Job ID = 11245239 sra ファイルのダウンロード中... Completed: 563478K bytes transferred in 8 seconds (576416K 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: SINGLE fastq に変換中... Read 20784027 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4717381/SRR7878704.sra Written 20784027 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4717381/SRR7878704.sra 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: 00:05:03 20784027 reads; of these: 20784027 (100.00%) were unpaired; of these: 864191 (4.16%) aligned 0 times 16865340 (81.15%) aligned exactly 1 time 3054496 (14.70%) aligned >1 times 95.84% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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_rmdupse_core] 8350466 / 19919836 = 0.4192 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, 10 Oct 2018 00:07:29: # Command line: callpeak -t SRX4717381.bam -f BAM -g 12100000 -n SRX4717381.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4717381.05 # format = BAM # ChIP-seq file = ['SRX4717381.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, 10 Oct 2018 00:07:29: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:07:29: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:07:29: # Command line: callpeak -t SRX4717381.bam -f BAM -g 12100000 -n SRX4717381.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4717381.20 # format = BAM # ChIP-seq file = ['SRX4717381.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, 10 Oct 2018 00:07:29: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:07:29: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:07:29: # Command line: callpeak -t SRX4717381.bam -f BAM -g 12100000 -n SRX4717381.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4717381.10 # format = BAM # ChIP-seq file = ['SRX4717381.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, 10 Oct 2018 00:07:29: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:07:29: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:07:36: 1000000 INFO @ Wed, 10 Oct 2018 00:07:36: 1000000 INFO @ Wed, 10 Oct 2018 00:07:36: 1000000 INFO @ Wed, 10 Oct 2018 00:07:42: 2000000 INFO @ Wed, 10 Oct 2018 00:07:42: 2000000 INFO @ Wed, 10 Oct 2018 00:07:42: 2000000 INFO @ Wed, 10 Oct 2018 00:07:49: 3000000 INFO @ Wed, 10 Oct 2018 00:07:49: 3000000 INFO @ Wed, 10 Oct 2018 00:07:49: 3000000 INFO @ Wed, 10 Oct 2018 00:07:55: 4000000 INFO @ Wed, 10 Oct 2018 00:07:55: 4000000 INFO @ Wed, 10 Oct 2018 00:07:56: 4000000 INFO @ Wed, 10 Oct 2018 00:08:02: 5000000 INFO @ Wed, 10 Oct 2018 00:08:02: 5000000 INFO @ Wed, 10 Oct 2018 00:08:03: 5000000 INFO @ Wed, 10 Oct 2018 00:08:08: 6000000 INFO @ Wed, 10 Oct 2018 00:08:09: 6000000 INFO @ Wed, 10 Oct 2018 00:08:09: 6000000 INFO @ Wed, 10 Oct 2018 00:08:15: 7000000 INFO @ Wed, 10 Oct 2018 00:08:16: 7000000 INFO @ Wed, 10 Oct 2018 00:08:16: 7000000 INFO @ Wed, 10 Oct 2018 00:08:21: 8000000 INFO @ Wed, 10 Oct 2018 00:08:22: 8000000 INFO @ Wed, 10 Oct 2018 00:08:23: 8000000 INFO @ Wed, 10 Oct 2018 00:08:27: 9000000 INFO @ Wed, 10 Oct 2018 00:08:29: 9000000 INFO @ Wed, 10 Oct 2018 00:08:30: 9000000 INFO @ Wed, 10 Oct 2018 00:08:34: 10000000 INFO @ Wed, 10 Oct 2018 00:08:36: 10000000 INFO @ Wed, 10 Oct 2018 00:08:38: 10000000 INFO @ Wed, 10 Oct 2018 00:08:40: 11000000 INFO @ Wed, 10 Oct 2018 00:08:43: 11000000 INFO @ Wed, 10 Oct 2018 00:08:44: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:08:44: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:08:44: #1 total tags in treatment: 11569370 INFO @ Wed, 10 Oct 2018 00:08:44: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:08:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:08:44: #1 tags after filtering in treatment: 11569370 INFO @ Wed, 10 Oct 2018 00:08:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:08:44: #1 finished! INFO @ Wed, 10 Oct 2018 00:08:44: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:08:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:08:45: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:08:45: 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, 10 Oct 2018 00:08:45: Process for pairing-model is terminated! cat: SRX4717381.10_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 `SRX4717381.10_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 `SRX4717381.10_*.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 `SRX4717381.10_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, 10 Oct 2018 00:08:45: 11000000 INFO @ Wed, 10 Oct 2018 00:08:47: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:08:47: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:08:47: #1 total tags in treatment: 11569370 INFO @ Wed, 10 Oct 2018 00:08:47: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:08:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:08:47: #1 tags after filtering in treatment: 11569370 INFO @ Wed, 10 Oct 2018 00:08:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:08:47: #1 finished! INFO @ Wed, 10 Oct 2018 00:08:47: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:08:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:08:48: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:08:48: 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, 10 Oct 2018 00:08:48: Process for pairing-model is terminated! cat: SRX4717381.20_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 `SRX4717381.20_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 `SRX4717381.20_*.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 `SRX4717381.20_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, 10 Oct 2018 00:08:49: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:08:49: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:08:49: #1 total tags in treatment: 11569370 INFO @ Wed, 10 Oct 2018 00:08:49: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:08:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:08:49: #1 tags after filtering in treatment: 11569370 INFO @ Wed, 10 Oct 2018 00:08:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:08:49: #1 finished! INFO @ Wed, 10 Oct 2018 00:08:49: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:08:50: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:08:50: 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, 10 Oct 2018 00:08:50: Process for pairing-model is terminated! cat: SRX4717381.05_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 `SRX4717381.05_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 `SRX4717381.05_*.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 `SRX4717381.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。