Job ID = 10536518 sra ファイルのダウンロード中... Completed: 1781580K bytes transferred in 37 seconds (390167K 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 46517807 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671211/SRR6696963.sra Written 46517807 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: 00:32:40 46517807 reads; of these: 46517807 (100.00%) were paired; of these: 7920454 (17.03%) aligned concordantly 0 times 32918732 (70.77%) aligned concordantly exactly 1 time 5678621 (12.21%) aligned concordantly >1 times ---- 7920454 pairs aligned concordantly 0 times; of these: 530490 (6.70%) aligned discordantly 1 time ---- 7389964 pairs aligned 0 times concordantly or discordantly; of these: 14779928 mates make up the pairs; of these: 14282983 (96.64%) aligned 0 times 164684 (1.11%) aligned exactly 1 time 332261 (2.25%) aligned >1 times 84.65% overall alignment rate Time searching: 00:32:40 Overall time: 00:32:40 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 36 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] 13498199 / 38969956 = 0.3464 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 10:52:14: # Command line: callpeak -t SRX3671211.bam -f BAM -g 12100000 -n SRX3671211.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671211.10 # format = BAM # ChIP-seq file = ['SRX3671211.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 10:52:14: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:52:14: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:52:14: # Command line: callpeak -t SRX3671211.bam -f BAM -g 12100000 -n SRX3671211.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671211.20 # format = BAM # ChIP-seq file = ['SRX3671211.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 10:52:14: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:52:14: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:52:14: # Command line: callpeak -t SRX3671211.bam -f BAM -g 12100000 -n SRX3671211.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671211.05 # format = BAM # ChIP-seq file = ['SRX3671211.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 10:52:14: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:52:14: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:52:20: 1000000 INFO @ Thu, 05 Apr 2018 10:52:20: 1000000 INFO @ Thu, 05 Apr 2018 10:52:20: 1000000 INFO @ Thu, 05 Apr 2018 10:52:25: 2000000 INFO @ Thu, 05 Apr 2018 10:52:25: 2000000 INFO @ Thu, 05 Apr 2018 10:52:25: 2000000 INFO @ Thu, 05 Apr 2018 10:52:31: 3000000 INFO @ Thu, 05 Apr 2018 10:52:31: 3000000 INFO @ Thu, 05 Apr 2018 10:52:32: 3000000 INFO @ Thu, 05 Apr 2018 10:52:37: 4000000 INFO @ Thu, 05 Apr 2018 10:52:37: 4000000 INFO @ Thu, 05 Apr 2018 10:52:38: 4000000 INFO @ Thu, 05 Apr 2018 10:52:43: 5000000 INFO @ Thu, 05 Apr 2018 10:52:43: 5000000 INFO @ Thu, 05 Apr 2018 10:52:44: 5000000 INFO @ Thu, 05 Apr 2018 10:52:51: 6000000 INFO @ Thu, 05 Apr 2018 10:52:53: 6000000 INFO @ Thu, 05 Apr 2018 10:52:54: 6000000 INFO @ Thu, 05 Apr 2018 10:52:59: 7000000 INFO @ Thu, 05 Apr 2018 10:53:00: 7000000 INFO @ Thu, 05 Apr 2018 10:53:03: 7000000 INFO @ Thu, 05 Apr 2018 10:53:04: 8000000 INFO @ Thu, 05 Apr 2018 10:53:08: 8000000 INFO @ Thu, 05 Apr 2018 10:53:11: 9000000 INFO @ Thu, 05 Apr 2018 10:53:12: 8000000 INFO @ Thu, 05 Apr 2018 10:53:16: 9000000 INFO @ Thu, 05 Apr 2018 10:53:19: 10000000 INFO @ Thu, 05 Apr 2018 10:53:20: 9000000 INFO @ Thu, 05 Apr 2018 10:53:21: 10000000 INFO @ Thu, 05 Apr 2018 10:53:24: 11000000 INFO @ Thu, 05 Apr 2018 10:53:26: 10000000 INFO @ Thu, 05 Apr 2018 10:53:26: 11000000 INFO @ Thu, 05 Apr 2018 10:53:30: 12000000 INFO @ Thu, 05 Apr 2018 10:53:31: 11000000 INFO @ Thu, 05 Apr 2018 10:53:32: 12000000 INFO @ Thu, 05 Apr 2018 10:53:35: 13000000 INFO @ Thu, 05 Apr 2018 10:53:37: 13000000 INFO @ Thu, 05 Apr 2018 10:53:37: 12000000 INFO @ Thu, 05 Apr 2018 10:53:41: 14000000 INFO @ Thu, 05 Apr 2018 10:53:42: 14000000 INFO @ Thu, 05 Apr 2018 10:53:42: 13000000 INFO @ Thu, 05 Apr 2018 