Job ID = 10608975 sra ファイルのダウンロード中... Completed: 2600022K bytes transferred in 286 seconds (74377K 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 20657972 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2741982/SRR5453816.sra Written 20657972 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: 00:26:18 20657972 reads; of these: 20657972 (100.00%) were paired; of these: 1566834 (7.58%) aligned concordantly 0 times 17409597 (84.28%) aligned concordantly exactly 1 time 1681541 (8.14%) aligned concordantly >1 times ---- 1566834 pairs aligned concordantly 0 times; of these: 486621 (31.06%) aligned discordantly 1 time ---- 1080213 pairs aligned 0 times concordantly or discordantly; of these: 2160426 mates make up the pairs; of these: 1302049 (60.27%) aligned 0 times 691407 (32.00%) aligned exactly 1 time 166970 (7.73%) aligned >1 times 96.85% overall alignment rate Time searching: 00:26:18 Overall time: 00:26:18 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 20 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] 833127 / 19545171 = 0.0426 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 23:43:20: # Command line: callpeak -t SRX2741982.bam -f BAM -g 12100000 -n SRX2741982.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2741982.05 # format = BAM # ChIP-seq file = ['SRX2741982.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 23:43:20: #1 read tag files... INFO @ Thu, 03 May 2018 23:43:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:43:20: # Command line: callpeak -t SRX2741982.bam -f BAM -g 12100000 -n SRX2741982.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2741982.10 # format = BAM # ChIP-seq file = ['SRX2741982.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 23:43:20: #1 read tag files... INFO @ Thu, 03 May 2018 23:43:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:43:20: # Command line: callpeak -t SRX2741982.bam -f BAM -g 12100000 -n SRX2741982.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2741982.20 # format = BAM # ChIP-seq file = ['SRX2741982.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 23:43:20: #1 read tag files... INFO @ Thu, 03 May 2018 23:43:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:43:28: 1000000 INFO @ Thu, 03 May 2018 23:43:29: 1000000 INFO @ Thu, 03 May 2018 23:43:29: 1000000 INFO @ Thu, 03 May 2018 23:43:36: 2000000 INFO @ Thu, 03 May 2018 23:43:37: 2000000 INFO @ Thu, 03 May 2018 23:43:37: 2000000 INFO @ Thu, 03 May 2018 23:43:44: 3000000 INFO @ Thu, 03 May 2018 23:43:46: 3000000 INFO @ Thu, 03 May 2018 23:43:46: 3000000 INFO @ Thu, 03 May 2018 23:43:51: 4000000 INFO @ Thu, 03 May 2018 23:43:54: 4000000 INFO @ Thu, 03 May 2018 23:43:54: 4000000 INFO @ Thu, 03 May 2018 23:43:59: 5000000 INFO @ Thu, 03 May 2018 23:44:02: 5000000 INFO @ Thu, 03 May 2018 23:44:02: 5000000 INFO @ Thu, 03 May 2018 23:44:07: 6000000 INFO @ Thu, 03 May 2018 23:44:11: 6000000 INFO @ Thu, 03 May 2018 23:44:11: 6000000 INFO @ Thu, 03 May 2018 23:44:14: 7000000 INFO @ Thu, 03 May 2018 23:44:19: 7000000 INFO @ Thu, 03 May 2018 23:44:19: 7000000 INFO @ Thu, 03 May 2018 23:44:22: 8000000 INFO @ Thu, 03 May 2018 23:44:27: 8000000 INFO @ Thu, 03 May 2018 23:44:27: 8000000 INFO @ Thu, 03 May 2018 23:44:30: 9000000 INFO @ Thu, 03 May 2018 23:44:36: 9000000 INFO @ Thu, 03 May 2018 23:44:36: 9000000 INFO @ Thu, 03 May 2018 23:44:37: 10000000 INFO @ Thu, 03 May 2018 23:44:44: 10000000 INFO @ Thu, 03 May 2018 23:44:44: 10000000 INFO @ Thu, 03 May 2018 23:44:45: 11000000 INFO @ Thu, 03 May 2018 23:44:52: 11000000 INFO @ Thu, 03 May 2018 23:44:52: 11000000 INFO @ Thu, 03 May 2018 23:44:52: 12000000 INFO @ Thu, 03 May 2018 23:45:00: 13000000 INFO @ Thu, 03 May 2018 23:45:00: 12000000 INFO @ Thu, 03 May 2018 23:45:00: 12000000 INFO @ Thu, 03 May 2018 23:45:08: 14000000 INFO @ Thu, 03 May 2018 23:45:09: 13000000 INFO @ Thu, 03 May 2018 23:45:09: 13000000 INFO @ Thu, 03 May 2018 23:45:15: 15000000 INFO @ Thu, 03 May 2018 23:45:17: 14000000 INFO @ Thu, 03 May 2018 23:45:17: 14000000 INFO @ Thu, 03 May 2018 23:45:23: 16000000 INFO @ Thu, 03 May 2018 23:45:25: 15000000 INFO @ Thu, 03 May 2018 23:45:25: 15000000 INFO @ Thu, 03 May 2018 23:45:31: 17000000 INFO @ Thu, 03 May 2018 23:45:34: 16000000 INFO @ Thu, 03 May 2018 23:45:34: 16000000 INFO @ Thu, 03 May 2018 23:45:38: 18000000 INFO @ Thu, 03 May 2018 23:45:42: 17000000 INFO @ Thu, 03 May 2018 23:45:42: 17000000 INFO @ Thu, 03 May 2018 23:45:46: 19000000 INFO @ Thu, 03 May 2018 23:45:50: 18000000 INFO @ Thu, 03 May 2018 23:45:50: 18000000 INFO @ Thu, 03 May 2018 23:45:53: 20000000 INFO @ Thu, 03 May 2018 23:45:58: 19000000 INFO @ Thu, 03 May 2018 23:45:58: 19000000 INFO @ Thu, 03 May 2018 23:46:01: 21000000 INFO @ Thu, 03 May 2018 23:46:07: 20000000 INFO @ Thu, 03 May 2018 23:46:07: 20000000 INFO @ Thu, 03 May 2018 23:46:09: 22000000 INFO @ Thu, 03 May 2018 23:46:15: 21000000 INFO @ Thu, 03 May 2018 23:46:15: 21000000 INFO @ Thu, 03 May 2018 23:46:16: 23000000 INFO @ Thu, 03 May 2018 23:46:23: 22000000 INFO @ Thu, 03 May 2018 23:46:23: 22000000 INFO @ Thu, 03 May 2018 23:46:24: 24000000 INFO @ Thu, 03 May 2018 23:46:32: 23000000 INFO @ Thu, 03 May 2018 23:46:32: 23000000 INFO @ Thu, 03 May 2018 23:46:32: 25000000 INFO @ Thu, 03 May 2018 23:46:39: 26000000 INFO @ Thu, 03 May 2018 23:46:40: 24000000 INFO @ Thu, 03 May 2018 23:46:40: 24000000 INFO @ Thu, 03 May 2018 23:46:47: 27000000 INFO @ Thu, 03 May 2018 23:46:48: 25000000 INFO @ Thu, 03 May 2018 23:46:48: 25000000 INFO @ Thu, 03 May 2018 23:46:54: 28000000 INFO @ Thu, 03 May 2018 23:46:56: 26000000 INFO @ Thu, 03 May 2018 23:46:56: 26000000 INFO @ Thu, 03 May 2018 23:47:02: 29000000 INFO @ Thu, 03 May 2018 23:47:05: 27000000 INFO @ Thu, 03 May 2018 23:47:05: 27000000 INFO @ Thu, 03 May 2018 23:47:10: 30000000 INFO @ Thu, 03 May 2018 23:47:13: 28000000 INFO @ Thu, 03 May 2018 23:47:13: 28000000 INFO @ Thu, 03 May 2018 23:47:17: 31000000 INFO @ Thu, 03 May 2018 23:47:21: 29000000 INFO @ Thu, 03 May 2018 23:47:21: 29000000 INFO @ Thu, 03 May 2018 23:47:25: 32000000 INFO @ Thu, 03 May 2018 23:47:30: 30000000 INFO @ Thu, 03 May 2018 23:47:30: 30000000 INFO @ Thu, 03 May 2018 23:47:33: 33000000 INFO @ Thu, 03 May 2018 23:47:38: 31000000 INFO @ Thu, 03 May 2018 23:47:38: 31000000 INFO @ Thu, 03 May 2018 23:47:40: 34000000 INFO @ Thu, 03 May 2018 23:47:46: 32000000 INFO @ Thu, 03 May 2018 23:47:46: 32000000 INFO @ Thu, 03 May 2018 23:47:47: 35000000 INFO @ Thu, 03 May 2018 23:47:53: 33000000 INFO @ Thu, 03 May 2018 23:47:53: 33000000 INFO @ Thu, 03 May 2018 23:47:55: 36000000 INFO @ Thu, 03 May 2018 23:48:01: 34000000 INFO @ Thu, 03 May 2018 23:48:01: 34000000 INFO @ Thu, 03 May 2018 23:48:02: 37000000 INFO @ Thu, 03 May 2018 23:48:09: 35000000 INFO @ Thu, 03 May 2018 23:48:09: 35000000 INFO @ Thu, 03 May 2018 23:48:09: 38000000 INFO @ Thu, 03 May 2018 