Job ID = 9732086 sra ファイルのダウンロード中... Completed: 500225K bytes transferred in 13 seconds (293608K bits/sec), in 1 file, 2 directories. 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 21581612 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675876/SRR5380652.sra Written 21581612 spots total 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: 00:09:37 21581612 reads; of these: 21581612 (100.00%) were paired; of these: 6103734 (28.28%) aligned concordantly 0 times 13412615 (62.15%) aligned concordantly exactly 1 time 2065263 (9.57%) aligned concordantly >1 times ---- 6103734 pairs aligned concordantly 0 times; of these: 812348 (13.31%) aligned discordantly 1 time ---- 5291386 pairs aligned 0 times concordantly or discordantly; of these: 10582772 mates make up the pairs; of these: 9462316 (89.41%) aligned 0 times 722771 (6.83%) aligned exactly 1 time 397685 (3.76%) aligned >1 times 78.08% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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 12 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] 2687561 / 15864297 = 0.1694 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 @ Sun, 03 Sep 2017 19:43:04: # Command line: callpeak -t SRX2675876.bam -f BAM -g 12100000 -n SRX2675876.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675876.20 # format = BAM # ChIP-seq file = ['SRX2675876.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 @ Sun, 03 Sep 2017 19:43:04: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:04: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:04: # Command line: callpeak -t SRX2675876.bam -f BAM -g 12100000 -n SRX2675876.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675876.05 # format = BAM # ChIP-seq file = ['SRX2675876.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 @ Sun, 03 Sep 2017 19:43:04: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:04: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:04: # Command line: callpeak -t SRX2675876.bam -f BAM -g 12100000 -n SRX2675876.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675876.10 # format = BAM # ChIP-seq file = ['SRX2675876.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 @ Sun, 03 Sep 2017 19:43:04: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:04: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:09: 1000000 INFO @ Sun, 03 Sep 2017 19:43:09: 1000000 INFO @ Sun, 03 Sep 2017 19:43:09: 1000000 INFO @ Sun, 03 Sep 2017 19:43:13: 2000000 INFO @ Sun, 03 Sep 2017 19:43:13: 2000000 INFO @ Sun, 03 Sep 2017 19:43:13: 2000000 INFO @ Sun, 03 Sep 2017 19:43:18: 3000000 INFO @ Sun, 03 Sep 2017 19:43:18: 3000000 INFO @ Sun, 03 Sep 2017 19:43:18: 3000000 INFO @ Sun, 03 Sep 2017 19:43:22: 4000000 INFO @ Sun, 03 Sep 2017 19:43:22: 4000000 INFO @ Sun, 03 Sep 2017 19:43:23: 4000000 INFO @ Sun, 03 Sep 2017 19:43:27: 5000000 INFO @ Sun, 03 Sep 2017 19:43:27: 5000000 INFO @ Sun, 03 Sep 2017 19:43:27: 5000000 INFO @ Sun, 03 Sep 2017 19:43:31: 6000000 INFO @ Sun, 03 Sep 2017 19:43:32: 6000000 INFO @ Sun, 03 Sep 2017 19:43:32: 6000000 INFO @ Sun, 03 Sep 2017 19:43:36: 7000000 INFO @ Sun, 03 Sep 2017 19:43:36: 7000000 INFO @ Sun, 03 Sep 2017 19:43:37: 7000000 INFO @ Sun, 03 Sep 2017 19:43:41: 8000000 INFO @ Sun, 03 Sep 2017 19:43:41: 8000000 INFO @ Sun, 03 Sep 2017 19:43:41: 8000000 INFO @ Sun, 03 Sep 2017 19:43:45: 9000000 INFO @ Sun, 03 Sep 2017 19:43:45: 9000000 INFO @ Sun, 03 Sep 2017 19:43:46: 9000000 INFO @ Sun, 03 Sep 2017 19:43:50: 10000000 INFO @ Sun, 03 Sep 2017 19:43:50: 10000000 INFO @ Sun, 03 Sep 2017 19:43:50: 10000000 INFO @ Sun, 03 Sep 2017 19:43:54: 11000000 INFO @ Sun, 03 Sep 2017 19:43:54: 11000000 INFO @ Sun, 03 Sep 2017 19:43:55: 11000000 INFO @ Sun, 03 Sep 2017 19:43:59: 12000000 INFO @ Sun, 03 Sep 2017 19:43:59: 12000000 INFO @ Sun, 03 Sep 2017 19:43:59: 12000000 INFO @ Sun, 03 Sep 2017 19:44:03: 13000000 INFO @ Sun, 03 Sep 2017 19:44:03: 13000000 INFO @ Sun, 03 Sep 2017 19:44:04: 13000000 INFO @ Sun, 03 Sep 2017 19:44:08: 14000000 INFO @ Sun, 03 Sep 2017 19:44:08: 14000000 INFO @ Sun, 03 Sep 2017 19:44:08: 14000000 INFO @ Sun, 03 Sep 2017 19:44:12: 15000000 INFO @ Sun, 03 Sep 2017 19:44:12: 15000000 INFO @ Sun, 03 Sep 2017 19:44:13: 15000000 INFO @ Sun, 03 Sep 2017 19:44:17: 16000000 INFO @ Sun, 03 Sep 2017 19:44:17: 16000000 INFO @ Sun, 03 Sep 2017 19:44:18: 16000000 INFO @ Sun, 03 Sep 2017 19:44:21: 17000000 INFO @ Sun, 03 Sep 2017 19:44:21: 17000000 INFO @ Sun, 03 Sep 2017 19:44:22: 17000000 INFO @ Sun, 03 Sep 2017 19:44:26: 18000000 INFO @ Sun, 03 Sep 2017 19:44:26: 