Job ID = 9161950 sra ファイルのダウンロード中... Completed: 1381141K bytes transferred in 15 seconds (738075K 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 22351818 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423684/SRR2930973.sra Written 22351818 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: 00:15:17 22351818 reads; of these: 22351818 (100.00%) were paired; of these: 6160965 (27.56%) aligned concordantly 0 times 13643049 (61.04%) aligned concordantly exactly 1 time 2547804 (11.40%) aligned concordantly >1 times ---- 6160965 pairs aligned concordantly 0 times; of these: 362844 (5.89%) aligned discordantly 1 time ---- 5798121 pairs aligned 0 times concordantly or discordantly; of these: 11596242 mates make up the pairs; of these: 11327321 (97.68%) aligned 0 times 109734 (0.95%) aligned exactly 1 time 159187 (1.37%) aligned >1 times 74.66% overall alignment rate Time searching: 00:15:17 Overall time: 00:15:17 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] 2915331 / 16535497 = 0.1763 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 05:29:34: # Command line: callpeak -t SRX1423684.bam -f BAM -g 12100000 -n SRX1423684.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423684.05 # format = BAM # ChIP-seq file = ['SRX1423684.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 05:29:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:29:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:29:34: # Command line: callpeak -t SRX1423684.bam -f BAM -g 12100000 -n SRX1423684.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423684.20 # format = BAM # ChIP-seq file = ['SRX1423684.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 05:29:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:29:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:29:34: # Command line: callpeak -t SRX1423684.bam -f BAM -g 12100000 -n SRX1423684.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423684.10 # format = BAM # ChIP-seq file = ['SRX1423684.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 05:29:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:29:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:29:40: 1000000 INFO @ Wed, 28 Jun 2017 05:29:40: 1000000 INFO @ Wed, 28 Jun 2017 05:29:40: 1000000 INFO @ Wed, 28 Jun 2017 05:29:45: 2000000 INFO @ Wed, 28 Jun 2017 05:29:46: 2000000 INFO @ Wed, 28 Jun 2017 05:29:46: 2000000 INFO @ Wed, 28 Jun 2017 05:29:52: 3000000 INFO @ Wed, 28 Jun 2017 05:29:52: 3000000 INFO @ Wed, 28 Jun 2017 05:29:54: 3000000 INFO @ Wed, 28 Jun 2017 05:29:58: 4000000 INFO @ Wed, 28 Jun 2017 05:29:58: 4000000 INFO @ Wed, 28 Jun 2017 05:30:00: 4000000 INFO @ Wed, 28 Jun 2017 05:30:03: 5000000 INFO @ Wed, 28 Jun 2017 05:30:05: 5000000 INFO @ Wed, 28 Jun 2017 05:30:06: 5000000 INFO @ Wed, 28 Jun 2017 05:30:09: 6000000 INFO @ Wed, 28 Jun 2017 05:30:11: 6000000 INFO @ Wed, 28 Jun 2017 05:30:13: 6000000 INFO @ Wed, 28 Jun 2017 05:30:16: 7000000 INFO @ Wed, 28 Jun 2017 05:30:17: 7000000 INFO @ Wed, 28 Jun 2017 05:30:19: 7000000 INFO @ Wed, 28 Jun 2017 05:30:21: 8000000 INFO @ Wed, 28 Jun 2017 05:30:23: 8000000 INFO @ Wed, 28 Jun 2017 05:30:26: 8000000 INFO @ Wed, 28 Jun 2017 05:30:27: 9000000 INFO @ Wed, 28 Jun 2017 05:30:29: 9000000 INFO @ Wed, 28 Jun 2017 05:30:32: 9000000 INFO @ Wed, 28 Jun 2017 05:30:34: 10000000 INFO @ Wed, 28 Jun 2017 05:30:36: 10000000 INFO @ Wed, 28 Jun 2017 05:30:39: 10000000 INFO @ Wed, 28 Jun 2017 05:30:41: 11000000 INFO @ Wed, 28 Jun 2017 05:30:44: 11000000 INFO @ Wed, 28 Jun 2017 05:30:46: 11000000 INFO @ Wed, 28 Jun 2017 05:30:48: 12000000 INFO @ Wed, 28 Jun 2017 05:30:50: 12000000 INFO @ Wed, 28 Jun 2017 05:30:53: 12000000 INFO @ Wed, 28 Jun 2017 05:30:55: 13000000 INFO @ Wed, 28 Jun 2017 05:30:55: 13000000 INFO @ Wed, 28 Jun 2017 05:31:00: 13000000 INFO @ Wed, 28 Jun 2017 05:31:01: 14000000 INFO @ Wed, 28 Jun 2017 05:31:02: 14000000 INFO @ Wed, 28 Jun 2017 05:31:07: 14000000 INFO @ Wed, 28 Jun 2017 05:31:07: 15000000 INFO @ Wed, 28 Jun 2017 05:31:09: 15000000 INFO @ Wed, 28 Jun 2017 05:31:12: 16000000 INFO @ Wed, 28 Jun 2017 05:31:14: 15000000 INFO @ Wed, 28 Jun 2017 05:31:16: 16000000 INFO @ Wed, 28 Jun 2017 05:31:18: 17000000 INFO @ Wed, 28 Jun 2017 05:31:20: 16000000 INFO @ Wed, 28 Jun 2017 05:31:22: 17000000 INFO @ Wed, 28 Jun 2017 05:31:24: 18000000 INFO @ Wed, 28 Jun 2017 05:31:27: 17000000 INFO @ Wed, 28 Jun 2017 05:31:29: 18000000 INFO @ Wed, 28 Jun 2017 