10:53:48: 15000000 INFO @ Thu, 05 Apr 2018 10:53:49: 15000000 INFO @ Thu, 05 Apr 2018 10:53:49: 14000000 INFO @ Thu, 05 Apr 2018 10:53:53: 16000000 INFO @ Thu, 05 Apr 2018 10:53:54: 16000000 INFO @ Thu, 05 Apr 2018 10:53:54: 15000000 INFO @ Thu, 05 Apr 2018 10:53:58: 17000000 INFO @ Thu, 05 Apr 2018 10:53:59: 16000000 INFO @ Thu, 05 Apr 2018 10:54:00: 17000000 INFO @ Thu, 05 Apr 2018 10:54:04: 17000000 INFO @ Thu, 05 Apr 2018 10:54:04: 18000000 INFO @ Thu, 05 Apr 2018 10:54:05: 18000000 INFO @ Thu, 05 Apr 2018 10:54:09: 18000000 INFO @ Thu, 05 Apr 2018 10:54:10: 19000000 INFO @ Thu, 05 Apr 2018 10:54:11: 19000000 INFO @ Thu, 05 Apr 2018 10:54:15: 19000000 INFO @ Thu, 05 Apr 2018 10:54:16: 20000000 INFO @ Thu, 05 Apr 2018 10:54:17: 20000000 INFO @ Thu, 05 Apr 2018 10:54:20: 20000000 INFO @ Thu, 05 Apr 2018 10:54:22: 21000000 INFO @ Thu, 05 Apr 2018 10:54:23: 21000000 INFO @ Thu, 05 Apr 2018 10:54:25: 21000000 INFO @ Thu, 05 Apr 2018 10:54:27: 22000000 INFO @ Thu, 05 Apr 2018 10:54:28: 22000000 INFO @ Thu, 05 Apr 2018 10:54:31: 22000000 INFO @ Thu, 05 Apr 2018 10:54:33: 23000000 INFO @ Thu, 05 Apr 2018 10:54:34: 23000000 INFO @ Thu, 05 Apr 2018 10:54:36: 23000000 INFO @ Thu, 05 Apr 2018 10:54:38: 24000000 INFO @ Thu, 05 Apr 2018 10:54:39: 24000000 INFO @ Thu, 05 Apr 2018 10:54:41: 24000000 INFO @ Thu, 05 Apr 2018 10:54:44: 25000000 INFO @ Thu, 05 Apr 2018 10:54:45: 25000000 INFO @ Thu, 05 Apr 2018 10:54:48: 25000000 INFO @ Thu, 05 Apr 2018 10:54:50: 26000000 INFO @ Thu, 05 Apr 2018 10:54:53: 26000000 INFO @ Thu, 05 Apr 2018 10:54:55: 26000000 INFO @ Thu, 05 Apr 2018 10:54:56: 27000000 INFO @ Thu, 05 Apr 2018 10:54:58: 27000000 INFO @ Thu, 05 Apr 2018 10:55:00: 27000000 INFO @ Thu, 05 Apr 2018 10:55:02: 28000000 INFO @ Thu, 05 Apr 2018 10:55:03: 28000000 INFO @ Thu, 05 Apr 2018 10:55:05: 28000000 INFO @ Thu, 05 Apr 2018 10:55:07: 29000000 INFO @ Thu, 05 Apr 2018 10:55:09: 29000000 INFO @ Thu, 05 Apr 2018 10:55:11: 29000000 INFO @ Thu, 05 Apr 2018 10:55:13: 30000000 INFO @ Thu, 05 Apr 2018 10:55:15: 30000000 INFO @ Thu, 05 Apr 2018 10:55:17: 30000000 INFO @ Thu, 05 Apr 2018 10:55:18: 31000000 INFO @ Thu, 05 Apr 2018 10:55:20: 31000000 INFO @ Thu, 05 Apr 2018 10:55:23: 31000000 INFO @ Thu, 05 Apr 2018 10:55:24: 32000000 INFO @ Thu, 05 Apr 2018 10:55:25: 32000000 INFO @ Thu, 05 Apr 2018 10:55:28: 32000000 INFO @ Thu, 05 Apr 2018 10:55:29: 33000000 INFO @ Thu, 05 Apr 2018 10:55:31: 33000000 INFO @ Thu, 05 Apr 2018 10:55:34: 33000000 INFO @ Thu, 05 Apr 2018 10:55:34: 34000000 INFO @ Thu, 05 Apr 2018 10:55:37: 34000000 INFO @ Thu, 05 Apr 2018 10:55:39: 34000000 INFO @ Thu, 05 Apr 2018 10:55:39: 35000000 INFO @ Thu, 05 Apr 2018 10:55:42: 35000000 INFO @ Thu, 05 Apr 2018 10:55:45: 36000000 INFO @ Thu, 05 Apr 2018 10:55:46: 35000000 INFO @ Thu, 05 Apr 2018 10:55:50: 36000000 INFO @ Thu, 05 Apr 2018 10:55:53: 37000000 INFO @ Thu, 05 Apr 2018 10:55:56: 36000000 INFO @ Thu, 05 Apr 2018 10:55:59: 37000000 INFO @ Thu, 05 Apr 2018 10:56:01: 38000000 INFO @ Thu, 05 Apr 2018 10:56:04: 38000000 INFO @ Thu, 05 Apr 2018 10:56:05: 37000000 INFO @ Thu, 05 Apr 2018 10:56:09: 39000000 INFO @ Thu, 05 Apr 2018 10:56:10: 39000000 INFO @ Thu, 05 Apr 2018 10:56:14: 38000000 INFO @ Thu, 05 Apr 2018 10:56:15: 40000000 INFO @ Thu, 05 Apr 2018 10:56:20: 40000000 INFO @ Thu, 05 Apr 2018 10:56:21: 41000000 INFO @ Thu, 05 Apr 2018 10:56:23: 39000000 INFO @ Thu, 05 Apr 2018 10:56:28: 42000000 INFO @ Thu, 05 Apr 2018 10:56:29: 41000000 INFO @ Thu, 05 Apr 2018 10:56:32: 40000000 INFO @ Thu, 05 Apr 2018 10:56:35: 42000000 INFO @ Thu, 05 Apr 2018 10:56:39: 43000000 INFO @ Thu, 05 Apr 2018 10:56:39: 41000000 INFO @ Thu, 05 Apr 2018 10:56:42: 43000000 INFO @ Thu, 05 Apr 2018 10:56:46: 42000000 INFO @ Thu, 05 Apr 2018 10:56:47: 44000000 INFO @ Thu, 05 Apr 2018 10:56:49: 44000000 INFO @ Thu, 05 Apr 2018 10:56:54: 43000000 INFO @ Thu, 05 Apr 2018 10:56:56: 45000000 INFO @ Thu, 05 Apr 2018 10:56:57: 45000000 INFO @ Thu, 05 Apr 2018 10:57:01: 44000000 