Job ID = 10254446 sra ファイルのダウンロード中... Completed: 275775K bytes transferred in 14 seconds (160009K bits/sec), in 1 file. Completed: 372829K bytes transferred in 10 seconds (287164K bits/sec), in 1 file. 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 4350348 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353384/SRR6246242.sra Written 4350348 spots total Written 6060211 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353384/SRR6246243.sra Written 6060211 spots total rm: cannot remove `[DSE]RX*': 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: 00:07:32 10410559 reads; of these: 10410559 (100.00%) were paired; of these: 1633344 (15.69%) aligned concordantly 0 times 8380456 (80.50%) aligned concordantly exactly 1 time 396759 (3.81%) aligned concordantly >1 times ---- 1633344 pairs aligned concordantly 0 times; of these: 860219 (52.67%) aligned discordantly 1 time ---- 773125 pairs aligned 0 times concordantly or discordantly; of these: 1546250 mates make up the pairs; of these: 1037073 (67.07%) aligned 0 times 406848 (26.31%) aligned exactly 1 time 102329 (6.62%) aligned >1 times 95.02% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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] 59265 / 9425298 = 0.0063 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, 06 Dec 2017 18:22:00: # Command line: callpeak -t SRX3353384.bam -f BAM -g 12100000 -n SRX3353384.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3353384.10 # format = BAM # ChIP-seq file = ['SRX3353384.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, 06 Dec 2017 18:22:00: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:22:00: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:22:00: # Command line: callpeak -t SRX3353384.bam -f BAM -g 12100000 -n SRX3353384.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3353384.05 # format = BAM # ChIP-seq file = ['SRX3353384.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, 06 Dec 2017 18:22:00: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:22:00: # Command line: callpeak -t SRX3353384.bam -f BAM -g 12100000 -n SRX3353384.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3353384.20 # format = BAM # ChIP-seq file = ['SRX3353384.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, 06 Dec 2017 18:22:00: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:22:00: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:22:00: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:22:05: 1000000 INFO @ Wed, 06 Dec 2017 18:22:05: 1000000 INFO @ Wed, 06 Dec 2017 18:22:05: 1000000 INFO @ Wed, 06 Dec 2017 18:22:10: 2000000 INFO @ Wed, 06 Dec 2017 18:22:11: 2000000 INFO @ Wed, 06 Dec 2017 18:22:11: 2000000 INFO @ Wed, 06 Dec 2017 18:22:16: 3000000 INFO @ Wed, 06 Dec 2017 18:22:16: 3000000 INFO @ Wed, 06 Dec 2017 18:22:17: 3000000 INFO @ Wed, 06 Dec 2017 18:22:21: 4000000 INFO @ Wed, 06 Dec 2017 18:22:22: 4000000 INFO @ Wed, 06 Dec 2017 18:22:23: 4000000 INFO @ Wed, 06 Dec 2017 18:22:26: 5000000 INFO @ Wed, 06 Dec 2017 18:22:28: 5000000 INFO @ Wed, 06 Dec 2017 18:22:29: 5000000 INFO @ Wed, 06 Dec 2017 18:22:32: 6000000 INFO @ Wed, 06 Dec 2017 18:22:34: 6000000 INFO @ Wed, 06 Dec 2017 18:22:35: 6000000 INFO @ Wed, 06 Dec 2017 18:22:37: 7000000 INFO @ Wed, 06 Dec 2017 18:22:39: 7000000 INFO @ Wed, 06 Dec 2017 18:22:41: 7000000 INFO @ Wed, 06 Dec 2017 18:22:42: 8000000 INFO @ Wed, 06 Dec 2017 18:22:45: 8000000 INFO @ Wed, 06 Dec 2017 18:22:47: 8000000 INFO @ Wed, 06 Dec 2017 18:22:47: 9000000 INFO @ Wed, 06 Dec 2017 18:22:51: 9000000 INFO @ Wed, 06 Dec 2017 18:22:53: 10000000 INFO @ Wed, 06 Dec 2017 18:22:53: 9000000 INFO @ Wed, 06 Dec 2017 18:22:57: 10000000 INFO @ Wed, 06 Dec 2017 18:22:58: 11000000 INFO @ Wed, 06 Dec 2017 18:22:59: 10000000 INFO @ Wed, 06 Dec 2017 18:23:02: 11000000 INFO @ Wed, 06 Dec 2017 18:23:03: 12000000 INFO @ Wed, 06 Dec 2017 18:23:05: 11000000 INFO @ Wed, 06 Dec 2017 18:23:08: 12000000 INFO @ Wed, 06 Dec 2017 18:23:09: 13000000 INFO @ Wed, 06 Dec 2017 18:23:11: 12000000 INFO @ Wed, 06 Dec 2017 18:23:14: 13000000 INFO @ Wed, 06 Dec 2017 