18000000 INFO @ Sun, 03 Sep 2017 19:44:27: 18000000 INFO @ Sun, 03 Sep 2017 19:44:30: 19000000 INFO @ Sun, 03 Sep 2017 19:44:30: 19000000 INFO @ Sun, 03 Sep 2017 19:44:31: 19000000 INFO @ Sun, 03 Sep 2017 19:44:34: 20000000 INFO @ Sun, 03 Sep 2017 19:44:35: 20000000 INFO @ Sun, 03 Sep 2017 19:44:36: 20000000 INFO @ Sun, 03 Sep 2017 19:44:39: 21000000 INFO @ Sun, 03 Sep 2017 19:44:39: 21000000 INFO @ Sun, 03 Sep 2017 19:44:40: 21000000 INFO @ Sun, 03 Sep 2017 19:44:43: 22000000 INFO @ Sun, 03 Sep 2017 19:44:44: 22000000 INFO @ Sun, 03 Sep 2017 19:44:45: 22000000 INFO @ Sun, 03 Sep 2017 19:44:48: 23000000 INFO @ Sun, 03 Sep 2017 19:44:48: 23000000 INFO @ Sun, 03 Sep 2017 19:44:49: 23000000 INFO @ Sun, 03 Sep 2017 19:44:52: 24000000 INFO @ Sun, 03 Sep 2017 19:44:53: 24000000 INFO @ Sun, 03 Sep 2017 19:44:54: 24000000 INFO @ Sun, 03 Sep 2017 19:44:57: 25000000 INFO @ Sun, 03 Sep 2017 19:44:57: 25000000 INFO @ Sun, 03 Sep 2017 19:44:58: 25000000 INFO @ Sun, 03 Sep 2017 19:45:01: 26000000 INFO @ Sun, 03 Sep 2017 19:45:01: 26000000 INFO @ Sun, 03 Sep 2017 19:45:03: 26000000 INFO @ Sun, 03 Sep 2017 19:45:06: 27000000 INFO @ Sun, 03 Sep 2017 19:45:06: 27000000 INFO @ Sun, 03 Sep 2017 19:45:07: 27000000 INFO @ Sun, 03 Sep 2017 19:45:10: 28000000 INFO @ Sun, 03 Sep 2017 19:45:10: 28000000 INFO @ Sun, 03 Sep 2017 19:45:12: 28000000 INFO @ Sun, 03 Sep 2017 19:45:12: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:12: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:12: #1 total tags in treatment: 12796237 INFO @ Sun, 03 Sep 2017 19:45:12: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:45:12: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:12: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:12: #1 total tags in treatment: 12796237 INFO @ Sun, 03 Sep 2017 19:45:12: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:45:12: #1 tags after filtering in treatment: 5647378 INFO @ Sun, 03 Sep 2017 19:45:12: #1 Redundant rate of treatment: 0.56 INFO @ Sun, 03 Sep 2017 19:45:12: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:12: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:12: #1 tags after filtering in treatment: 5647378 INFO @ Sun, 03 Sep 2017 19:45:12: #1 Redundant rate of treatment: 0.56 INFO @ Sun, 03 Sep 2017 19:45:12: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:12: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:13: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:13: 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 @ Sun, 03 Sep 2017 19:45:13: Process for pairing-model is terminated! cat: SRX2675876.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Sun, 03 Sep 2017 19:45:13: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:13: 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 @ Sun, 03 Sep 2017 19:45:13: Process for pairing-model is terminated! cat: SRX2675876.20_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): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675876.10_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 `SRX2675876.10_*.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 `SRX2675876.10_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 pass1 - making usageList (0 chroms): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675876.20_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 `SRX2675876.20_*.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 `SRX2675876.20_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 @ Sun, 03 Sep 2017 19:45:14: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:14: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:14: #1 total tags in treatment: 12796237 INFO @ Sun, 03 Sep 2017 19:45:14: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 19:45:14: #1 tags after filtering in treatment: 5647378 INFO @ Sun, 03 Sep 2017 19:45:14: #1 Redundant rate of treatment: 0.56 INFO @ Sun, 03 Sep 2017 19:45:14: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:14: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:14: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:14: 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 @ Sun, 03 Sep 2017 19:45:14: Process for pairing-model is terminated! cat: SRX2675876.05_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): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675876.05_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 `SRX2675876.05_*.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 `SRX2675876.05_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。