Job ID = 10536497 sra ファイルのダウンロード中... Completed: 1144607K bytes transferred in 19 seconds (483328K 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 27406758 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671193/SRR6696945.sra Written 27406758 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: 00:19:09 27406758 reads; of these: 27406758 (100.00%) were paired; of these: 5142738 (18.76%) aligned concordantly 0 times 19543011 (71.31%) aligned concordantly exactly 1 time 2721009 (9.93%) aligned concordantly >1 times ---- 5142738 pairs aligned concordantly 0 times; of these: 172118 (3.35%) aligned discordantly 1 time ---- 4970620 pairs aligned 0 times concordantly or discordantly; of these: 9941240 mates make up the pairs; of these: 9769330 (98.27%) aligned 0 times 83319 (0.84%) aligned exactly 1 time 88591 (0.89%) aligned >1 times 82.18% overall alignment rate Time searching: 00:19:09 Overall time: 00:19:09 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] 5520644 / 22384506 = 0.2466 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 10:18:45: # Command line: callpeak -t SRX3671193.bam -f BAM -g 12100000 -n SRX3671193.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671193.10 # format = BAM # ChIP-seq file = ['SRX3671193.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 10:18:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:18:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:18:45: # Command line: callpeak -t SRX3671193.bam -f BAM -g 12100000 -n SRX3671193.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671193.20 # format = BAM # ChIP-seq file = ['SRX3671193.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 10:18:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:18:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:18:45: # Command line: callpeak -t SRX3671193.bam -f BAM -g 12100000 -n SRX3671193.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671193.05 # format = BAM # ChIP-seq file = ['SRX3671193.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 10:18:45: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:18:45: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:18:51: 1000000 INFO @ Thu, 05 Apr 2018 10:18:51: 1000000 INFO @ Thu, 05 Apr 2018 10:18:51: 1000000 INFO @ Thu, 05 Apr 2018 10:18:56: 2000000 INFO @ Thu, 05 Apr 2018 10:18:56: 2000000 INFO @ Thu, 05 Apr 2018 10:18:56: 2000000 INFO @ Thu, 05 Apr 2018 10:19:01: 3000000 INFO @ Thu, 05 Apr 2018 10:19:01: 3000000 INFO @ Thu, 05 Apr 2018 10:19:01: 3000000 INFO @ Thu, 05 Apr 2018 10:19:06: 4000000 INFO @ Thu, 05 Apr 2018 10:19:06: 4000000 INFO @ Thu, 05 Apr 2018 10:19:06: 4000000 INFO @ Thu, 05 Apr 2018 10:19:11: 5000000 INFO @ Thu, 05 Apr 2018 10:19:11: 5000000 INFO @ Thu, 05 Apr 2018 10:19:12: 5000000 INFO @ Thu, 05 Apr 2018 10:19:16: 6000000 INFO @ Thu, 05 Apr 2018 10:19:16: 6000000 INFO @ Thu, 05 Apr 2018 10:19:17: 6000000 INFO @ Thu, 05 Apr 2018 10:19:21: 7000000 INFO @ Thu, 05 Apr 2018 10:19:22: 7000000 INFO @ Thu, 05 Apr 2018 10:19:22: 7000000 INFO @ Thu, 05 Apr 2018 10:19:27: 8000000 INFO @ Thu, 05 Apr 2018 10:19:27: 8000000 INFO @ Thu, 05 Apr 2018 10:19:27: 8000000 INFO @ Thu, 05 Apr 2018 10:19:32: 9000000 INFO @ Thu, 05 Apr 2018 10:19:32: 9000000 INFO @ Thu, 05 Apr 2018 10:19:33: 9000000 INFO @ Thu, 05 Apr 2018 10:19:37: 10000000 INFO @ Thu, 05 Apr 2018 10:19:38: 10000000 INFO @ Thu, 05 Apr 2018 10:19:38: 10000000 INFO @ Thu, 05 Apr 2018 10:19:42: 11000000 INFO @ Thu, 05 Apr 2018 10:19:43: 11000000 INFO @ Thu, 05 Apr 2018 10:19:43: 11000000 INFO @ Thu, 05 Apr 2018 10:19:48: 12000000 INFO @ Thu, 05 Apr 2018 10:19:48: 12000000 INFO @ Thu, 05 Apr 2018 10:19:49: 12000000 INFO @ Thu, 05 Apr 2018 10:19:53: 13000000 INFO @ Thu, 05 Apr 2018 10:19:54: 13000000 INFO @ Thu, 05 Apr 2018 10:19:54: 13000000 INFO @ Thu, 05 Apr 2018 10:19:58: 14000000 INFO @ Thu, 05 Apr 2018 10:19:59: 14000000 INFO @ Thu, 05 Apr 2018 10:19:59: 14000000 INFO @ Thu, 05 Apr 2018 10:20:03: 15000000 INFO @ Thu, 05 Apr 2018 10:20:04: 15000000 INFO @ Thu, 05 Apr 2018 10:20:05: 15000000 INFO @ Thu, 05 Apr 2018 10:20:09: 16000000 INFO @ Thu, 05 Apr 2018 10:20:09: 16000000 INFO @ Thu, 05 Apr 2018 10:20:10: 16000000 INFO @ Thu, 05 Apr 2018 10:20:14: 17000000 INFO @ Thu, 05 Apr 2018 10:20:15: 17000000 INFO @ Thu, 05 Apr 2018 10:20:15: 17000000 INFO @ Thu, 05 Apr 2018 10:20:19: 18000000 INFO @ Thu, 05 Apr 2018 10:20:20: 18000000 INFO @ Thu, 05 Apr 2018 10:20:21: 18000000 INFO @ Thu, 05 Apr 2018 10:20:25: 19000000 INFO @ Thu, 05 Apr 2018 10:20:25: 19000000 INFO @ Thu, 05 Apr 2018 10:20:26: 19000000 INFO @ Thu, 05 Apr 2018 10:20:30: 20000000 INFO @ Thu, 05 Apr 2018 10:20:30: 20000000 INFO @ Thu, 05 Apr 2018 10:20:31: 20000000 INFO @ Thu, 05 Apr 2018 10:20:35: 21000000 INFO @ Thu, 05 Apr 2018 10:20:35: 21000000 INFO @ Thu, 05 Apr 2018 10:20:37: 21000000 INFO @ Thu, 05 Apr 2018 10:20:41: 22000000 INFO @ Thu, 05 