23:48:12: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:48:12: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:48:12: #1 total tags in treatment: 18263584 INFO @ Thu, 03 May 2018 23:48:12: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:48:12: #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 23:48:13: #1 tags after filtering in treatment: 11499887 INFO @ Thu, 03 May 2018 23:48:13: #1 Redundant rate of treatment: 0.37 INFO @ Thu, 03 May 2018 23:48:13: #1 finished! INFO @ Thu, 03 May 2018 23:48:13: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:48:13: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:48:13: 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 23:48:13: Process for pairing-model is terminated! cat: SRX2741982.05_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 `SRX2741982.05_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 `SRX2741982.05_*.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 `SRX2741982.05_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 23:48:17: 36000000 INFO @ Thu, 03 May 2018 23:48:17: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 03 May 2018 23:48:24: 37000000 INFO @ Thu, 03 May 2018 23:48:24: 37000000 INFO @ Thu, 03 May 2018 23:48:32: 38000000 INFO @ Thu, 03 May 2018 23:48:32: 38000000 INFO @ Thu, 03 May 2018 23:48:34: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:48:34: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:48:34: #1 total tags in treatment: 18263584 INFO @ Thu, 03 May 2018 23:48:34: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:48:34: #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 23:48:34: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:48:34: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:48:34: #1 total tags in treatment: 18263584 INFO @ Thu, 03 May 2018 23:48:34: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:48:34: #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 23:48:35: #1 tags after filtering in treatment: 11499887 INFO @ Thu, 03 May 2018 23:48:35: #1 Redundant rate of treatment: 0.37 INFO @ Thu, 03 May 2018 23:48:35: #1 finished! INFO @ Thu, 03 May 2018 23:48:35: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:48:35: #1 tags after filtering in treatment: 11499887 INFO @ Thu, 03 May 2018 23:48:35: #1 Redundant rate of treatment: 0.37 INFO @ Thu, 03 May 2018 23:48:35: #1 finished! INFO @ Thu, 03 May 2018 23:48:35: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:48:36: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:48:36: 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 23:48:36: Process for pairing-model is terminated! cat: SRX2741982.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Thu, 03 May 2018 23:48:36: #2 number of paired peaks: 0 WARNING @ Thu, 03 May 2018 23:48:36: 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 23:48:36: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2741982.20_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 `SRX2741982.20_*.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 `SRX2741982.20_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 cat: SRX2741982.10_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 `SRX2741982.10_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 `SRX2741982.10_*.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 `SRX2741982.10_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。