Job ID = 9384123 sra ファイルのダウンロード中... Completed: 974099K bytes transferred in 21 seconds (374262K 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 7167391 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2963107/SRR5763438.sra Written 7167391 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: 00:08:07 7167391 reads; of these: 7167391 (100.00%) were paired; of these: 973360 (13.58%) aligned concordantly 0 times 5618532 (78.39%) aligned concordantly exactly 1 time 575499 (8.03%) aligned concordantly >1 times ---- 973360 pairs aligned concordantly 0 times; of these: 148813 (15.29%) aligned discordantly 1 time ---- 824547 pairs aligned 0 times concordantly or discordantly; of these: 1649094 mates make up the pairs; of these: 1485239 (90.06%) aligned 0 times 113174 (6.86%) aligned exactly 1 time 50681 (3.07%) aligned >1 times 89.64% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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 8 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] 127078 / 6333875 = 0.0201 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 @ Sun, 06 Aug 2017 00:56:41: # Command line: callpeak -t SRX2963107.bam -f BAM -g 12100000 -n SRX2963107.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2963107.10 # format = BAM # ChIP-seq file = ['SRX2963107.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 @ Sun, 06 Aug 2017 00:56:41: #1 read tag files... INFO @ Sun, 06 Aug 2017 00:56:41: #1 read treatment tags... INFO @ Sun, 06 Aug 2017 00:56:41: # Command line: callpeak -t SRX2963107.bam -f BAM -g 12100000 -n SRX2963107.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2963107.05 # format = BAM # ChIP-seq file = ['SRX2963107.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 @ Sun, 06 Aug 2017 00:56:41: #1 read tag files... INFO @ Sun, 06 Aug 2017 00:56:41: #1 read treatment tags... INFO @ Sun, 06 Aug 2017 00:56:41: # Command line: callpeak -t SRX2963107.bam -f BAM -g 12100000 -n SRX2963107.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2963107.20 # format = BAM # ChIP-seq file = ['SRX2963107.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 @ Sun, 06 Aug 2017 00:56:41: #1 read tag files... INFO @ Sun, 06 Aug 2017 00:56:41: #1 read treatment tags... INFO @ Sun, 06 Aug 2017 00:56:48: 1000000 INFO @ Sun, 06 Aug 2017 00:56:48: 1000000 INFO @ Sun, 06 Aug 2017 00:56:48: 1000000 INFO @ Sun, 06 Aug 2017 00:56:55: 2000000 INFO @ Sun, 06 Aug 2017 00:56:55: 2000000 INFO @ Sun, 06 Aug 2017 00:56:55: 2000000 INFO @ Sun, 06 Aug 2017 00:57:02: 3000000 INFO @ Sun, 06 Aug 2017 00:57:02: 3000000 INFO @ Sun, 06 Aug 2017 00:57:02: 3000000 INFO @ Sun, 06 Aug 2017 00:57:08: 4000000 INFO @ Sun, 06 Aug 2017 00:57:09: 4000000 INFO @ Sun, 06 Aug 2017 00:57:09: 4000000 INFO @ Sun, 06 Aug 2017 00:57:15: 5000000 INFO @ Sun, 06 Aug 2017 00:57:16: 5000000 INFO @ Sun, 06 Aug 2017 00:57:16: 5000000 INFO @ Sun, 06 Aug 2017 00:57:22: 6000000 INFO @ Sun, 06 Aug 2017 00:57:22: 6000000 INFO @ Sun, 06 Aug 2017 00:57:24: 6000000 INFO @ Sun, 06 Aug 2017 00:57:29: 7000000 INFO @ Sun, 06 Aug 2017 00:57:29: 7000000 INFO @ Sun, 06 Aug 2017 00:57:31: 7000000 INFO @ Sun, 06 Aug 2017 00:57:36: 8000000 INFO @ Sun, 06 Aug 2017 00:57:36: 8000000 INFO @ Sun, 06 Aug 2017 00:57:38: 8000000 INFO @ Sun, 06 Aug 2017 00:57:42: 9000000 INFO @ Sun, 06 Aug 2017 00:57:43: 9000000 INFO @ Sun, 06 Aug 2017 00:57:45: 9000000 INFO @ Sun, 06 Aug 2017 00:57:49: 10000000 INFO @ Sun, 06 Aug 2017 00:57:51: 10000000 INFO @ Sun, 06 Aug 2017 00:57:54: 10000000 INFO @ Sun, 06 Aug 2017 00:57:57: 11000000 INFO @ Sun, 06 Aug 2017 00:57:59: 11000000 INFO @ Sun, 06 Aug 2017 00:58:01: 11000000 