Job ID = 10536489 sra ファイルのダウンロード中... Completed: 1502837K bytes transferred in 54 seconds (226112K 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 35822305 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671185/SRR6696937.sra Written 35822305 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 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: 00:21:24 35822305 reads; of these: 35822305 (100.00%) were paired; of these: 11841682 (33.06%) aligned concordantly 0 times 21212660 (59.22%) aligned concordantly exactly 1 time 2767963 (7.73%) aligned concordantly >1 times ---- 11841682 pairs aligned concordantly 0 times; of these: 26987 (0.23%) aligned discordantly 1 time ---- 11814695 pairs aligned 0 times concordantly or discordantly; of these: 23629390 mates make up the pairs; of these: 23409352 (99.07%) aligned 0 times 184358 (0.78%) aligned exactly 1 time 35680 (0.15%) aligned >1 times 67.33% overall alignment rate Time searching: 00:21:24 Overall time: 00:21:24 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 20 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] 13326967 / 23998080 = 0.5553 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 @ Thu, 05 Apr 2018 10:17:41: # Command line: callpeak -t SRX3671185.bam -f BAM -g 12100000 -n SRX3671185.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671185.10 # format = BAM # ChIP-seq file = ['SRX3671185.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 @ Thu, 05 Apr 2018 10:17:41: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:17:41: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:17:41: # Command line: callpeak -t SRX3671185.bam -f BAM -g 12100000 -n SRX3671185.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671185.05 # format = BAM # ChIP-seq file = ['SRX3671185.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 @ Thu, 05 Apr 2018 10:17:41: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:17:41: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:17:41: # Command line: callpeak -t SRX3671185.bam -f BAM -g 12100000 -n SRX3671185.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671185.20 # format = BAM # ChIP-seq file = ['SRX3671185.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 @ Thu, 05 Apr 2018 10:17:41: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:17:41: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:17:46: 1000000 INFO @ Thu, 05 Apr 2018 10:17:47: 1000000 INFO @ Thu, 05 Apr 2018 10:17:47: 1000000 INFO @ Thu, 05 Apr 2018 10:17:52: 2000000 INFO @ Thu, 05 Apr 2018 10:17:52: 2000000 INFO @ Thu, 05 Apr 2018 10:17:52: 2000000 INFO @ Thu, 05 Apr 2018 10:17:57: 3000000 INFO @ Thu, 05 Apr 2018 10:17:57: 3000000 INFO @ Thu, 05 Apr 2018 10:17:57: 3000000 INFO @ Thu, 05 Apr 2018 10:18:02: 4000000 INFO @ Thu, 05 Apr 2018 10:18:02: 4000000 INFO @ Thu, 05 Apr 2018 10:18:03: 4000000 INFO @ Thu, 05 Apr 2018 10:18:07: 5000000 INFO @ Thu, 05 Apr 2018 10:18:08: 5000000 INFO @ Thu, 05 Apr 2018 10:18:08: 5000000 INFO @ Thu, 05 Apr 2018 10:18:13: 6000000 INFO @ Thu, 05 Apr 2018 10:18:13: 6000000 INFO @ Thu, 05 Apr 2018 10:18:14: 6000000 INFO @ Thu, 05 Apr 2018 10:18:18: 7000000 INFO @ Thu, 05 Apr 2018 10:18:19: 7000000 INFO @ Thu, 05 Apr 2018 10:18:19: 7000000 INFO @ Thu, 05 Apr 2018 10:18:23: 8000000 INFO @ Thu, 05 Apr 2018 10:18:24: 8000000 INFO @ Thu, 05 Apr 2018 10:18:25: 8000000 INFO @ Thu, 05 Apr 2018 10:18:29: 9000000 INFO @ Thu, 05 Apr 2018 10:18:31: 9000000 INFO @ Thu, 05 Apr 2018 10:18:32: 9000000 INFO @ Thu, 05 Apr 2018 10:18:35: 10000000 INFO @ Thu, 05 Apr 2018 10:18:37: 10000000 INFO @ Thu, 05 Apr 2018 10:18:38: 10000000 INFO @ Thu, 05 Apr 2018 10:18:42: 11000000 INFO @ Thu, 05 Apr 2018 10:18:44: 11000000 INFO @ Thu, 05 Apr 2018 10:18:45: 11000000 INFO @ Thu, 05 Apr 2018 10:18:48: 12000000 INFO @ Thu, 05 Apr 2018 10:18:51: 12000000 INFO @ Thu, 05 Apr 2018 10:18:52: 12000000 INFO @ Thu, 05 Apr 2018 10:18:55: 13000000 INFO @ Thu, 05 Apr 2018 10:18:57: 13000000 INFO @ Thu, 05 Apr 2018 10:18:59: 13000000 INFO @ Thu, 05 Apr 2018 10:19:01: 14000000 INFO @ Thu, 05 Apr 2018 10:19:04: 14000000 INFO @ Thu, 05 Apr 2018 10:19:05: 14000000 INFO @ Thu, 05 Apr 2018 10:19:08: 15000000 