Job ID = 9161953 sra ファイルのダウンロード中... Completed: 1459192K bytes transferred in 16 seconds (705652K 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 23691663 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423687/SRR2930976.sra Written 23691663 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: 00:14:34 23691663 reads; of these: 23691663 (100.00%) were paired; of these: 7592367 (32.05%) aligned concordantly 0 times 14225886 (60.05%) aligned concordantly exactly 1 time 1873410 (7.91%) aligned concordantly >1 times ---- 7592367 pairs aligned concordantly 0 times; of these: 457583 (6.03%) aligned discordantly 1 time ---- 7134784 pairs aligned 0 times concordantly or discordantly; of these: 14269568 mates make up the pairs; of these: 13999783 (98.11%) aligned 0 times 116270 (0.81%) aligned exactly 1 time 153515 (1.08%) aligned >1 times 70.45% overall alignment rate Time searching: 00:14:34 Overall time: 00:14:34 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 16 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] 3867792 / 16535946 = 0.2339 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 05:29:35: # Command line: callpeak -t SRX1423687.bam -f BAM -g 12100000 -n SRX1423687.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423687.05 # format = BAM # ChIP-seq file = ['SRX1423687.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 05:29:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:29:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:29:35: # Command line: callpeak -t SRX1423687.bam -f BAM -g 12100000 -n SRX1423687.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423687.10 # format = BAM # ChIP-seq file = ['SRX1423687.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 05:29:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:29:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:29:35: # Command line: callpeak -t SRX1423687.bam -f BAM -g 12100000 -n SRX1423687.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423687.20 # format = BAM # ChIP-seq file = ['SRX1423687.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 05:29:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:29:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:29:42: 1000000 INFO @ Wed, 28 Jun 2017 05:29:42: 1000000 INFO @ Wed, 28 Jun 2017 05:29:42: 1000000 INFO @ Wed, 28 Jun 2017 05:29:48: 2000000 INFO @ Wed, 28 Jun 2017 05:29:49: 2000000 INFO @ Wed, 28 Jun 2017 05:29:49: 2000000 INFO @ Wed, 28 Jun 2017 05:29:55: 3000000 INFO @ Wed, 28 Jun 2017 05:29:55: 3000000 INFO @ Wed, 28 Jun 2017 05:29:55: 3000000 INFO @ Wed, 28 Jun 2017 05:30:00: 4000000 INFO @ Wed, 28 Jun 2017 05:30:02: 4000000 INFO @ Wed, 28 Jun 2017 05:30:02: 4000000 INFO @ Wed, 28 Jun 2017 05:30:07: 5000000 INFO @ Wed, 28 Jun 2017 05:30:09: 5000000 INFO @ Wed, 28 Jun 2017 05:30:09: 5000000 INFO @ Wed, 28 Jun 2017 05:30:13: 6000000 INFO @ Wed, 28 Jun 2017 05:30:16: 6000000 INFO @ Wed, 28 Jun 2017 05:30:16: 6000000 INFO @ Wed, 28 Jun 2017 05:30:18: 7000000 INFO @ Wed, 28 Jun 2017 05:30:23: 7000000 INFO @ Wed, 28 Jun 2017 05:30:23: 7000000 INFO @ Wed, 28 Jun 2017 05:30:24: 8000000 INFO @ Wed, 28 Jun 2017 05:30:30: 8000000 INFO @ Wed, 28 Jun 2017 05:30:30: 8000000 INFO @ Wed, 28 Jun 2017 05:30:30: 9000000 INFO @ Wed, 28 Jun 2017 05:30:35: 10000000 INFO @ Wed, 28 Jun 2017 05:30:37: 9000000 INFO @ Wed, 28 Jun 2017 05:30:37: 9000000 INFO @ Wed, 28 Jun 2017 05:30:41: 11000000 INFO @ Wed, 28 Jun 2017 05:30:44: 10000000 INFO @ Wed, 28 Jun 2017 05:30:44: 10000000 INFO @ Wed, 28 Jun 2017 05:30:46: 12000000 INFO @ Wed, 28 Jun 2017 05:30:51: 11000000 INFO @ Wed, 28 Jun 2017 05:30:51: 11000000 INFO @ Wed, 28 Jun 2017 05:30:52: 13000000 INFO @ Wed, 28 Jun 2017 05:30:57: 14000000 INFO @ Wed, 28 Jun 2017 05:30:58: 12000000 INFO @ Wed, 28 Jun 2017 05:30:58: 12000000 INFO @ Wed, 28 Jun 2017 05:31:03: 15000000 INFO @ Wed, 28 Jun 2017 05:31:05: 13000000 INFO @ Wed, 28 Jun 2017 05:31:05: 13000000 INFO @ Wed, 28 Jun 2017 05:31:08: 16000000 INFO @ Wed, 28 Jun 2017 05:31:12: 14000000 INFO @ Wed, 28 Jun 2017 05:31:12: 14000000 INFO @ Wed, 28 Jun 2017 05:31:14: 17000000 INFO @ Wed, 28 Jun 2017 05:31:19: 15000000 INFO @ Wed, 28 Jun 2017 05:31:19: 15000000 INFO @ Wed, 28 Jun 2017 05:31:20: 18000000 INFO @ Wed, 28 Jun 2017 05:31:25: 