INFO @ Sun, 06 Aug 2017 00:58:03: 12000000 INFO @ Sun, 06 Aug 2017 00:58:06: 12000000 INFO @ Sun, 06 Aug 2017 00:58:07: #1 tag size is determined as 101 bps INFO @ Sun, 06 Aug 2017 00:58:07: #1 tag size = 101 INFO @ Sun, 06 Aug 2017 00:58:07: #1 total tags in treatment: 6068622 INFO @ Sun, 06 Aug 2017 00:58:07: #1 user defined the maximum tags... INFO @ Sun, 06 Aug 2017 00:58:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 06 Aug 2017 00:58:07: #1 tags after filtering in treatment: 5142687 INFO @ Sun, 06 Aug 2017 00:58:07: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 06 Aug 2017 00:58:07: #1 finished! INFO @ Sun, 06 Aug 2017 00:58:07: #2 Build Peak Model... INFO @ Sun, 06 Aug 2017 00:58:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 06 Aug 2017 00:58:08: #2 number of paired peaks: 0 WARNING @ Sun, 06 Aug 2017 00:58:08: 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 @ Sun, 06 Aug 2017 00:58:08: Process for pairing-model is terminated! cat: SRX2963107.20_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 `SRX2963107.20_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 `SRX2963107.20_*.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 `SRX2963107.20_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 @ Sun, 06 Aug 2017 00:58:08: 12000000 INFO @ Sun, 06 Aug 2017 00:58:10: #1 tag size is determined as 101 bps INFO @ Sun, 06 Aug 2017 00:58:10: #1 tag size = 101 INFO @ Sun, 06 Aug 2017 00:58:10: #1 total tags in treatment: 6068622 INFO @ Sun, 06 Aug 2017 00:58:10: #1 user defined the maximum tags... INFO @ Sun, 06 Aug 2017 00:58:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 06 Aug 2017 00:58:10: #1 tags after filtering in treatment: 5142687 INFO @ Sun, 06 Aug 2017 00:58:10: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 06 Aug 2017 00:58:10: #1 finished! INFO @ Sun, 06 Aug 2017 00:58:10: #2 Build Peak Model... INFO @ Sun, 06 Aug 2017 00:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 06 Aug 2017 00:58:10: #2 number of paired peaks: 0 WARNING @ Sun, 06 Aug 2017 00:58:10: 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 @ Sun, 06 Aug 2017 00:58:10: Process for pairing-model is terminated! cat: SRX2963107.05_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 `SRX2963107.05_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 `SRX2963107.05_*.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 `SRX2963107.05_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 @ Sun, 06 Aug 2017 00:58:13: #1 tag size is determined as 101 bps INFO @ Sun, 06 Aug 2017 00:58:13: #1 tag size = 101 INFO @ Sun, 06 Aug 2017 00:58:13: #1 total tags in treatment: 6068622 INFO @ Sun, 06 Aug 2017 00:58:13: #1 user defined the maximum tags... INFO @ Sun, 06 Aug 2017 00:58:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 06 Aug 2017 00:58:13: #1 tags after filtering in treatment: 5142687 INFO @ Sun, 06 Aug 2017 00:58:13: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 06 Aug 2017 00:58:13: #1 finished! INFO @ Sun, 06 Aug 2017 00:58:13: #2 Build Peak Model... INFO @ Sun, 06 Aug 2017 00:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 06 Aug 2017 00:58:13: #2 number of paired peaks: 0 WARNING @ Sun, 06 Aug 2017 00:58:13: 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 @ Sun, 06 Aug 2017 00:58:13: Process for pairing-model is terminated! cat: SRX2963107.10_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 `SRX2963107.10_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 `SRX2963107.10_*.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 `SRX2963107.10_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。