INFO @ Thu, 05 Apr 2018 10:57:03: 46000000 INFO @ Thu, 05 Apr 2018 10:57:03: 46000000 INFO @ Thu, 05 Apr 2018 10:57:07: 45000000 INFO @ Thu, 05 Apr 2018 10:57:08: 47000000 INFO @ Thu, 05 Apr 2018 10:57:08: 47000000 INFO @ Thu, 05 Apr 2018 10:57:12: 46000000 INFO @ Thu, 05 Apr 2018 10:57:13: 48000000 INFO @ Thu, 05 Apr 2018 10:57:14: 48000000 INFO @ Thu, 05 Apr 2018 10:57:17: 47000000 INFO @ Thu, 05 Apr 2018 10:57:19: 49000000 INFO @ Thu, 05 Apr 2018 10:57:19: 49000000 INFO @ Thu, 05 Apr 2018 10:57:22: 48000000 INFO @ Thu, 05 Apr 2018 10:57:24: 50000000 INFO @ Thu, 05 Apr 2018 10:57:24: 50000000 INFO @ Thu, 05 Apr 2018 10:57:27: 49000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 10:57:29: 51000000 INFO @ Thu, 05 Apr 2018 10:57:30: 51000000 INFO @ Thu, 05 Apr 2018 10:57:32: 50000000 INFO @ Thu, 05 Apr 2018 10:57:33: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:57:33: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:57:33: #1 total tags in treatment: 25301662 INFO @ Thu, 05 Apr 2018 10:57:33: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:57:33: #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 10:57:34: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:57:34: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:57:34: #1 total tags in treatment: 25301662 INFO @ Thu, 05 Apr 2018 10:57:34: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:57:34: #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 10:57:34: #1 tags after filtering in treatment: 8106895 INFO @ Thu, 05 Apr 2018 10:57:34: #1 Redundant rate of treatment: 0.68 INFO @ Thu, 05 Apr 2018 10:57:34: #1 finished! INFO @ Thu, 05 Apr 2018 10:57:34: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:57:35: #1 tags after filtering in treatment: 8106895 INFO @ Thu, 05 Apr 2018 10:57:35: #1 Redundant rate of treatment: 0.68 INFO @ Thu, 05 Apr 2018 10:57:35: #1 finished! INFO @ Thu, 05 Apr 2018 10:57:35: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:57:35: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:57:35: 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 10:57:35: Process for pairing-model is terminated! cat: SRX3671211.05_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 `SRX3671211.05_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 `SRX3671211.05_*.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 `SRX3671211.05_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 10:57:35: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:57:35: 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 10:57:35: Process for pairing-model is terminated! cat: SRX3671211.20_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 `SRX3671211.20_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 `SRX3671211.20_*.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 `SRX3671211.20_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 10:57:37: 51000000 INFO @ Thu, 05 Apr 2018 10:57:41: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:57:41: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:57:41: #1 total tags in treatment: 25301662 INFO @ Thu, 05 Apr 2018 10:57:41: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:57:41: #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 10:57:42: #1 tags after filtering in treatment: 8106895 INFO @ Thu, 05 Apr 2018 10:57:42: #1 Redundant rate of treatment: 0.68 INFO @ Thu, 05 Apr 2018 10:57:42: #1 finished! INFO @ Thu, 05 Apr 2018 10:57:42: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:57:42: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:57:42: 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 10:57:42: Process for pairing-model is terminated! cat: SRX3671211.10_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 `SRX3671211.10_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 `SRX3671211.10_*.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 `SRX3671211.10_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 BigWig に変換しました。