Job ID = 11245237 sra ファイルのダウンロード中... Completed: 688769K bytes transferred in 10 seconds (557438K 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 24990336 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4717379/SRR7878702.sra Written 24990336 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4717379/SRR7878702.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:49 24990336 reads; of these: 24990336 (100.00%) were unpaired; of these: 1243874 (4.98%) aligned 0 times 21831939 (87.36%) aligned exactly 1 time 1914523 (7.66%) aligned >1 times 95.02% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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] 14106467 / 23746462 = 0.5940 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 00:08:18: # Command line: callpeak -t SRX4717379.bam -f BAM -g 12100000 -n SRX4717379.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4717379.05 # format = BAM # ChIP-seq file = ['SRX4717379.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 00:08:18: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:08:18: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:08:18: # Command line: callpeak -t SRX4717379.bam -f BAM -g 12100000 -n SRX4717379.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4717379.20 # format = BAM # ChIP-seq file = ['SRX4717379.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 00:08:18: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:08:18: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:08:18: # Command line: callpeak -t SRX4717379.bam -f BAM -g 12100000 -n SRX4717379.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4717379.10 # format = BAM # ChIP-seq file = ['SRX4717379.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 00:08:18: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:08:18: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:08:25: 1000000 INFO @ Wed, 10 Oct 2018 00:08:25: 1000000 INFO @ Wed, 10 Oct 2018 00:08:26: 1000000 INFO @ Wed, 10 Oct 2018 00:08:32: 2000000 INFO @ Wed, 10 Oct 2018 00:08:33: 2000000 INFO @ Wed, 10 Oct 2018 00:08:33: 2000000 INFO @ Wed, 10 Oct 2018 00:08:39: 3000000 INFO @ Wed, 10 Oct 2018 00:08:40: 3000000 INFO @ Wed, 10 Oct 2018 00:08:40: 3000000 INFO @ Wed, 10 Oct 2018 00:08:46: 4000000 INFO @ Wed, 10 Oct 2018 00:08:46: 4000000 INFO @ Wed, 10 Oct 2018 00:08:47: 4000000 INFO @ Wed, 10 Oct 2018 00:08:53: 5000000 INFO @ Wed, 10 Oct 2018 00:08:54: 5000000 INFO @ Wed, 10 Oct 2018 00:08:55: 5000000 INFO @ Wed, 10 Oct 2018 00:09:00: 6000000 INFO @ Wed, 10 Oct 2018 00:09:01: 6000000 INFO @ Wed, 10 Oct 2018 00:09:03: 6000000 INFO @ Wed, 10 Oct 2018 00:09:07: 7000000 INFO @ Wed, 10 Oct 2018 00:09:08: 7000000 INFO @ Wed, 10 Oct 2018 00:09:10: 7000000 INFO @ Wed, 10 Oct 2018 00:09:13: 8000000 INFO @ Wed, 10 Oct 2018 00:09:16: 8000000 INFO @ Wed, 10 Oct 2018 00:09:18: 8000000 INFO @ Wed, 10 Oct 2018 00:09:20: 9000000 INFO @ Wed, 10 Oct 2018 00:09:23: 9000000 INFO @ Wed, 10 Oct 2018 00:09:24: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:09:24: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:09:24: #1 total tags in treatment: 9639995 INFO @ Wed, 10 Oct 2018 00:09:24: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:09:24: #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 00:09:24: #1 tags after filtering in treatment: 9639995 INFO @ Wed, 10 Oct 2018 00:09:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:09:24: #1 finished! INFO @ Wed, 10 Oct 2018 00:09:24: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:09:25: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:09:25: 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 00:09:25: Process for pairing-model is terminated! cat: SRX4717379.05_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 `SRX4717379.05_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 `SRX4717379.05_*.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 `SRX4717379.05_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, 10 Oct 2018 00:09:25: 9000000 INFO @ Wed, 10 Oct 2018 00:09:27: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:09:27: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:09:27: #1 total tags in treatment: 9639995 INFO @ Wed, 10 Oct 2018 00:09:27: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:09:27: #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 00:09:27: #1 tags after filtering in treatment: 9639995 INFO @ Wed, 10 Oct 2018 00:09:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:09:27: #1 finished! INFO @ Wed, 10 Oct 2018 00:09:27: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:09:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:09:28: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:09:28: 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 00:09:28: Process for pairing-model is terminated! cat: SRX4717379.10_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 `SRX4717379.10_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 `SRX4717379.10_*.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 `SRX4717379.10_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 00:09:30: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:09:30: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:09:30: #1 total tags in treatment: 9639995 INFO @ Wed, 10 Oct 2018 00:09:30: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:09:30: #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 00:09:30: #1 tags after filtering in treatment: 9639995 INFO @ Wed, 10 Oct 2018 00:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:09:30: #1 finished! INFO @ Wed, 10 Oct 2018 00:09:30: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:09:30: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:09:30: 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 00:09:30: Process for pairing-model is terminated! cat: SRX4717379.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4717379.20_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 `SRX4717379.20_*.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 `SRX4717379.20_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。