Job ID = 9732096 sra ファイルのダウンロード中... Completed: 327439K bytes transferred in 9 seconds (271091K 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 13993778 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675887/SRR5380663.sra Written 13993778 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: 00:06:11 13993778 reads; of these: 13993778 (100.00%) were paired; of these: 3249433 (23.22%) aligned concordantly 0 times 9792769 (69.98%) aligned concordantly exactly 1 time 951576 (6.80%) aligned concordantly >1 times ---- 3249433 pairs aligned concordantly 0 times; of these: 698620 (21.50%) aligned discordantly 1 time ---- 2550813 pairs aligned 0 times concordantly or discordantly; of these: 5101626 mates make up the pairs; of these: 4566441 (89.51%) aligned 0 times 355490 (6.97%) aligned exactly 1 time 179695 (3.52%) aligned >1 times 83.68% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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 8 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] 1432990 / 11395324 = 0.1258 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 19:43:54: # Command line: callpeak -t SRX2675887.bam -f BAM -g 12100000 -n SRX2675887.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675887.10 # format = BAM # ChIP-seq file = ['SRX2675887.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 19:43:54: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:54: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:54: # Command line: callpeak -t SRX2675887.bam -f BAM -g 12100000 -n SRX2675887.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675887.05 # format = BAM # ChIP-seq file = ['SRX2675887.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 19:43:54: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:54: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:54: # Command line: callpeak -t SRX2675887.bam -f BAM -g 12100000 -n SRX2675887.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675887.20 # format = BAM # ChIP-seq file = ['SRX2675887.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 19:43:54: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:43:54: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:43:59: 1000000 INFO @ Sun, 03 Sep 2017 19:44:00: 1000000 INFO @ Sun, 03 Sep 2017 19:44:00: 1000000 INFO @ Sun, 03 Sep 2017 19:44:05: 2000000 INFO @ Sun, 03 Sep 2017 19:44:05: 2000000 INFO @ Sun, 03 Sep 2017 19:44:06: 2000000 INFO @ Sun, 03 Sep 2017 19:44:10: 3000000 INFO @ Sun, 03 Sep 2017 19:44:11: 3000000 INFO @ Sun, 03 Sep 2017 19:44:12: 3000000 INFO @ Sun, 03 Sep 2017 19:44:16: 4000000 INFO @ Sun, 03 Sep 2017 19:44:16: 4000000 INFO @ Sun, 03 Sep 2017 19:44:18: 4000000 INFO @ Sun, 03 Sep 2017 19:44:21: 5000000 INFO @ Sun, 03 Sep 2017 19:44:22: 5000000 INFO @ Sun, 03 Sep 2017 19:44:24: 5000000 INFO @ Sun, 03 Sep 2017 19:44:27: 6000000 INFO @ Sun, 03 Sep 2017 19:44:27: 6000000 INFO @ Sun, 03 Sep 2017 19:44:29: 6000000 INFO @ Sun, 03 Sep 2017 19:44:32: 7000000 INFO @ Sun, 03 Sep 2017 19:44:33: 7000000 INFO @ Sun, 03 Sep 2017 19:44:35: 7000000 INFO @ Sun, 03 Sep 2017 19:44:38: 8000000 INFO @ Sun, 03 Sep 2017 19:44:38: 8000000 INFO @ Sun, 03 Sep 2017 19:44:41: 8000000 INFO @ Sun, 03 Sep 2017 19:44:43: 9000000 INFO @ Sun, 03 Sep 2017 19:44:44: 9000000 INFO @ Sun, 03 Sep 2017 19:44:47: 9000000 INFO @ Sun, 03 Sep 2017 19:44:49: 10000000 INFO @ Sun, 03 Sep 2017 19:44:49: 10000000 INFO @ Sun, 03 Sep 2017 19:44:53: 10000000 INFO @ Sun, 03 Sep 2017 19:44:55: 11000000 INFO @ Sun, 03 Sep 2017 19:44:55: 11000000 INFO @ Sun, 03 Sep 2017 19:44:58: 11000000 INFO @ Sun, 03 Sep 2017 19:45:00: 12000000 INFO @ Sun, 03 Sep 2017 19:45:00: 12000000 INFO @ Sun, 03 Sep 2017 19:45:04: 12000000 INFO @ Sun, 03 Sep 2017 19:45:05: 13000000 INFO @ Sun, 03 Sep 2017 19:45:06: 13000000 INFO @ Sun, 03 Sep 2017 19:45:10: 13000000 INFO @ Sun, 03 Sep 2017 19:45:11: 14000000 INFO @ Sun, 03 Sep 2017 19:45:12: 14000000 INFO @ Sun, 03 Sep 2017 19:45:16: 14000000 INFO @ Sun, 03 Sep 2017 19:45:16: 15000000 INFO @ Sun, 