05:31:29: 19000000 INFO @ Wed, 28 Jun 2017 05:31:34: 18000000 INFO @ Wed, 28 Jun 2017 05:31:35: 20000000 INFO @ Wed, 28 Jun 2017 05:31:36: 19000000 INFO @ Wed, 28 Jun 2017 05:31:40: 21000000 INFO @ Wed, 28 Jun 2017 05:31:41: 19000000 INFO @ Wed, 28 Jun 2017 05:31:43: 20000000 INFO @ Wed, 28 Jun 2017 05:31:46: 22000000 INFO @ Wed, 28 Jun 2017 05:31:48: 20000000 INFO @ Wed, 28 Jun 2017 05:31:50: 21000000 INFO @ Wed, 28 Jun 2017 05:31:52: 23000000 INFO @ Wed, 28 Jun 2017 05:31:55: 21000000 INFO @ Wed, 28 Jun 2017 05:31:57: 22000000 INFO @ Wed, 28 Jun 2017 05:31:57: 24000000 INFO @ Wed, 28 Jun 2017 05:32:02: 22000000 INFO @ Wed, 28 Jun 2017 05:32:03: 25000000 INFO @ Wed, 28 Jun 2017 05:32:04: 23000000 INFO @ Wed, 28 Jun 2017 05:32:09: 23000000 INFO @ Wed, 28 Jun 2017 05:32:09: 26000000 INFO @ Wed, 28 Jun 2017 05:32:10: 24000000 INFO @ Wed, 28 Jun 2017 05:32:14: 27000000 INFO @ Wed, 28 Jun 2017 05:32:15: 24000000 INFO @ Wed, 28 Jun 2017 05:32:17: 25000000 INFO @ Wed, 28 Jun 2017 05:32:17: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:32:17: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:32:17: #1 total tags in treatment: 13295518 INFO @ Wed, 28 Jun 2017 05:32:17: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:32:17: #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 05:32:18: #1 tags after filtering in treatment: 9201721 INFO @ Wed, 28 Jun 2017 05:32:18: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 28 Jun 2017 05:32:18: #1 finished! INFO @ Wed, 28 Jun 2017 05:32:18: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:32:18: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:32:18: 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 05:32:18: Process for pairing-model is terminated! cat: SRX1423684.20_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 `SRX1423684.20_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 `SRX1423684.20_*.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 `SRX1423684.20_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: 25000000 INFO @ Wed, 28 Jun 2017 05:32:24: 26000000 INFO @ Wed, 28 Jun 2017 05:32:29: 26000000 INFO @ Wed, 28 Jun 2017 05:32:31: 27000000 INFO @ Wed, 28 Jun 2017 05:32:35: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:32:35: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:32:35: #1 total tags in treatment: 13295518 INFO @ Wed, 28 Jun 2017 05:32:35: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:32:35: #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 05:32:35: #1 tags after filtering in treatment: 9201721 INFO @ Wed, 28 Jun 2017 05:32:35: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 28 Jun 2017 05:32:35: #1 finished! INFO @ Wed, 28 Jun 2017 05:32:35: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:32:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:32:36: 27000000 INFO @ Wed, 28 Jun 2017 05:32:36: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:32:36: 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 05:32:36: Process for pairing-model is terminated! cat: SRX1423684.05_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 `SRX1423684.05_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 `SRX1423684.05_*.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 `SRX1423684.05_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 05:32:39: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:32:39: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:32:39: #1 total tags in treatment: 13295518 INFO @ Wed, 28 Jun 2017 05:32:39: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:32:39: #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 05:32:39: #1 tags after filtering in treatment: 9201721 INFO @ Wed, 28 Jun 2017 05:32:39: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 28 Jun 2017 05:32:39: #1 finished! INFO @ Wed, 28 Jun 2017 05:32:39: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:32:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:32:40: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:32:40: 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 05:32:40: Process for pairing-model is terminated! cat: SRX1423684.10_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 `SRX1423684.10_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 `SRX1423684.10_*.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 `SRX1423684.10_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。