Job ID = 9161917 sra ファイルのダウンロード中... Completed: 1547053K bytes transferred in 18 seconds (673229K 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 12111607 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1406638/SRR2889258.sra Written 12111607 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: 00:11:16 12111607 reads; of these: 12111607 (100.00%) were paired; of these: 5575579 (46.04%) aligned concordantly 0 times 5413951 (44.70%) aligned concordantly exactly 1 time 1122077 (9.26%) aligned concordantly >1 times ---- 5575579 pairs aligned concordantly 0 times; of these: 192265 (3.45%) aligned discordantly 1 time ---- 5383314 pairs aligned 0 times concordantly or discordantly; of these: 10766628 mates make up the pairs; of these: 10308935 (95.75%) aligned 0 times 291053 (2.70%) aligned exactly 1 time 166640 (1.55%) aligned >1 times 57.44% overall alignment rate Time searching: 00:11:16 Overall time: 00:11:16 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] 208036 / 6693062 = 0.0311 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 @ Wed, 28 Jun 2017 05:16:53: # Command line: callpeak -t SRX1406638.bam -f BAM -g 12100000 -n SRX1406638.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1406638.05 # format = BAM # ChIP-seq file = ['SRX1406638.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 @ Wed, 28 Jun 2017 05:16:53: # Command line: callpeak -t SRX1406638.bam -f BAM -g 12100000 -n SRX1406638.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1406638.20 # format = BAM # ChIP-seq file = ['SRX1406638.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 @ Wed, 28 Jun 2017 05:16:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:16:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:16:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:16:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:16:53: # Command line: callpeak -t SRX1406638.bam -f BAM -g 12100000 -n SRX1406638.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1406638.10 # format = BAM # ChIP-seq file = ['SRX1406638.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 @ Wed, 28 Jun 2017 05:16:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:16:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:17:02: 1000000 INFO @ Wed, 28 Jun 2017 05:17:03: 1000000 INFO @ Wed, 28 Jun 2017 05:17:04: 1000000 INFO @ Wed, 28 Jun 2017 05:17:12: 2000000 INFO @ Wed, 28 Jun 2017 05:17:13: 2000000 INFO @ Wed, 28 Jun 2017 05:17:14: 2000000 INFO @ Wed, 28 Jun 2017 05:17:21: 3000000 INFO @ Wed, 28 Jun 2017 05:17:23: 3000000 INFO @ Wed, 28 Jun 2017 05:17:25: 3000000 INFO @ Wed, 28 Jun 2017 05:17:30: 4000000 INFO @ Wed, 28 Jun 2017 05:17:33: 4000000 INFO @ Wed, 28 Jun 2017 05:17:36: 4000000 INFO @ Wed, 28 Jun 2017 05:17:40: 5000000 INFO @ Wed, 28 Jun 2017 05:17:43: 5000000 INFO @ Wed, 28 Jun 2017 05:17:46: 5000000 INFO @ Wed, 28 Jun 2017 05:17:49: 6000000 INFO @ Wed, 28 Jun 2017 05:17:53: 6000000 INFO @ Wed, 28 Jun 2017 05:17:56: 6000000 INFO @ Wed, 28 Jun 2017 05:17:58: 7000000 INFO @ Wed, 28 Jun 2017 05:18:03: 7000000 INFO @ Wed, 28 Jun 2017 05:18:07: 8000000 INFO @ Wed, 28 Jun 2017 05:18:07: 7000000 INFO @ Wed, 28 Jun 2017 05:18:13: 8000000 INFO @ Wed, 28 Jun 2017 05:18:16: 9000000 INFO @ Wed, 28 Jun 2017 05:18:17: 8000000 INFO @ Wed, 28 Jun 2017 05:18:23: 9000000 INFO @ Wed, 28 Jun 2017 05:18:25: 10000000 INFO @ Wed, 28 Jun 2017 05:18:28: 9000000 INFO @ Wed, 28 Jun 2017 05:18:33: 10000000 INFO @ Wed, 28 Jun 2017 05:18:34: 11000000 INFO @ Wed, 28 Jun 2017 05:18:38: 10000000 INFO @ Wed, 28 Jun 2017 05:18:43: 11000000 INFO @ Wed, 28 Jun 2017 05:18:43: 12000000 INFO @ Wed, 28 Jun 2017 05:18:49: 11000000 INFO @ Wed, 28 Jun 2017 05:18:52: 13000000 INFO @ Wed, 28 Jun 2017 05:18:53: 12000000 INFO @ Wed, 28 Jun 2017 05:18:57: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:18:57: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:18:57: #1 total tags in treatment: 6329980 INFO @ Wed, 28 Jun 2017 05:18:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:18:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:18:57: #1 tags after filtering in treatment: 4938180 INFO @ Wed, 28 Jun 2017 05:18:57: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 28 Jun 2017 05:18:57: #1 finished! INFO @ Wed, 28 Jun 2017 05:18:57: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:18:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:18:57: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:18:57: 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 @ Wed, 28 Jun 2017 05:18:57: Process for pairing-model is terminated! cat: SRX1406638.05_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1406638.05_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 `SRX1406638.05_*.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 `SRX1406638.05_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 @ Wed, 28 Jun 2017 05:19:00: 12000000 INFO @ Wed, 28 Jun 2017 05:19:03: 13000000 INFO @ Wed, 28 Jun 2017 05:19:08: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:19:08: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:19:08: #1 total tags in treatment: 6329980 INFO @ Wed, 28 Jun 2017 05:19:08: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:19:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:19:08: #1 tags after filtering in treatment: 4938180 INFO @ Wed, 28 Jun 2017 05:19:08: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 28 Jun 2017 05:19:08: #1 finished! INFO @ Wed, 28 Jun 2017 05:19:08: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:19:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:19:08: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:19:08: 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 @ Wed, 28 Jun 2017 05:19:08: Process for pairing-model is terminated! cat: SRX1406638.10_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 `SRX1406638.10_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 `SRX1406638.10_*.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 `SRX1406638.10_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 @ Wed, 28 Jun 2017 05:19:09: 13000000 INFO @ Wed, 28 Jun 2017 05:19:14: #1 tag size is determined as 100 bps INFO @ Wed, 28 Jun 2017 05:19:14: #1 tag size = 100 INFO @ Wed, 28 Jun 2017 05:19:14: #1 total tags in treatment: 6329980 INFO @ Wed, 28 Jun 2017 05:19:14: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:19:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:19:14: #1 tags after filtering in treatment: 4938180 INFO @ Wed, 28 Jun 2017 05:19:14: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 28 Jun 2017 05:19:14: #1 finished! INFO @ Wed, 28 Jun 2017 05:19:14: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:19:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:19:14: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:19:14: 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 @ Wed, 28 Jun 2017 05:19:14: Process for pairing-model is terminated! cat: SRX1406638.20_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 `SRX1406638.20_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 `SRX1406638.20_*.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 `SRX1406638.20_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。