INFO @ Thu, 05 Apr 2018 10:19:10: 15000000 INFO @ Thu, 05 Apr 2018 10:19:12: 15000000 INFO @ Thu, 05 Apr 2018 10:19:15: 16000000 INFO @ Thu, 05 Apr 2018 10:19:17: 16000000 INFO @ Thu, 05 Apr 2018 10:19:19: 16000000 INFO @ Thu, 05 Apr 2018 10:19:21: 17000000 INFO @ Thu, 05 Apr 2018 10:19:24: 17000000 INFO @ Thu, 05 Apr 2018 10:19:26: 17000000 INFO @ Thu, 05 Apr 2018 10:19:28: 18000000 INFO @ Thu, 05 Apr 2018 10:19:30: 18000000 INFO @ Thu, 05 Apr 2018 10:19:32: 18000000 INFO @ Thu, 05 Apr 2018 10:19:34: 19000000 INFO @ Thu, 05 Apr 2018 10:19:37: 19000000 INFO @ Thu, 05 Apr 2018 10:19:39: 19000000 INFO @ Thu, 05 Apr 2018 10:19:41: 20000000 INFO @ Thu, 05 Apr 2018 10:19:43: 20000000 INFO @ Thu, 05 Apr 2018 10:19:46: 20000000 INFO @ Thu, 05 Apr 2018 10:19:48: 21000000 INFO @ Thu, 05 Apr 2018 10:19:50: 21000000 INFO @ Thu, 05 Apr 2018 10:19:52: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:19:52: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:19:52: #1 total tags in treatment: 10659339 INFO @ Thu, 05 Apr 2018 10:19:52: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:19:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:19:52: #1 tags after filtering in treatment: 7962502 INFO @ Thu, 05 Apr 2018 10:19:52: #1 Redundant rate of treatment: 0.25 INFO @ Thu, 05 Apr 2018 10:19:52: #1 finished! INFO @ Thu, 05 Apr 2018 10:19:52: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:19:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:19:52: 21000000 INFO @ Thu, 05 Apr 2018 10:19:52: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:19:52: 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 @ Thu, 05 Apr 2018 10:19:52: Process for pairing-model is terminated! cat: SRX3671185.10_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 `SRX3671185.10_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 `SRX3671185.10_*.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 `SRX3671185.10_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 @ Thu, 05 Apr 2018 10:19:54: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:19:54: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:19:54: #1 total tags in treatment: 10659339 INFO @ Thu, 05 Apr 2018 10:19:54: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:19:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:19:54: #1 tags after filtering in treatment: 7962502 INFO @ Thu, 05 Apr 2018 10:19:54: #1 Redundant rate of treatment: 0.25 INFO @ Thu, 05 Apr 2018 10:19:54: #1 finished! INFO @ Thu, 05 Apr 2018 10:19:54: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:19:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:19:55: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:19:55: 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 @ Thu, 05 Apr 2018 10:19:55: Process for pairing-model is terminated! cat: SRX3671185.05_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 `SRX3671185.05_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 `SRX3671185.05_*.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 `SRX3671185.05_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 @ Thu, 05 Apr 2018 10:19:56: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:19:56: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:19:56: #1 total tags in treatment: 10659339 INFO @ Thu, 05 Apr 2018 10:19:56: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:19:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 10:19:56: #1 tags after filtering in treatment: 7962502 INFO @ Thu, 05 Apr 2018 10:19:56: #1 Redundant rate of treatment: 0.25 INFO @ Thu, 05 Apr 2018 10:19:56: #1 finished! INFO @ Thu, 05 Apr 2018 10:19:56: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:19:57: #2 number of paired peaks: 0 WARNING @ Thu, 05 Apr 2018 10:19:57: 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 @ Thu, 05 Apr 2018 10:19:57: Process for pairing-model is terminated! cat: SRX3671185.20_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 `SRX3671185.20_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 `SRX3671185.20_*.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 `SRX3671185.20_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。