Job ID = 9161944 sra ファイルのダウンロード中... Completed: 1377876K bytes transferred in 17 seconds (659604K 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 22933214 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423678/SRR2930967.sra Written 22933214 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: 00:12:20 22933214 reads; of these: 22933214 (100.00%) were paired; of these: 9800622 (42.74%) aligned concordantly 0 times 11640130 (50.76%) aligned concordantly exactly 1 time 1492462 (6.51%) aligned concordantly >1 times ---- 9800622 pairs aligned concordantly 0 times; of these: 65612 (0.67%) aligned discordantly 1 time ---- 9735010 pairs aligned 0 times concordantly or discordantly; of these: 19470020 mates make up the pairs; of these: 19256226 (98.90%) aligned 0 times 166093 (0.85%) aligned exactly 1 time 47701 (0.24%) aligned >1 times 58.02% overall alignment rate Time searching: 00:12:20 Overall time: 00:12:20 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] 945639 / 13182832 = 0.0717 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 05:23:34: # Command line: callpeak -t SRX1423678.bam -f BAM -g 12100000 -n SRX1423678.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423678.05 # format = BAM # ChIP-seq file = ['SRX1423678.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 05:23:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:23:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:23:34: # Command line: callpeak -t SRX1423678.bam -f BAM -g 12100000 -n SRX1423678.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423678.20 # format = BAM # ChIP-seq file = ['SRX1423678.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 05:23:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:23:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:23:34: # Command line: callpeak -t SRX1423678.bam -f BAM -g 12100000 -n SRX1423678.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423678.10 # format = BAM # ChIP-seq file = ['SRX1423678.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 05:23:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:23:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:23:43: 1000000 INFO @ Wed, 28 Jun 2017 05:23:43: 1000000 INFO @ Wed, 28 Jun 2017 05:23:43: 1000000 INFO @ Wed, 28 Jun 2017 05:23:51: 2000000 INFO @ Wed, 28 Jun 2017 05:23:52: 2000000 INFO @ Wed, 28 Jun 2017 05:23:52: 2000000 INFO @ Wed, 28 Jun 2017 05:24:01: 3000000 INFO @ Wed, 28 Jun 2017 05:24:01: 3000000 INFO @ Wed, 28 Jun 2017 05:24:01: 3000000 INFO @ Wed, 28 Jun 2017 05:24:10: 4000000 INFO @ Wed, 28 Jun 2017 05:24:10: 4000000 INFO @ Wed, 28 Jun 2017 05:24:10: 4000000 INFO @ Wed, 28 Jun 2017 05:24:19: 5000000 INFO @ Wed, 28 Jun 2017 05:24:19: 5000000 INFO @ Wed, 28 Jun 2017 05:24:19: 5000000 INFO @ Wed, 28 Jun 2017 05:24:27: 6000000 INFO @ Wed, 28 Jun 2017 05:24:28: 6000000 INFO @ Wed, 28 Jun 2017 05:24:28: 6000000 INFO @ Wed, 28 Jun 2017 05:24:36: 7000000 INFO @ Wed, 28 Jun 2017 05:24:36: 7000000 INFO @ Wed, 28 Jun 2017 05:24:36: 7000000 INFO @ Wed, 28 Jun 2017 05:24:43: 8000000 INFO @ Wed, 28 Jun 2017 05:24:44: 8000000 INFO @ Wed, 28 Jun 2017 05:24:44: 8000000 INFO @ Wed, 28 Jun 2017 05:24:50: 9000000 INFO @ Wed, 28 Jun 2017 05:24:51: 9000000 INFO @ Wed, 28 Jun 2017 05:24:51: 9000000 INFO @ Wed, 28 Jun 2017 05:24:57: 10000000 INFO @ Wed, 28 Jun 2017 05:24:58: 10000000 INFO @ Wed, 28 Jun 2017 05:24:58: 10000000 INFO @ Wed, 28 Jun 2017 05:25:04: 11000000 INFO @ Wed, 28 Jun 2017 05:25:05: 11000000 INFO @ Wed, 28 Jun 2017 05:25:05: 11000000 INFO @ Wed, 28 Jun 2017 05:25:11: 12000000 INFO @ Wed, 28 Jun 2017 05:25:12: 12000000 INFO @ Wed, 28 Jun 2017 05:25:12: 12000000 INFO @ Wed, 28 Jun 2017 05:25:18: 13000000 INFO @ Wed, 28 Jun 2017 05:25:19: 13000000 INFO @ Wed, 28 Jun 2017 05:25:19: 13000000 INFO @ Wed, 28 Jun 2017 05:25:25: 14000000 INFO @ Wed, 28 Jun 2017 05:25:26: 14000000 INFO @ Wed, 28 Jun 2017 05:25:26: 14000000 INFO @ Wed, 28 Jun 2017 05:25:33: 15000000 INFO @ Wed, 28 Jun 2017 05:25:33: 15000000 INFO @ Wed, 28 Jun 2017 05:25:33: 15000000 INFO @ Wed, 28 Jun 2017 05:25:40: 16000000 INFO @ Wed, 28 Jun 2017 05:25:40: 16000000 INFO @ Wed, 28 Jun 2017 05:25:41: 16000000 INFO @ Wed, 28 Jun 2017 05:25:47: 