16000000 INFO @ Wed, 28 Jun 2017 05:31:26: 16000000 INFO @ Wed, 28 Jun 2017 05:31:26: 19000000 INFO @ Wed, 28 Jun 2017 05:31:32: 20000000 INFO @ Wed, 28 Jun 2017 05:31:32: 17000000 INFO @ Wed, 28 Jun 2017 05:31:32: 17000000 INFO @ Wed, 28 Jun 2017 05:31:37: 21000000 INFO @ Wed, 28 Jun 2017 05:31:38: 18000000 INFO @ Wed, 28 Jun 2017 05:31:38: 18000000 INFO @ Wed, 28 Jun 2017 05:31:42: 22000000 INFO @ Wed, 28 Jun 2017 05:31:44: 19000000 INFO @ Wed, 28 Jun 2017 05:31:44: 19000000 INFO @ Wed, 28 Jun 2017 05:31:48: 23000000 INFO @ Wed, 28 Jun 2017 05:31:50: 20000000 INFO @ Wed, 28 Jun 2017 05:31:50: 20000000 INFO @ Wed, 28 Jun 2017 05:31:53: 24000000 INFO @ Wed, 28 Jun 2017 05:31:55: 21000000 INFO @ Wed, 28 Jun 2017 05:31:56: 21000000 INFO @ Wed, 28 Jun 2017 05:31:58: 25000000 INFO @ Wed, 28 Jun 2017 05:32:01: 22000000 INFO @ Wed, 28 Jun 2017 05:32:01: 22000000 INFO @ Wed, 28 Jun 2017 05:32:01: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:32:01: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:32:01: #1 total tags in treatment: 12289022 INFO @ Wed, 28 Jun 2017 05:32:01: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:32:01: #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 05:32:02: #1 tags after filtering in treatment: 8951922 INFO @ Wed, 28 Jun 2017 05:32:02: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:32:02: #1 finished! INFO @ Wed, 28 Jun 2017 05:32:02: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:32:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:32:02: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:32:02: 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 05:32:02: Process for pairing-model is terminated! cat: SRX1423687.05_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 `SRX1423687.05_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 `SRX1423687.05_*.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 `SRX1423687.05_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 05:32:07: 23000000 INFO @ Wed, 28 Jun 2017 05:32:07: 23000000 INFO @ Wed, 28 Jun 2017 05:32:12: 24000000 INFO @ Wed, 28 Jun 2017 05:32:12: 24000000 INFO @ Wed, 28 Jun 2017 05:32:18: 25000000 INFO @ Wed, 28 Jun 2017 05:32:18: 25000000 INFO @ Wed, 28 Jun 2017 05:32:21: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:32:21: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:32:21: #1 total tags in treatment: 12289022 INFO @ Wed, 28 Jun 2017 05:32:21: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:32:21: #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 05:32:22: #1 tags after filtering in treatment: 8951922 INFO @ Wed, 28 Jun 2017 05:32:22: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:32:22: #1 finished! INFO @ Wed, 28 Jun 2017 05:32:22: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:32:22: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:32:22: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:32:22: #1 total tags in treatment: 12289022 INFO @ Wed, 28 Jun 2017 05:32:22: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:32:22: #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 05:32:22: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:32:22: 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 05:32:22: Process for pairing-model is terminated! cat: SRX1423687.20_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 `SRX1423687.20_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 `SRX1423687.20_*.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 `SRX1423687.20_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 05:32:22: #1 tags after filtering in treatment: 8951922 INFO @ Wed, 28 Jun 2017 05:32:22: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:32:22: #1 finished! INFO @ Wed, 28 Jun 2017 05:32:22: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:32:23: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:32:23: 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 05:32:23: Process for pairing-model is terminated! cat: SRX1423687.10_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 `SRX1423687.10_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 `SRX1423687.10_*.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 `SRX1423687.10_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。