Job ID = 11296932 sra ファイルのダウンロード中... Completed: 175436K bytes transferred in 4 seconds (301168K 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 8899118 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856347/SRR6908164.sra Written 8899118 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856347/SRR6908164.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: 00:01:41 8899118 reads; of these: 8899118 (100.00%) were unpaired; of these: 288198 (3.24%) aligned 0 times 6992443 (78.57%) aligned exactly 1 time 1618477 (18.19%) aligned >1 times 96.76% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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_rmdupse_core] 2483403 / 8610920 = 0.2884 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 @ Mon, 05 Nov 2018 17:59:48: # Command line: callpeak -t SRX3856347.bam -f BAM -g 12100000 -n SRX3856347.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856347.05 # format = BAM # ChIP-seq file = ['SRX3856347.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 @ Mon, 05 Nov 2018 17:59:48: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:59:48: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:59:48: # Command line: callpeak -t SRX3856347.bam -f BAM -g 12100000 -n SRX3856347.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856347.20 # format = BAM # ChIP-seq file = ['SRX3856347.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 @ Mon, 05 Nov 2018 17:59:48: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:59:48: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:59:48: # Command line: callpeak -t SRX3856347.bam -f BAM -g 12100000 -n SRX3856347.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856347.10 # format = BAM # ChIP-seq file = ['SRX3856347.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 @ Mon, 05 Nov 2018 17:59:48: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:59:48: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:59:55: 1000000 INFO @ Mon, 05 Nov 2018 17:59:55: 1000000 INFO @ Mon, 05 Nov 2018 17:59:57: 1000000 INFO @ Mon, 05 Nov 2018 18:00:00: 2000000 INFO @ Mon, 05 Nov 2018 18:00:02: 2000000 INFO @ Mon, 05 Nov 2018 18:00:05: 2000000 INFO @ Mon, 05 Nov 2018 18:00:06: 3000000 INFO @ Mon, 05 Nov 2018 18:00:09: 3000000 INFO @ Mon, 05 Nov 2018 18:00:12: 3000000 INFO @ Mon, 05 Nov 2018 18:00:12: 4000000 INFO @ Mon, 05 Nov 2018 18:00:16: 4000000 INFO @ Mon, 05 Nov 2018 18:00:18: 5000000 INFO @ Mon, 05 Nov 2018 18:00:20: 4000000 INFO @ Mon, 05 Nov 2018 18:00:23: 5000000 INFO @ Mon, 05 Nov 2018 18:00:24: 6000000 INFO @ Mon, 05 Nov 2018 18:00:25: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:00:25: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:00:25: #1 total tags in treatment: 6127517 INFO @ Mon, 05 Nov 2018 18:00:25: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:00:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:00:25: #1 tags after filtering in treatment: 6127517 INFO @ Mon, 05 Nov 2018 18:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:00:25: #1 finished! INFO @ Mon, 05 Nov 2018 18:00:25: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:00:26: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:00:26: 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 @ Mon, 05 Nov 2018 18:00:26: Process for pairing-model is terminated! cat: SRX3856347.20_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 `SRX3856347.20_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 `SRX3856347.20_*.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 `SRX3856347.20_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 @ Mon, 05 Nov 2018 18:00:27: 5000000 INFO @ Mon, 05 Nov 2018 18:00:29: 6000000 INFO @ Mon, 05 Nov 2018 18:00:30: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:00:30: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:00:30: #1 total tags in treatment: 6127517 INFO @ Mon, 05 Nov 2018 18:00:30: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:00:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:00:30: #1 tags after filtering in treatment: 6127517 INFO @ Mon, 05 Nov 2018 18:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:00:30: #1 finished! INFO @ Mon, 05 Nov 2018 18:00:30: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:00:30: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:00:30: 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 @ Mon, 05 Nov 2018 18:00:30: Process for pairing-model is terminated! cat: SRX3856347.10_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 `SRX3856347.10_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 `SRX3856347.10_*.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 `SRX3856347.10_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 @ Mon, 05 Nov 2018 18:00:33: 6000000 INFO @ Mon, 05 Nov 2018 18:00:34: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:00:34: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:00:34: #1 total tags in treatment: 6127517 INFO @ Mon, 05 Nov 2018 18:00:34: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:00:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 18:00:34: #1 tags after filtering in treatment: 6127517 INFO @ Mon, 05 Nov 2018 18:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:00:34: #1 finished! INFO @ Mon, 05 Nov 2018 18:00:34: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:00:34: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:00:34: 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 @ Mon, 05 Nov 2018 18:00:34: Process for pairing-model is terminated! cat: SRX3856347.05_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 `SRX3856347.05_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 `SRX3856347.05_*.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 `SRX3856347.05_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。