Job ID = 9732058 sra ファイルのダウンロード中... Completed: 330320K bytes transferred in 11 seconds (236854K 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 15069997 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2675858/SRR5380635.sra Written 15069997 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: 00:07:42 15069997 reads; of these: 15069997 (100.00%) were paired; of these: 3645052 (24.19%) aligned concordantly 0 times 10013468 (66.45%) aligned concordantly exactly 1 time 1411477 (9.37%) aligned concordantly >1 times ---- 3645052 pairs aligned concordantly 0 times; of these: 678858 (18.62%) aligned discordantly 1 time ---- 2966194 pairs aligned 0 times concordantly or discordantly; of these: 5932388 mates make up the pairs; of these: 5281636 (89.03%) aligned 0 times 400557 (6.75%) aligned exactly 1 time 250195 (4.22%) aligned >1 times 82.48% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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] 2013245 / 11982353 = 0.1680 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 19:31:25: # Command line: callpeak -t SRX2675858.bam -f BAM -g 12100000 -n SRX2675858.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2675858.05 # format = BAM # ChIP-seq file = ['SRX2675858.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 19:31:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:31:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:31:25: # Command line: callpeak -t SRX2675858.bam -f BAM -g 12100000 -n SRX2675858.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2675858.10 # format = BAM # ChIP-seq file = ['SRX2675858.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 19:31:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:31:25: # Command line: callpeak -t SRX2675858.bam -f BAM -g 12100000 -n SRX2675858.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2675858.20 # format = BAM # ChIP-seq file = ['SRX2675858.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 19:31:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:31:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 19:31:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 19:31:31: 1000000 INFO @ Sun, 03 Sep 2017 19:31:31: 1000000 INFO @ Sun, 03 Sep 2017 19:31:31: 1000000 INFO @ Sun, 03 Sep 2017 19:31:36: 2000000 INFO @ Sun, 03 Sep 2017 19:31:37: 2000000 INFO @ Sun, 03 Sep 2017 19:31:37: 2000000 INFO @ Sun, 03 Sep 2017 19:31:41: 3000000 INFO @ Sun, 03 Sep 2017 19:31:43: 3000000 INFO @ Sun, 03 Sep 2017 19:31:43: 3000000 INFO @ Sun, 03 Sep 2017 19:31:46: 4000000 INFO @ Sun, 03 Sep 2017 19:31:48: 4000000 INFO @ Sun, 03 Sep 2017 19:31:49: 4000000 INFO @ Sun, 03 Sep 2017 19:31:52: 5000000 INFO @ Sun, 03 Sep 2017 19:31:54: 5000000 INFO @ Sun, 03 Sep 2017 19:31:55: 5000000 INFO @ Sun, 03 Sep 2017 19:31:57: 6000000 INFO @ Sun, 03 Sep 2017 19:32:00: 6000000 INFO @ Sun, 03 Sep 2017 19:32:01: 6000000 INFO @ Sun, 03 Sep 2017 19:32:02: 7000000 INFO @ Sun, 03 Sep 2017 19:32:06: 7000000 INFO @ Sun, 03 Sep 2017 19:32:07: 8000000 INFO @ Sun, 03 Sep 2017 19:32:07: 7000000 INFO @ Sun, 03 Sep 2017 19:32:12: 9000000 INFO @ Sun, 03 Sep 2017 19:32:12: 8000000 INFO @ Sun, 03 Sep 2017 19:32:13: 8000000 INFO @ Sun, 03 Sep 2017 19:32:17: 10000000 INFO @ Sun, 03 Sep 2017 19:32:18: 9000000 INFO @ Sun, 03 Sep 2017 19:32:20: 9000000 INFO @ Sun, 03 Sep 2017 19:32:22: 11000000 INFO @ Sun, 03 Sep 2017 19:32:25: 10000000 INFO @ Sun, 03 Sep 2017 19:32:26: 10000000 INFO @ Sun, 03 Sep 2017 19:32:28: 12000000 INFO @ Sun, 03 Sep 2017 19:32:31: 11000000 INFO @ Sun, 03 Sep 2017 19:32:32: 11000000 INFO @ Sun, 03 Sep 2017 19:32:33: 13000000 INFO @ Sun, 03 Sep 2017 19:32:37: 12000000 INFO @ Sun, 03 Sep 2017 19:32:38: 14000000 INFO @ Sun, 03 Sep 2017 19:32:38: 12000000 INFO @ Sun, 03 Sep 2017 19:32:43: 15000000 INFO @ Sun, 03 Sep 2017 19:32:43: 13000000 INFO @ Sun, 03 Sep 2017 19:32:44: 13000000 INFO @ Sun, 03 Sep 2017 19:32:48: 16000000 INFO @ Sun, 03 Sep 2017 19:32:49: 14000000 INFO @ Sun, 03 Sep 2017 