Job ID = 10536386 sra ファイルのダウンロード中... Completed: 1411602K bytes transferred in 52 seconds (218789K 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 35437976 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671143/SRR6696895.sra Written 35437976 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: 00:23:05 35437976 reads; of these: 35437976 (100.00%) were paired; of these: 6653424 (18.77%) aligned concordantly 0 times 24077137 (67.94%) aligned concordantly exactly 1 time 4707415 (13.28%) aligned concordantly >1 times ---- 6653424 pairs aligned concordantly 0 times; of these: 54587 (0.82%) aligned discordantly 1 time ---- 6598837 pairs aligned 0 times concordantly or discordantly; of these: 13197674 mates make up the pairs; of these: 12764978 (96.72%) aligned 0 times 337884 (2.56%) aligned exactly 1 time 94812 (0.72%) aligned >1 times 81.99% overall alignment rate Time searching: 00:23:05 Overall time: 00:23:05 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 24 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] 10799202 / 28802464 = 0.3749 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 09:49:14: # Command line: callpeak -t SRX3671143.bam -f BAM -g 12100000 -n SRX3671143.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671143.05 # format = BAM # ChIP-seq file = ['SRX3671143.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 09:49:14: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:49:14: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:49:14: # Command line: callpeak -t SRX3671143.bam -f BAM -g 12100000 -n SRX3671143.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671143.20 # format = BAM # ChIP-seq file = ['SRX3671143.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 09:49:14: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:49:14: # Command line: callpeak -t SRX3671143.bam -f BAM -g 12100000 -n SRX3671143.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671143.10 # format = BAM # ChIP-seq file = ['SRX3671143.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 09:49:14: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:49:14: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:49:14: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:49:21: 1000000 INFO @ Thu, 05 Apr 2018 09:49:21: 1000000 INFO @ Thu, 05 Apr 2018 09:49:21: 1000000 INFO @ Thu, 05 Apr 2018 09:49:27: 2000000 INFO @ Thu, 05 Apr 2018 09:49:27: 2000000 INFO @ Thu, 05 Apr 2018 09:49:27: 2000000 INFO @ Thu, 05 Apr 2018 09:49:34: 3000000 INFO @ Thu, 05 Apr 2018 09:49:34: 3000000 INFO @ Thu, 05 Apr 2018 09:49:35: 3000000 INFO @ Thu, 05 Apr 2018 09:49:40: 4000000 INFO @ Thu, 05 Apr 2018 09:49:41: 4000000 INFO @ Thu, 05 Apr 2018 09:49:41: 4000000 INFO @ Thu, 05 Apr 2018 09:49:46: 5000000 INFO @ Thu, 05 Apr 2018 09:49:48: 5000000 INFO @ Thu, 05 Apr 2018 09:49:48: 5000000 INFO @ Thu, 05 Apr 2018 09:49:53: 6000000 INFO @ Thu, 05 Apr 2018 09:49:54: 6000000 INFO @ Thu, 05 Apr 2018 09:49:55: 6000000 INFO @ Thu, 05 Apr 2018 09:50:00: 7000000 INFO @ Thu, 05 Apr 2018 09:50:02: 7000000 INFO @ Thu, 05 Apr 2018 09:50:02: 7000000 INFO @ Thu, 05 Apr 2018 09:50:06: 8000000 INFO @ Thu, 05 Apr 2018 09:50:08: 8000000 INFO @ Thu, 05 Apr 2018 09:50:08: 8000000 INFO @ Thu, 05 Apr 2018 09:50:13: 9000000 INFO @ Thu, 05 Apr 2018 09:50:14: 9000000 INFO @ Thu, 05 Apr 2018 09:50:15: 