Apr 2018 10:20:41: 22000000 INFO @ Thu, 05 Apr 2018 10:20:42: 22000000 INFO @ Thu, 05 Apr 2018 10:20:46: 23000000 INFO @ Thu, 05 Apr 2018 10:20:46: 23000000 INFO @ Thu, 05 Apr 2018 10:20:47: 23000000 INFO @ Thu, 05 Apr 2018 10:20:51: 24000000 INFO @ Thu, 05 Apr 2018 10:20:52: 24000000 INFO @ Thu, 05 Apr 2018 10:20:53: 24000000 INFO @ Thu, 05 Apr 2018 10:20:56: 25000000 INFO @ Thu, 05 Apr 2018 10:20:57: 25000000 INFO @ Thu, 05 Apr 2018 10:20:58: 25000000 INFO @ Thu, 05 Apr 2018 10:21:02: 26000000 INFO @ Thu, 05 Apr 2018 10:21:02: 26000000 INFO @ Thu, 05 Apr 2018 10:21:03: 26000000 INFO @ Thu, 05 Apr 2018 10:21:07: 27000000 INFO @ Thu, 05 Apr 2018 10:21:08: 27000000 INFO @ Thu, 05 Apr 2018 10:21:09: 27000000 INFO @ Thu, 05 Apr 2018 10:21:12: 28000000 INFO @ Thu, 05 Apr 2018 10:21:13: 28000000 INFO @ Thu, 05 Apr 2018 10:21:14: 28000000 INFO @ Thu, 05 Apr 2018 10:21:17: 29000000 INFO @ Thu, 05 Apr 2018 10:21:18: 29000000 INFO @ Thu, 05 Apr 2018 10:21:19: 29000000 INFO @ Thu, 05 Apr 2018 10:21:22: 30000000 INFO @ Thu, 05 Apr 2018 10:21:23: 30000000 INFO @ Thu, 05 Apr 2018 10:21:25: 30000000 INFO @ Thu, 05 Apr 2018 10:21:27: 31000000 INFO @ Thu, 05 Apr 2018 10:21:29: 31000000 INFO @ Thu, 05 Apr 2018 10:21:30: 31000000 INFO @ Thu, 05 Apr 2018 10:21:32: 32000000 INFO @ Thu, 05 Apr 2018 10:21:34: 32000000 INFO @ Thu, 05 Apr 2018 10:21:35: 32000000 INFO @ Thu, 05 Apr 2018 10:21:38: 33000000 INFO @ Thu, 05 Apr 2018 10:21:39: 33000000 INFO @ Thu, 05 Apr 2018 10:21:41: 33000000 INFO @ Thu, 05 Apr 2018 10:21:43: 34000000 INFO @ Thu, 05 Apr 2018 10:21:43: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:21:43: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:21:43: #1 total tags in treatment: 16782586 INFO @ Thu, 05 Apr 2018 10:21:43: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:21:43: #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 10:21:43: #1 tags after filtering in treatment: 6671883 INFO @ Thu, 05 Apr 2018 10:21:43: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:21:43: #1 finished! INFO @ Thu, 05 Apr 2018 10:21:43: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:21:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:21:44: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:21:44: 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 10:21:44: Process for pairing-model is terminated! cat: SRX3671193.20_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 `SRX3671193.20_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 `SRX3671193.20_*.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 `SRX3671193.20_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 10:21:44: 34000000 INFO @ Thu, 05 Apr 2018 10:21:45: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:21:45: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:21:45: #1 total tags in treatment: 16782586 INFO @ Thu, 05 Apr 2018 10:21:45: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:21:45: #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 10:21:45: #1 tags after filtering in treatment: 6671883 INFO @ Thu, 05 Apr 2018 10:21:45: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:21:45: #1 finished! INFO @ Thu, 05 Apr 2018 10:21:45: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:21:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:21:45: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:21:45: 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 10:21:45: Process for pairing-model is terminated! cat: SRX3671193.05_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 `SRX3671193.05_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 `SRX3671193.05_*.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 `SRX3671193.05_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 10:21:46: 34000000 INFO @ Thu, 05 Apr 2018 10:21:46: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:21:46: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:21:46: #1 total tags in treatment: 16782586 INFO @ Thu, 05 Apr 2018 10:21:46: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:21:46: #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 10:21:46: #1 tags after filtering in treatment: 6671883 INFO @ Thu, 05 Apr 2018 10:21:46: #1 Redundant rate of treatment: 0.60 INFO @ Thu, 05 Apr 2018 10:21:46: #1 finished! INFO @ Thu, 05 Apr 2018 10:21:46: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:21:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:21:47: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:21:47: 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 10:21:47: Process for pairing-model is terminated! cat: SRX3671193.10_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 `SRX3671193.10_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 `SRX3671193.10_*.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 `SRX3671193.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。