Job ID = 9162105 sra ファイルのダウンロード中... Completed: 1561036K bytes transferred in 13 seconds (948899K 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 31807019 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1631843/SRR3225779.sra Written 31807019 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: 00:19:53 31807019 reads; of these: 31807019 (100.00%) were paired; of these: 12035871 (37.84%) aligned concordantly 0 times 17613947 (55.38%) aligned concordantly exactly 1 time 2157201 (6.78%) aligned concordantly >1 times ---- 12035871 pairs aligned concordantly 0 times; of these: 443660 (3.69%) aligned discordantly 1 time ---- 11592211 pairs aligned 0 times concordantly or discordantly; of these: 23184422 mates make up the pairs; of these: 22789646 (98.30%) aligned 0 times 232984 (1.00%) aligned exactly 1 time 161792 (0.70%) aligned >1 times 64.18% overall alignment rate Time searching: 00:19:53 Overall time: 00:19:53 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 20 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] 11231065 / 20206436 = 0.5558 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 06:24:11: # Command line: callpeak -t SRX1631843.bam -f BAM -g 12100000 -n SRX1631843.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1631843.20 # format = BAM # ChIP-seq file = ['SRX1631843.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 06:24:11: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:24:11: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:24:11: # Command line: callpeak -t SRX1631843.bam -f BAM -g 12100000 -n SRX1631843.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1631843.05 # format = BAM # ChIP-seq file = ['SRX1631843.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 06:24:11: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:24:11: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:24:11: # Command line: callpeak -t SRX1631843.bam -f BAM -g 12100000 -n SRX1631843.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1631843.10 # format = BAM # ChIP-seq file = ['SRX1631843.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 06:24:11: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:24:11: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:24:16: 1000000 INFO @ Wed, 28 Jun 2017 06:24:17: 1000000 INFO @ Wed, 28 Jun 2017 06:24:17: 1000000 INFO @ Wed, 28 Jun 2017 06:24:22: 2000000 INFO @ Wed, 28 Jun 2017 06:24:22: 2000000 INFO @ Wed, 28 Jun 2017 06:24:22: 2000000 INFO @ Wed, 28 Jun 2017 06:24:28: 3000000 INFO @ Wed, 28 Jun 2017 06:24:28: 3000000 INFO @ Wed, 28 Jun 2017 06:24:28: 3000000 INFO @ Wed, 28 Jun 2017 06:24:34: 4000000 INFO @ Wed, 28 Jun 2017 06:24:34: 4000000 INFO @ Wed, 28 Jun 2017 06:24:34: 4000000 INFO @ Wed, 28 Jun 2017 06:24:39: 5000000 INFO @ Wed, 28 Jun 2017 06:24:40: 5000000 INFO @ Wed, 28 Jun 2017 06:24:40: 5000000 INFO @ Wed, 28 Jun 2017 06:24:45: 6000000 INFO @ Wed, 28 Jun 2017 06:24:45: 6000000 INFO @ Wed, 28 Jun 2017 06:24:45: 6000000 INFO @ Wed, 28 Jun 2017 06:24:51: 7000000 INFO @ Wed, 28 Jun 2017 06:24:51: 7000000 INFO @ Wed, 28 Jun 2017 06:24:51: 7000000 INFO @ Wed, 28 Jun 2017 06:24:56: 8000000 INFO @ Wed, 28 Jun 2017 06:24:57: 8000000 INFO @ Wed, 28 Jun 2017 06:24:57: 8000000 INFO @ Wed, 28 Jun 2017 06:25:02: 9000000 INFO @ Wed, 28 Jun 2017 06:25:03: 9000000 INFO @ Wed, 28 Jun 2017 06:25:03: 9000000 INFO @ Wed, 28 Jun 2017 06:25:07: 10000000 INFO @ Wed, 28 Jun 2017 06:25:08: 10000000 INFO @ Wed, 28 Jun 2017 06:25:08: 10000000 INFO @ Wed, 28 Jun 2017 06:25:13: 11000000 INFO @ Wed, 28 Jun 2017 06:25:14: 11000000 INFO @ Wed, 28 Jun 2017 06:25:14: 11000000 INFO @ Wed, 28 Jun 2017 06:25:19: 12000000 INFO @ Wed, 28 Jun 2017 06:25:20: 12000000 INFO @ Wed, 28 Jun 2017 06:25:20: 12000000 INFO @ Wed, 28 Jun 2017 06:25:25: 13000000 INFO @ Wed, 28 Jun 2017 06:25:25: 13000000 INFO @ Wed, 28 Jun 2017 06:25:25: 13000000 INFO @ Wed, 28 Jun 2017 06:25:31: 14000000 INFO @ Wed, 28 Jun 2017 06:25:31: 14000000 INFO @ Wed, 28 Jun 2017 06:25:31: 14000000 INFO @ Wed, 28 Jun 2017 06:25:36: 15000000 INFO @ Wed, 28 Jun 2017 06:25:37: 15000000 INFO @ Wed, 28 Jun 2017 06:25:37: 15000000 INFO @ Wed, 28 Jun 2017 06:25:42: 16000000 INFO @ Wed, 28 Jun 2017 06:25:42: 16000000 INFO @ Wed, 28 Jun 2017 06:25:42: 16000000 INFO @ Wed, 28 Jun 2017 06:25:48: 17000000 INFO @ Wed, 28 Jun 2017 06:25:48: 17000000 INFO @ Wed, 28 Jun 2017 06:25:48: 17000000 INFO @ Wed, 28 Jun 2017 06:25:54: 18000000 INFO @ Wed, 28 Jun 2017 06:25:54: 18000000 INFO @ Wed, 28 Jun 2017 06:25:54: 18000000 INFO @ Wed, 28 Jun 2017 06:25:56: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:25:56: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:25:56: #1 total tags in treatment: 8691391 INFO @ Wed, 28 Jun 2017 06:25:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:25:56: #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 06:25:56: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:25:56: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:25:56: #1 total tags in treatment: 8691391 INFO @ Wed, 28 Jun 2017 06:25:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:25:56: #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 06:25:56: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:25:56: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:25:56: #1 total tags in treatment: 8691391 INFO @ Wed, 28 Jun 2017 06:25:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:25:56: #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 06:25:56: #1 tags after filtering in treatment: 6170486 INFO @ Wed, 28 Jun 2017 06:25:56: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 06:25:56: #1 finished! INFO @ Wed, 28 Jun 2017 06:25:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:25:56: #1 tags after filtering in treatment: 6170486 INFO @ Wed, 28 Jun 2017 06:25:56: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 06:25:56: #1 finished! INFO @ Wed, 28 Jun 2017 06:25:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:25:56: #1 tags after filtering in treatment: 6170486 INFO @ Wed, 28 Jun 2017 06:25:56: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 06:25:56: #1 finished! INFO @ Wed, 28 Jun 2017 06:25:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:25:56: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:25:56: 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 06:25:56: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 06:25:56: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:25:56: 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 06:25:56: Process for pairing-model is terminated! cat: SRX1631843.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX1631843.20_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) pass1 - making usageList (0 chroms): 0 millis rm: cannot remove `SRX1631843.05_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 `SRX1631843.05_*.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 `SRX1631843.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling rm: cannot remove `SRX1631843.20_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 `SRX1631843.20_*.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 `SRX1631843.20_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 06:25:56: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:25:56: 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 06:25:56: Process for pairing-model is terminated! cat: SRX1631843.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1631843.10_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 `SRX1631843.10_*.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 `SRX1631843.10_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。