17000000 INFO @ Wed, 28 Jun 2017 05:25:47: 17000000 INFO @ Wed, 28 Jun 2017 05:25:48: 17000000 INFO @ Wed, 28 Jun 2017 05:25:54: 18000000 INFO @ Wed, 28 Jun 2017 05:25:55: 18000000 INFO @ Wed, 28 Jun 2017 05:25:56: 18000000 INFO @ Wed, 28 Jun 2017 05:26:01: 19000000 INFO @ Wed, 28 Jun 2017 05:26:02: 19000000 INFO @ Wed, 28 Jun 2017 05:26:03: 19000000 INFO @ Wed, 28 Jun 2017 05:26:08: 20000000 INFO @ Wed, 28 Jun 2017 05:26:09: 20000000 INFO @ Wed, 28 Jun 2017 05:26:11: 20000000 INFO @ Wed, 28 Jun 2017 05:26:15: 21000000 INFO @ Wed, 28 Jun 2017 05:26:17: 21000000 INFO @ Wed, 28 Jun 2017 05:26:18: 21000000 INFO @ Wed, 28 Jun 2017 05:26:22: 22000000 INFO @ Wed, 28 Jun 2017 05:26:25: 22000000 INFO @ Wed, 28 Jun 2017 05:26:27: 22000000 INFO @ Wed, 28 Jun 2017 05:26:29: 23000000 INFO @ Wed, 28 Jun 2017 05:26:33: 23000000 INFO @ Wed, 28 Jun 2017 05:26:34: 23000000 INFO @ Wed, 28 Jun 2017 05:26:37: 24000000 INFO @ Wed, 28 Jun 2017 05:26:41: 24000000 INFO @ Wed, 28 Jun 2017 05:26:42: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:26:42: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:26:42: #1 total tags in treatment: 12187948 INFO @ Wed, 28 Jun 2017 05:26:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:26:42: #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 05:26:43: 24000000 INFO @ Wed, 28 Jun 2017 05:26:43: #1 tags after filtering in treatment: 8888471 INFO @ Wed, 28 Jun 2017 05:26:43: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:26:43: #1 finished! INFO @ Wed, 28 Jun 2017 05:26:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:26:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:26:43: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:26:43: 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 05:26:43: Process for pairing-model is terminated! cat: SRX1423678.05_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 `SRX1423678.05_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 `SRX1423678.05_*.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 `SRX1423678.05_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 05:26:46: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:26:46: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:26:46: #1 total tags in treatment: 12187948 INFO @ Wed, 28 Jun 2017 05:26:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:26:46: #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 05:26:47: #1 tags after filtering in treatment: 8888471 INFO @ Wed, 28 Jun 2017 05:26:47: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:26:47: #1 finished! INFO @ Wed, 28 Jun 2017 05:26:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:26:47: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:26:47: 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 05:26:47: Process for pairing-model is terminated! cat: SRX1423678.20_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 `SRX1423678.20_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 `SRX1423678.20_*.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 `SRX1423678.20_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 05:26:48: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:26:48: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:26:48: #1 total tags in treatment: 12187948 INFO @ Wed, 28 Jun 2017 05:26:48: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:26:48: #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 05:26:48: #1 tags after filtering in treatment: 8888471 INFO @ Wed, 28 Jun 2017 05:26:48: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 28 Jun 2017 05:26:48: #1 finished! INFO @ Wed, 28 Jun 2017 05:26:48: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:26:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:26:49: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 05:26:49: 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 05:26:49: Process for pairing-model is terminated! cat: SRX1423678.10_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 `SRX1423678.10_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 `SRX1423678.10_*.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 `SRX1423678.10_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。