19:32:50: 14000000 INFO @ Sun, 03 Sep 2017 19:32:53: 17000000 INFO @ Sun, 03 Sep 2017 19:32:55: 15000000 INFO @ Sun, 03 Sep 2017 19:32:57: 15000000 INFO @ Sun, 03 Sep 2017 19:32:58: 18000000 INFO @ Sun, 03 Sep 2017 19:33:01: 16000000 INFO @ Sun, 03 Sep 2017 19:33:03: 16000000 INFO @ Sun, 03 Sep 2017 19:33:04: 19000000 INFO @ Sun, 03 Sep 2017 19:33:07: 17000000 INFO @ Sun, 03 Sep 2017 19:33:09: 20000000 INFO @ Sun, 03 Sep 2017 19:33:10: 17000000 INFO @ Sun, 03 Sep 2017 19:33:12: 18000000 INFO @ Sun, 03 Sep 2017 19:33:14: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:33:14: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:33:14: #1 total tags in treatment: 9432179 INFO @ Sun, 03 Sep 2017 19:33:14: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:33:14: #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 19:33:14: #1 tags after filtering in treatment: 4383822 INFO @ Sun, 03 Sep 2017 19:33:14: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:33:14: #1 finished! INFO @ Sun, 03 Sep 2017 19:33:14: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:33:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:33:14: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:33:14: 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 19:33:14: Process for pairing-model is terminated! cat: SRX2675858.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675858.20_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 `SRX2675858.20_*.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 `SRX2675858.20_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 19:33:16: 18000000 INFO @ Sun, 03 Sep 2017 19:33:18: 19000000 INFO @ Sun, 03 Sep 2017 19:33:21: 19000000 INFO @ Sun, 03 Sep 2017 19:33:24: 20000000 INFO @ Sun, 03 Sep 2017 19:33:27: 20000000 INFO @ Sun, 03 Sep 2017 19:33:28: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:33:28: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:33:28: #1 total tags in treatment: 9432179 INFO @ Sun, 03 Sep 2017 19:33:28: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:33:28: #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 19:33:28: #1 tags after filtering in treatment: 4383822 INFO @ Sun, 03 Sep 2017 19:33:28: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:33:28: #1 finished! INFO @ Sun, 03 Sep 2017 19:33:28: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:33:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:33:29: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:33:29: 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 19:33:29: Process for pairing-model is terminated! cat: SRX2675858.05_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 `SRX2675858.05_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 `SRX2675858.05_*.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 `SRX2675858.05_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 19:33:32: #1 tag size is determined as 25 bps INFO @ Sun, 03 Sep 2017 19:33:32: #1 tag size = 25 INFO @ Sun, 03 Sep 2017 19:33:32: #1 total tags in treatment: 9432179 INFO @ Sun, 03 Sep 2017 19:33:32: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 19:33:32: #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 19:33:32: #1 tags after filtering in treatment: 4383822 INFO @ Sun, 03 Sep 2017 19:33:32: #1 Redundant rate of treatment: 0.54 INFO @ Sun, 03 Sep 2017 19:33:32: #1 finished! INFO @ Sun, 03 Sep 2017 19:33:32: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 19:33:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 19:33:32: #2 number of paired peaks: 0 WARNING @ Sun, 03 Sep 2017 19:33:32: 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 19:33:32: Process for pairing-model is terminated! cat: SRX2675858.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2675858.10_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 `SRX2675858.10_*.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 `SRX2675858.10_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。