Job ID = 9161658 sra ファイルのダウンロード中... Completed: 942362K bytes transferred in 9 seconds (784982K 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 10711204 spots for /home/okishinya/chipatlas/results/sacCer3/SRX047391/SRR124142.sra Written 10711204 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: 00:10:22 10711204 reads; of these: 10711204 (100.00%) were paired; of these: 651178 (6.08%) aligned concordantly 0 times 8591494 (80.21%) aligned concordantly exactly 1 time 1468532 (13.71%) aligned concordantly >1 times ---- 651178 pairs aligned concordantly 0 times; of these: 17022 (2.61%) aligned discordantly 1 time ---- 634156 pairs aligned 0 times concordantly or discordantly; of these: 1268312 mates make up the pairs; of these: 1057665 (83.39%) aligned 0 times 171337 (13.51%) aligned exactly 1 time 39310 (3.10%) aligned >1 times 95.06% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 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 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] 2679205 / 10070384 = 0.2660 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 04:35:33: # Command line: callpeak -t SRX047391.bam -f BAM -g 12100000 -n SRX047391.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX047391.20 # format = BAM # ChIP-seq file = ['SRX047391.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 04:35:33: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:35:33: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:35:33: # Command line: callpeak -t SRX047391.bam -f BAM -g 12100000 -n SRX047391.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX047391.05 # format = BAM # ChIP-seq file = ['SRX047391.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 04:35:33: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:35:33: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:35:33: # Command line: callpeak -t SRX047391.bam -f BAM -g 12100000 -n SRX047391.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX047391.10 # format = BAM # ChIP-seq file = ['SRX047391.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 04:35:33: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:35:33: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:35:41: 1000000 INFO @ Wed, 28 Jun 2017 04:35:42: 1000000 INFO @ Wed, 28 Jun 2017 04:35:42: 1000000 INFO @ Wed, 28 Jun 2017 04:35:50: 2000000 INFO @ Wed, 28 Jun 2017 04:35:50: 2000000 INFO @ Wed, 28 Jun 2017 04:35:51: 2000000 INFO @ Wed, 28 Jun 2017 04:35:58: 3000000 INFO @ Wed, 28 Jun 2017 04:35:59: 3000000 INFO @ Wed, 28 Jun 2017 04:36:00: 3000000 INFO @ Wed, 28 Jun 2017 04:36:07: 4000000 INFO @ Wed, 28 Jun 2017 04:36:07: 4000000 INFO @ Wed, 28 Jun 2017 04:36:08: 4000000 INFO @ Wed, 28 Jun 2017 04:36:16: 5000000 INFO @ Wed, 28 Jun 2017 04:36:16: 5000000 INFO @ Wed, 28 Jun 2017 04:36:17: 5000000 INFO @ Wed, 28 Jun 2017 04:36:25: 6000000 INFO @ Wed, 28 Jun 2017 04:36:25: 6000000 INFO @ Wed, 28 Jun 2017 04:36:26: 6000000 INFO @ Wed, 28 Jun 2017 04:36:34: 7000000 INFO @ Wed, 28 Jun 2017 04:36:34: 7000000 INFO @ Wed, 28 Jun 2017 04:36:35: 7000000 INFO @ Wed, 28 Jun 2017 04:36:43: 8000000 INFO @ Wed, 28 Jun 2017 04:36:43: 8000000 INFO @ Wed, 28 Jun 2017 04:36:44: 8000000 INFO @ Wed, 28 Jun 2017 04:36:52: 9000000 INFO @ Wed, 28 Jun 2017 04:36:52: 9000000 INFO @ Wed, 28 Jun 2017 04:36:54: 9000000 INFO @ Wed, 28 Jun 2017 04:37:00: 10000000 INFO @ Wed, 28 Jun 2017 04:37:01: 10000000 INFO @ Wed, 28 Jun 2017 04:37:03: 10000000 INFO @ Wed, 28 Jun 2017 04:37:08: 11000000 INFO @ Wed, 28 Jun 2017 04:37:09: 11000000 INFO @ Wed, 28 Jun 2017 04:37:13: 11000000 INFO @ Wed, 28 Jun 2017 04:37:17: 12000000 INFO @ Wed, 28 Jun 2017 04:37:18: 12000000 INFO @ Wed, 28 Jun 2017 04:37:23: 12000000 INFO @ Wed, 28 Jun 2017 04:37:25: 13000000 INFO @ Wed, 28 Jun 2017 04:37:26: 13000000 INFO @ Wed, 28 Jun 2017 04:37:32: 13000000 INFO @ Wed, 28 Jun 2017 04:37:33: 14000000 INFO @ Wed, 28 Jun 2017 04:37:35: 14000000 INFO @ Wed, 28 Jun 2017 04:37:41: 14000000 INFO @ Wed, 28 Jun 2017 04:37:41: 15000000 INFO @ Wed, 28 Jun 2017 04:37:42: #1 tag size is determined as 76 bps INFO @ Wed, 28 Jun 2017 04:37:42: #1 tag size = 76 INFO @ Wed, 28 Jun 2017 04:37:42: #1 total tags in treatment: 7380834 INFO @ Wed, 28 Jun 2017 04:37:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:37:42: #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 04:37:42: #1 tags after filtering in treatment: 4012152 INFO @ Wed, 28 Jun 2017 04:37:42: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 28 Jun 2017 04:37:42: #1 finished! INFO @ Wed, 28 Jun 2017 04:37:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:37:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:37:42: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:37:42: 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 04:37:42: Process for pairing-model is terminated! cat: SRX047391.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX047391.20_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 `SRX047391.20_*.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 `SRX047391.20_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 04:37:43: 15000000 INFO @ Wed, 28 Jun 2017 04:37:43: #1 tag size is determined as 76 bps INFO @ Wed, 28 Jun 2017 04:37:43: #1 tag size = 76 INFO @ Wed, 28 Jun 2017 04:37:43: #1 total tags in treatment: 7380834 INFO @ Wed, 28 Jun 2017 04:37:43: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:37:43: #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 04:37:43: #1 tags after filtering in treatment: 4012152 INFO @ Wed, 28 Jun 2017 04:37:43: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 28 Jun 2017 04:37:43: #1 finished! INFO @ Wed, 28 Jun 2017 04:37:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:37:43: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:37:43: 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 04:37:43: Process for pairing-model is terminated! cat: SRX047391.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX047391.05_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 `SRX047391.05_*.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 `SRX047391.05_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 04:37:48: 15000000 INFO @ Wed, 28 Jun 2017 04:37:48: #1 tag size is determined as 76 bps INFO @ Wed, 28 Jun 2017 04:37:48: #1 tag size = 76 INFO @ Wed, 28 Jun 2017 04:37:48: #1 total tags in treatment: 7380834 INFO @ Wed, 28 Jun 2017 04:37:48: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:37:48: #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 04:37:48: #1 tags after filtering in treatment: 4012152 INFO @ Wed, 28 Jun 2017 04:37:48: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 28 Jun 2017 04:37:48: #1 finished! INFO @ Wed, 28 Jun 2017 04:37:48: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:37:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:37:49: #2 number of paired peaks: 0 WARNING @ Wed, 28 Jun 2017 04:37:49: 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 04:37:49: Process for pairing-model is terminated! cat: SRX047391.10_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 `SRX047391.10_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 `SRX047391.10_*.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 `SRX047391.10_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。