9000000 INFO @ Thu, 05 Apr 2018 09:50:19: 10000000 INFO @ Thu, 05 Apr 2018 09:50:21: 10000000 INFO @ Thu, 05 Apr 2018 09:50:21: 10000000 INFO @ Thu, 05 Apr 2018 09:50:25: 11000000 INFO @ Thu, 05 Apr 2018 09:50:27: 11000000 INFO @ Thu, 05 Apr 2018 09:50:28: 11000000 INFO @ Thu, 05 Apr 2018 09:50:32: 12000000 INFO @ Thu, 05 Apr 2018 09:50:34: 12000000 INFO @ Thu, 05 Apr 2018 09:50:35: 12000000 INFO @ Thu, 05 Apr 2018 09:50:38: 13000000 INFO @ Thu, 05 Apr 2018 09:50:41: 13000000 INFO @ Thu, 05 Apr 2018 09:50:41: 13000000 INFO @ Thu, 05 Apr 2018 09:50:44: 14000000 INFO @ Thu, 05 Apr 2018 09:50:47: 14000000 INFO @ Thu, 05 Apr 2018 09:50:48: 14000000 INFO @ Thu, 05 Apr 2018 09:50:51: 15000000 INFO @ Thu, 05 Apr 2018 09:50:54: 15000000 INFO @ Thu, 05 Apr 2018 09:50:55: 15000000 INFO @ Thu, 05 Apr 2018 09:50:57: 16000000 INFO @ Thu, 05 Apr 2018 09:51:01: 16000000 INFO @ Thu, 05 Apr 2018 09:51:01: 16000000 INFO @ Thu, 05 Apr 2018 09:51:03: 17000000 INFO @ Thu, 05 Apr 2018 09:51:07: 17000000 INFO @ Thu, 05 Apr 2018 09:51:08: 17000000 INFO @ Thu, 05 Apr 2018 09:51:10: 18000000 INFO @ Thu, 05 Apr 2018 09:51:14: 18000000 INFO @ Thu, 05 Apr 2018 09:51:15: 18000000 INFO @ Thu, 05 Apr 2018 09:51:16: 19000000 INFO @ Thu, 05 Apr 2018 09:51:21: 19000000 INFO @ Thu, 05 Apr 2018 09:51:22: 19000000 INFO @ Thu, 05 Apr 2018 09:51:22: 20000000 INFO @ Thu, 05 Apr 2018 09:51:28: 20000000 INFO @ Thu, 05 Apr 2018 09:51:28: 21000000 INFO @ Thu, 05 Apr 2018 09:51:29: 20000000 INFO @ Thu, 05 Apr 2018 09:51:34: 22000000 INFO @ Thu, 05 Apr 2018 09:51:35: 21000000 INFO @ Thu, 05 Apr 2018 09:51:35: 21000000 INFO @ Thu, 05 Apr 2018 09:51:41: 23000000 INFO @ Thu, 05 Apr 2018 09:51:42: 22000000 INFO @ Thu, 05 Apr 2018 09:51:42: 22000000 INFO @ Thu, 05 Apr 2018 09:51:47: 24000000 INFO @ Thu, 05 Apr 2018 09:51:48: 23000000 INFO @ Thu, 05 Apr 2018 09:51:48: 23000000 INFO @ Thu, 05 Apr 2018 09:51:54: 25000000 INFO @ Thu, 05 Apr 2018 09:51:54: 24000000 INFO @ Thu, 05 Apr 2018 09:51:54: 24000000 INFO @ Thu, 05 Apr 2018 09:52:00: 25000000 INFO @ Thu, 05 Apr 2018 09:52:00: 26000000 INFO @ Thu, 05 Apr 2018 09:52:01: 25000000 INFO @ Thu, 05 Apr 2018 09:52:06: 26000000 INFO @ Thu, 05 Apr 2018 09:52:08: 27000000 INFO @ Thu, 05 Apr 2018 09:52:08: 26000000 INFO @ Thu, 05 Apr 2018 09:52:13: 27000000 INFO @ Thu, 05 Apr 2018 09:52:14: 28000000 INFO @ Thu, 05 Apr 2018 09:52:15: 27000000 INFO @ Thu, 05 Apr 2018 09:52:19: 28000000 INFO @ Thu, 05 Apr 2018 09:52:21: 29000000 INFO @ Thu, 05 Apr 2018 09:52:22: 28000000 INFO @ Thu, 05 Apr 2018 09:52:25: 29000000 INFO @ Thu, 05 Apr 2018 09:52:28: 30000000 INFO @ Thu, 05 Apr 2018 09:52:29: 29000000 INFO @ Thu, 05 Apr 2018 09:52:32: 30000000 INFO @ Thu, 05 Apr 2018 09:52:34: 31000000 INFO @ Thu, 05 Apr 2018 09:52:35: 30000000 INFO @ Thu, 05 Apr 2018 09:52:38: 31000000 INFO @ Thu, 05 Apr 2018 09:52:41: 32000000 INFO @ Thu, 05 Apr 2018 09:52:42: 31000000 INFO @ Thu, 05 Apr 2018 09:52:44: 32000000 INFO @ Thu, 05 Apr 2018 09:52:48: 33000000 INFO @ Thu, 05 Apr 2018 09:52:49: 32000000 INFO @ Thu, 05 Apr 2018 09:52:50: 33000000 INFO @ Thu, 05 Apr 2018 09:52:55: 34000000 INFO @ Thu, 05 Apr 2018 09:52:56: 33000000 INFO @ Thu, 05 Apr 2018 09:52:56: 34000000 INFO @ Thu, 05 Apr 2018 09:53:02: 35000000 INFO @ Thu, 05 Apr 2018 09:53:03: 35000000 INFO @ Thu, 05 Apr 2018 09:53:03: 34000000 INFO @ Thu, 05 