Job ID = 9162106 sra ファイルのダウンロード中... Completed: 1382491K bytes transferred in 13 seconds (826288K 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 28550797 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1631844/SRR3225780.sra Written 28550797 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: 00:19:41 28550797 reads; of these: 28550797 (100.00%) were paired; of these: 8977517 (31.44%) aligned concordantly 0 times 17451455 (61.12%) aligned concordantly exactly 1 time 2121825 (7.43%) aligned concordantly >1 times ---- 8977517 pairs aligned concordantly 0 times; of these: 484094 (5.39%) aligned discordantly 1 time ---- 8493423 pairs aligned 0 times concordantly or discordantly; of these: 16986846 mates make up the pairs; of these: 16592780 (97.68%) aligned 0 times 225220 (1.33%) aligned exactly 1 time 168846 (0.99%) aligned >1 times 70.94% overall alignment rate Time searching: 00:19:41 Overall time: 00:19:41 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] 11877289 / 20048432 = 0.5924 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 06:23:26: # Command line: callpeak -t SRX1631844.bam -f BAM -g 12100000 -n SRX1631844.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1631844.05 # format = BAM # ChIP-seq file = ['SRX1631844.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 06:23:26: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:23:26: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:23:26: # Command line: callpeak -t SRX1631844.bam -f BAM -g 12100000 -n SRX1631844.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1631844.10 # format = BAM # ChIP-seq file = ['SRX1631844.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 06:23:26: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:23:26: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:23:26: # Command line: callpeak -t SRX1631844.bam -f BAM -g 12100000 -n SRX1631844.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1631844.20 # format = BAM # ChIP-seq file = ['SRX1631844.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 06:23:26: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:23:26: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:23:32: 1000000 INFO @ Wed, 28 Jun 2017 06:23:32: 1000000 INFO @ Wed, 28 Jun 2017 06:23:32: 1000000 INFO @ Wed, 28 Jun 2017 06:23:38: 2000000 INFO @ Wed, 28 Jun 2017 06:23:38: 2000000 INFO @ Wed, 28 Jun 2017 06:23:39: 2000000 INFO @ Wed, 28 Jun 2017 06:23:45: 3000000 INFO @ Wed, 28 Jun 2017 06:23:45: 3000000 INFO @ Wed, 28 Jun 2017 06:23:45: 3000000 INFO @ Wed, 28 Jun 2017 06:23:51: 4000000 INFO @ Wed, 28 Jun 2017 06:23:52: 4000000 INFO @ Wed, 28 Jun 2017 06:23:52: 4000000 INFO @ Wed, 28 Jun 2017 06:23:58: 5000000 INFO @ Wed, 28 Jun 2017 06:23:59: 5000000 INFO @ Wed, 28 Jun 2017 06:24:00: 5000000 INFO @ Wed, 28 Jun 2017 06:24:05: 6000000 INFO @ Wed, 28 Jun 2017 06:24:06: 6000000 INFO @ Wed, 28 Jun 2017 06:24:08: 6000000 INFO @ Wed, 28 Jun 2017 06:24:12: 7000000 INFO @ Wed, 28 Jun 2017 06:24:13: 7000000 INFO @ Wed, 28 Jun 2017 06:24:16: 7000000 INFO @ Wed, 28 Jun 2017 06:24:19: 8000000 INFO @ Wed, 28 Jun 2017 06:24:20: 8000000 INFO @ Wed, 28 Jun 2017 06:24:24: 8000000 INFO @ Wed, 28 Jun 2017 06:24:26: 9000000 INFO @ Wed, 28 Jun 2017 06:24:27: 9000000 INFO @ Wed, 28 Jun 2017 06:24:32: 9000000 INFO @ Wed, 28 Jun 2017 06:24:33: 10000000 INFO @ Wed, 28 Jun 2017 06:24:34: 10000000 INFO @ Wed, 28 Jun 2017 06:24:39: 10000000 INFO @ Wed, 28 Jun 2017 06:24:40: 11000000 INFO @ Wed, 28 Jun 2017 06:24:41: 11000000 INFO @ Wed, 28 Jun 2017 06:24:47: 12000000 INFO @ Wed, 28 Jun 2017 06:24:47: 11000000 INFO @ Wed, 28 Jun 2017 06:24:48: 12000000 INFO @ Wed, 28 Jun 2017 06:24:54: 13000000 INFO @ Wed, 28 Jun 2017 06:24:55: 13000000 INFO @ Wed, 28 Jun 2017 06:24:56: 12000000 INFO @ Wed, 28 Jun 2017 06:25:01: 14000000 INFO @ Wed, 28 Jun 2017 06:25:02: 14000000 INFO @ Wed, 28 Jun 2017 06:25:03: 13000000 INFO @ Wed, 28 Jun 2017 06:25:08: 15000000 INFO @ Wed, 28 Jun 2017 06:25:08: 15000000 INFO @ Wed, 28 Jun 2017 06:25:11: 14000000 INFO @ Wed, 28 Jun 2017 06:25:15: 16000000 INFO @ Wed, 28 Jun 2017 06:25:15: 16000000 INFO @ Wed, 28 Jun 2017 06:25:19: 15000000 INFO @ Wed, 28 Jun 2017 06:25:20: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:25:20: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:25:20: #1 total tags in treatment: 7877038 INFO @ Wed, 28 Jun 2017 06:25:20: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:25:20: #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 06:25:20: #1 tags after filtering in treatment: 5671971 INFO @ Wed, 28 Jun 2017 06:25:20: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 06:25:20: #1 finished! INFO @ Wed, 28 Jun 2017 06:25:20: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:25:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:25:20: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:25:20: 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 06:25:20: Process for pairing-model is terminated! cat: SRX1631844.05_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 `SRX1631844.05_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 `SRX1631844.05_*.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 `SRX1631844.05_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 06:25:21: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:25:21: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:25:21: #1 total tags in treatment: 7877038 INFO @ Wed, 28 Jun 2017 06:25:21: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:25:21: #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 06:25:21: #1 tags after filtering in treatment: 5671971 INFO @ Wed, 28 Jun 2017 06:25:21: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 06:25:21: #1 finished! INFO @ Wed, 28 Jun 2017 06:25:21: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:25:21: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:25:21: 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 06:25:21: Process for pairing-model is terminated! cat: SRX1631844.10_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 `SRX1631844.10_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 `SRX1631844.10_*.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 `SRX1631844.10_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 06:25:25: 16000000 INFO @ Wed, 28 Jun 2017 06:25:29: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:25:29: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:25:29: #1 total tags in treatment: 7877038 INFO @ Wed, 28 Jun 2017 06:25:29: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:25:29: #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 06:25:30: #1 tags after filtering in treatment: 5671971 INFO @ Wed, 28 Jun 2017 06:25:30: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 06:25:30: #1 finished! INFO @ Wed, 28 Jun 2017 06:25:30: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:25:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:25:30: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 06:25:30: 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 06:25:30: Process for pairing-model is terminated! cat: SRX1631844.20_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 `SRX1631844.20_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 `SRX1631844.20_*.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 `SRX1631844.20_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。