Job ID = 9161970 sra ファイルのダウンロード中... Completed: 868236K bytes transferred in 11 seconds (638621K 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 14462524 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423702/SRR2930991.sra Written 14462524 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: 00:10:52 14462524 reads; of these: 14462524 (100.00%) were paired; of these: 1243147 (8.60%) aligned concordantly 0 times 11630655 (80.42%) aligned concordantly exactly 1 time 1588722 (10.99%) aligned concordantly >1 times ---- 1243147 pairs aligned concordantly 0 times; of these: 19754 (1.59%) aligned discordantly 1 time ---- 1223393 pairs aligned 0 times concordantly or discordantly; of these: 2446786 mates make up the pairs; of these: 2287918 (93.51%) aligned 0 times 127116 (5.20%) aligned exactly 1 time 31752 (1.30%) aligned >1 times 92.09% overall alignment rate Time searching: 00:10:52 Overall time: 00:10:52 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] 5174651 / 13221830 = 0.3914 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 05:25:26: # Command line: callpeak -t SRX1423702.bam -f BAM -g 12100000 -n SRX1423702.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423702.05 # format = BAM # ChIP-seq file = ['SRX1423702.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 05:25:26: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:25:26: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:25:26: # Command line: callpeak -t SRX1423702.bam -f BAM -g 12100000 -n SRX1423702.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423702.10 # format = BAM # ChIP-seq file = ['SRX1423702.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 05:25:26: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:25:26: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:25:26: # Command line: callpeak -t SRX1423702.bam -f BAM -g 12100000 -n SRX1423702.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423702.20 # format = BAM # ChIP-seq file = ['SRX1423702.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 05:25:26: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:25:26: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:25:32: 1000000 INFO @ Wed, 28 Jun 2017 05:25:32: 1000000 INFO @ Wed, 28 Jun 2017 05:25:32: 1000000 INFO @ Wed, 28 Jun 2017 05:25:38: 2000000 INFO @ Wed, 28 Jun 2017 05:25:39: 2000000 INFO @ Wed, 28 Jun 2017 05:25:39: 2000000 INFO @ Wed, 28 Jun 2017 05:25:44: 3000000 INFO @ Wed, 28 Jun 2017 05:25:45: 3000000 INFO @ Wed, 28 Jun 2017 05:25:45: 3000000 INFO @ Wed, 28 Jun 2017 05:25:49: 4000000 INFO @ Wed, 28 Jun 2017 05:25:51: 4000000 INFO @ Wed, 28 Jun 2017 05:25:51: 4000000 INFO @ Wed, 28 Jun 2017 05:25:55: 5000000 INFO @ Wed, 28 Jun 2017 05:25:57: 5000000 INFO @ Wed, 28 Jun 2017 05:25:57: 5000000 INFO @ Wed, 28 Jun 2017 05:26:00: 6000000 INFO @ Wed, 28 Jun 2017 05:26:03: 6000000 INFO @ Wed, 28 Jun 2017 05:26:03: 6000000 INFO @ Wed, 28 Jun 2017 05:26:06: 7000000 INFO @ Wed, 28 Jun 2017 05:26:09: 7000000 INFO @ Wed, 28 Jun 2017 05:26:09: 7000000 INFO @ Wed, 28 Jun 2017 05:26:12: 8000000 INFO @ Wed, 28 Jun 2017 05:26:15: 8000000 INFO @ Wed, 28 Jun 2017 05:26:15: 8000000 INFO @ Wed, 28 Jun 2017 05:26:18: 9000000 INFO @ Wed, 28 Jun 2017 05:26:21: 9000000 INFO @ Wed, 28 Jun 2017 05:26:21: 9000000 INFO @ Wed, 28 Jun 2017 05:26:24: 10000000 INFO @ Wed, 28 Jun 2017 05:26:26: 10000000 INFO @ Wed, 28 Jun 2017 05:26:27: 10000000 INFO @ Wed, 28 Jun 2017 05:26:30: 11000000 INFO @ Wed, 28 Jun 2017 05:26:32: 11000000 INFO @ Wed, 28 Jun 2017 05:26:33: 11000000 INFO @ Wed, 28 Jun 2017 05:26:36: 12000000 INFO @ Wed, 28 Jun 2017 05:26:37: 12000000 INFO @ Wed, 28 Jun 2017 05:26:39: 12000000 INFO @ Wed, 28 Jun 2017 05:26:42: 13000000 INFO @ Wed, 28 Jun 2017 05:26:43: 13000000 INFO @ Wed, 28 Jun 2017 05:26:46: 13000000 INFO @ Wed, 28 Jun 2017 05:26:48: 14000000 INFO @ Wed, 28 Jun 2017 05:26:48: 14000000 INFO @ Wed, 28 Jun 2017 05:26:52: 14000000 INFO @ Wed, 28 Jun 2017 05:26:53: 15000000 INFO @ Wed, 28 Jun 2017 05:26:54: 15000000 INFO @ Wed, 28 Jun 2017 05:26:58: 15000000 INFO @ Wed, 28 Jun 2017 05:26:59: 16000000 INFO @ Wed, 28 Jun 2017 05:27:00: 16000000 INFO @ Wed, 28 Jun 2017 05:27:01: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:27:01: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:27:01: #1 total tags in treatment: 8045345 INFO @ Wed, 28 Jun 2017 05:27:01: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:27:01: #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 05:27:01: #1 tags after filtering in treatment: 6331397 INFO @ Wed, 28 Jun 2017 05:27:01: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 28 Jun 2017 05:27:01: #1 finished! INFO @ Wed, 28 Jun 2017 05:27:01: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:27:01: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:27:01: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:27:01: #1 total tags in treatment: 8045345 INFO @ Wed, 28 Jun 2017 05:27:01: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:27:01: #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 05:27:02: #1 tags after filtering in treatment: 6331397 INFO @ Wed, 28 Jun 2017 05:27:02: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 28 Jun 2017 05:27:02: #1 finished! INFO @ Wed, 28 Jun 2017 05:27:02: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:27:02: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:27:02: 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 05:27:02: Process for pairing-model is terminated! cat: SRX1423702.10_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 `SRX1423702.10_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 `SRX1423702.10_*.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 `SRX1423702.10_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 05:27:02: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:27:02: 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 05:27:02: Process for pairing-model is terminated! cat: SRX1423702.20_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 `SRX1423702.20_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 `SRX1423702.20_*.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 `SRX1423702.20_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 @ Wed, 28 Jun 2017 05:27:03: 16000000 INFO @ Wed, 28 Jun 2017 05:27:05: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:27:05: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:27:05: #1 total tags in treatment: 8045345 INFO @ Wed, 28 Jun 2017 05:27:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:27:05: #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 05:27:05: #1 tags after filtering in treatment: 6331397 INFO @ Wed, 28 Jun 2017 05:27:05: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 28 Jun 2017 05:27:05: #1 finished! INFO @ Wed, 28 Jun 2017 05:27:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:27:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:27:06: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:27:06: 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 05:27:06: Process for pairing-model is terminated! cat: SRX1423702.05_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 `SRX1423702.05_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 `SRX1423702.05_*.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 `SRX1423702.05_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。