO @ Thu, 05 Apr 2018 10:37:20: 27000000 INFO @ Thu, 05 Apr 2018 10:37:23: 29000000 INFO @ Thu, 05 Apr 2018 10:37:24: 31000000 INFO @ Thu, 05 Apr 2018 10:37:25: 28000000 INFO @ Thu, 05 Apr 2018 10:37:28: 30000000 INFO @ Thu, 05 Apr 2018 10:37:29: 32000000 INFO @ Thu, 05 Apr 2018 10:37:31: 29000000 INFO @ Thu, 05 Apr 2018 10:37:33: 31000000 INFO @ Thu, 05 Apr 2018 10:37:34: 33000000 INFO @ Thu, 05 Apr 2018 10:37:36: 30000000 INFO @ Thu, 05 Apr 2018 10:37:38: 32000000 INFO @ Thu, 05 Apr 2018 10:37:39: 34000000 INFO @ Thu, 05 Apr 2018 10:37:41: 31000000 INFO @ Thu, 05 Apr 2018 10:37:43: 33000000 INFO @ Thu, 05 Apr 2018 10:37:44: 35000000 INFO @ Thu, 05 Apr 2018 10:37:47: 32000000 INFO @ Thu, 05 Apr 2018 10:37:48: 36000000 INFO @ Thu, 05 Apr 2018 10:37:48: 34000000 INFO @ Thu, 05 Apr 2018 10:37:53: 33000000 INFO @ Thu, 05 Apr 2018 10:37:54: 37000000 INFO @ Thu, 05 Apr 2018 10:37:54: 35000000 INFO @ Thu, 05 Apr 2018 10:37:58: 34000000 INFO @ Thu, 05 Apr 2018 10:37:59: 38000000 INFO @ Thu, 05 Apr 2018 10:37:59: 36000000 INFO @ Thu, 05 Apr 2018 10:38:03: 35000000 INFO @ Thu, 05 Apr 2018 10:38:04: 39000000 INFO @ Thu, 05 Apr 2018 10:38:04: 37000000 INFO @ Thu, 05 Apr 2018 10:38:09: 36000000 INFO @ Thu, 05 Apr 2018 10:38:09: 40000000 INFO @ Thu, 05 Apr 2018 10:38:10: 38000000 INFO @ Thu, 05 Apr 2018 10:38:15: 41000000 INFO @ Thu, 05 Apr 2018 10:38:15: 39000000 INFO @ Thu, 05 Apr 2018 10:38:15: 37000000 INFO @ Thu, 05 Apr 2018 10:38:18: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:38:18: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:38:18: #1 total tags in treatment: 20570565 INFO @ Thu, 05 Apr 2018 10:38:18: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:38:18: #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 10:38:18: #1 tags after filtering in treatment: 7150770 INFO @ Thu, 05 Apr 2018 10:38:18: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:38:18: #1 finished! INFO @ Thu, 05 Apr 2018 10:38:18: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:38:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:38:19: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:38:19: 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 10:38:19: Process for pairing-model is terminated! cat: SRX3671202.20_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 `SRX3671202.20_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 `SRX3671202.20_*.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 `SRX3671202.20_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 10:38:20: 40000000 INFO @ Thu, 05 Apr 2018 10:38:20: 38000000 INFO @ Thu, 05 Apr 2018 10:38:25: 41000000 INFO @ Thu, 05 Apr 2018 10:38:26: 39000000 INFO @ Thu, 05 Apr 2018 10:38:28: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:38:28: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:38:28: #1 total tags in treatment: 20570565 INFO @ Thu, 05 Apr 2018 10:38:28: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:38:28: #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 10:38:28: #1 tags after filtering in treatment: 7150770 INFO @ Thu, 05 Apr 2018 10:38:28: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:38:28: #1 finished! INFO @ Thu, 05 Apr 2018 10:38:28: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:38:29: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:38:29: 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 10:38:29: Process for pairing-model is terminated! cat: SRX3671202.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671202.10_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 `SRX3671202.10_*.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 `SRX3671202.10_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 10:38:31: 40000000 INFO @ Thu, 05 Apr 2018 10:38:36: 41000000 INFO @ Thu, 05 Apr 2018 10:38:39: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:38:39: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:38:39: #1 total tags in treatment: 20570565 INFO @ Thu, 05 Apr 2018 10:38:39: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:38:39: #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 10:38:39: #1 tags after filtering in treatment: 7150770 INFO @ Thu, 05 Apr 2018 10:38:39: #1 Redundant rate of treatment: 0.65 INFO @ Thu, 05 Apr 2018 10:38:39: #1 finished! INFO @ Thu, 05 Apr 2018 10:38:39: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:38:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:38:40: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:38:40: 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 10:38:40: Process for pairing-model is terminated! cat: SRX3671202.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3671202.05_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 `SRX3671202.05_*.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 `SRX3671202.05_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。