Apr 2018 09:53:09: 36000000 INFO @ Thu, 05 Apr 2018 09:53:09: 36000000 INFO @ Thu, 05 Apr 2018 09:53:10: 35000000 INFO @ Thu, 05 Apr 2018 09:53:12: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:53:12: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:53:12: #1 total tags in treatment: 17988143 INFO @ Thu, 05 Apr 2018 09:53:12: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:53:12: #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 09:53:12: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:53:12: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:53:12: #1 total tags in treatment: 17988143 INFO @ Thu, 05 Apr 2018 09:53:12: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:53:12: #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 09:53:12: #1 tags after filtering in treatment: 11280338 INFO @ Thu, 05 Apr 2018 09:53:12: #1 Redundant rate of treatment: 0.37 INFO @ Thu, 05 Apr 2018 09:53:12: #1 finished! INFO @ Thu, 05 Apr 2018 09:53:12: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:53:13: #1 tags after filtering in treatment: 11280338 INFO @ Thu, 05 Apr 2018 09:53:13: #1 Redundant rate of treatment: 0.37 INFO @ Thu, 05 Apr 2018 09:53:13: #1 finished! INFO @ Thu, 05 Apr 2018 09:53:13: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:53:13: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:53:13: 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, 05 Apr 2018 09:53:13: Process for pairing-model is terminated! cat: SRX3671143.05_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 `SRX3671143.05_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 `SRX3671143.05_*.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 `SRX3671143.05_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 09:53:13: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:53:13: 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, 05 Apr 2018 09:53:13: Process for pairing-model is terminated! cat: SRX3671143.20_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 `SRX3671143.20_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 `SRX3671143.20_*.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 `SRX3671143.20_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 09:53:16: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Apr 2018 09:53:19: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:53:19: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:53:19: #1 total tags in treatment: 17988143 INFO @ Thu, 05 Apr 2018 09:53:19: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:53:19: #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 09:53:19: #1 tags after filtering in treatment: 11280338 INFO @ Thu, 05 Apr 2018 09:53:19: #1 Redundant rate of treatment: 0.37 INFO @ Thu, 05 Apr 2018 09:53:19: #1 finished! INFO @ Thu, 05 Apr 2018 09:53:19: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:53:20: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 09:53:20: 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 09:53:20: Process for pairing-model is terminated! cat: SRX3671143.10_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 `SRX3671143.10_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 `SRX3671143.10_*.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 `SRX3671143.10_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。