03 Sep 2017 19:45:17: 15000000 INFO @ Sun, 03 Sep 2017 19:45:21: 16000000 INFO @ Sun, 03 Sep 2017 19:45:21: 15000000 INFO @ Sun, 03 Sep 2017 19:45:23: 16000000 INFO @ Sun, 03 Sep 2017 19:45:26: 17000000 INFO @ Sun, 03 Sep 2017 19:45:27: 16000000 INFO @ Sun, 03 Sep 2017 19:45:28: 17000000 INFO @ Sun, 03 Sep 2017 19:45:31: 18000000 INFO @ Sun, 03 Sep 2017 19:45:33: 17000000 INFO @ Sun, 03 Sep 2017 19:45:34: 18000000 INFO @ Sun, 03 Sep 2017 19:45:37: 19000000 INFO @ Sun, 03 Sep 2017 19:45:39: 18000000 INFO @ Sun, 03 Sep 2017 19:45:40: 19000000 INFO @ Sun, 03 Sep 2017 19:45:42: 20000000 INFO @ Sun, 03 Sep 2017 19:45:44: 19000000 INFO @ Sun, 03 Sep 2017 19:45:45: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:45: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:45: #1 total tags in treatment: 9325865 INFO @ Sun, 03 Sep 2017 19:45:45: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:45: #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 19:45:45: #1 tags after filtering in treatment: 4319269 INFO @ Sun, 03 Sep 2017 19:45:45: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:45:45: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:45: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:45: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:45: 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 @ Sun, 03 Sep 2017 19:45:45: Process for pairing-model is terminated! cat: SRX2675887.10_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): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675887.10_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 `SRX2675887.10_*.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 `SRX2675887.10_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 INFO @ Sun, 03 Sep 2017 19:45:45: 20000000 INFO @ Sun, 03 Sep 2017 19:45:49: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:49: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:49: #1 total tags in treatment: 9325865 INFO @ Sun, 03 Sep 2017 19:45:49: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:49: #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 19:45:49: #1 tags after filtering in treatment: 4319269 INFO @ Sun, 03 Sep 2017 19:45:49: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:45:49: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:49: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:49: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:49: 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 19:45:49: Process for pairing-model is terminated! cat: SRX2675887.05_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 `SRX2675887.05_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 `SRX2675887.05_*.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 `SRX2675887.05_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 @ Sun, 03 Sep 2017 19:45:50: 20000000 INFO @ Sun, 03 Sep 2017 19:45:53: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:45:53: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:45:53: #1 total tags in treatment: 9325865 INFO @ Sun, 03 Sep 2017 19:45:53: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:45:53: #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 19:45:53: #1 tags after filtering in treatment: 4319269 INFO @ Sun, 03 Sep 2017 19:45:53: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:45:53: #1 finished! INFO @ Sun, 03 Sep 2017 19:45:53: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:45:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:45:53: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:45:53: 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 19:45:53: Process for pairing-model is terminated! cat: SRX2675887.20_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): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675887.20_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 `SRX2675887.20_*.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 `SRX2675887.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。