18:23:14: 14000000 INFO @ Wed, 06 Dec 2017 18:23:17: 13000000 INFO @ Wed, 06 Dec 2017 18:23:19: 15000000 INFO @ Wed, 06 Dec 2017 18:23:19: 14000000 INFO @ Wed, 06 Dec 2017 18:23:23: 14000000 INFO @ Wed, 06 Dec 2017 18:23:25: 16000000 INFO @ Wed, 06 Dec 2017 18:23:25: 15000000 INFO @ Wed, 06 Dec 2017 18:23:29: 15000000 INFO @ Wed, 06 Dec 2017 18:23:30: 17000000 INFO @ Wed, 06 Dec 2017 18:23:31: 16000000 INFO @ Wed, 06 Dec 2017 18:23:35: 18000000 INFO @ Wed, 06 Dec 2017 18:23:35: 16000000 INFO @ Wed, 06 Dec 2017 18:23:37: 17000000 INFO @ Wed, 06 Dec 2017 18:23:40: 19000000 INFO @ Wed, 06 Dec 2017 18:23:41: 17000000 INFO @ Wed, 06 Dec 2017 18:23:43: 18000000 INFO @ Wed, 06 Dec 2017 18:23:44: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:23:44: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:23:44: #1 total tags in treatment: 8720940 INFO @ Wed, 06 Dec 2017 18:23:44: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:23:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:23:44: #1 tags after filtering in treatment: 6483734 INFO @ Wed, 06 Dec 2017 18:23:44: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 06 Dec 2017 18:23:44: #1 finished! INFO @ Wed, 06 Dec 2017 18:23:44: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:23:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:23:45: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:23:45: 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, 06 Dec 2017 18:23:45: Process for pairing-model is terminated! cat: SRX3353384.10_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 `SRX3353384.10_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 `SRX3353384.10_*.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 `SRX3353384.10_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, 06 Dec 2017 18:23:47: 18000000 INFO @ Wed, 06 Dec 2017 18:23:49: 19000000 INFO @ Wed, 06 Dec 2017 18:23:53: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:23:53: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:23:53: #1 total tags in treatment: 8720940 INFO @ Wed, 06 Dec 2017 18:23:53: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:23:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:23:53: #1 tags after filtering in treatment: 6483734 INFO @ Wed, 06 Dec 2017 18:23:53: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 06 Dec 2017 18:23:53: #1 finished! INFO @ Wed, 06 Dec 2017 18:23:53: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:23:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:23:53: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:23:53: 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, 06 Dec 2017 18:23:53: Process for pairing-model is terminated! cat: SRX3353384.05_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 `SRX3353384.05_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 `SRX3353384.05_*.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 `SRX3353384.05_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, 06 Dec 2017 18:23:53: 19000000 INFO @ Wed, 06 Dec 2017 18:23:57: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:23:57: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:23:57: #1 total tags in treatment: 8720940 INFO @ Wed, 06 Dec 2017 18:23:57: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:23:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:23:57: #1 tags after filtering in treatment: 6483734 INFO @ Wed, 06 Dec 2017 18:23:57: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 06 Dec 2017 18:23:57: #1 finished! INFO @ Wed, 06 Dec 2017 18:23:57: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:23:58: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:23:58: 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, 06 Dec 2017 18:23:58: Process for pairing-model is terminated! cat: SRX3353384.20_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 `SRX3353384.20_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 `SRX3353384.20_*.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 `SRX3353384.20_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。