Job ID = 11296961 sra ファイルのダウンロード中... Completed: 205556K bytes transferred in 5 seconds (297786K 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 10448882 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856383/SRR6908201.sra Written 10448882 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856383/SRR6908201.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: 00:02:14 10448882 reads; of these: 10448882 (100.00%) were unpaired; of these: 511311 (4.89%) aligned 0 times 8449435 (80.86%) aligned exactly 1 time 1488136 (14.24%) aligned >1 times 95.11% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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_rmdupse_core] 2597745 / 9937571 = 0.2614 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 18:06:10: # Command line: callpeak -t SRX3856383.bam -f BAM -g 12100000 -n SRX3856383.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856383.20 # format = BAM # ChIP-seq file = ['SRX3856383.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 18:06:10: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:06:10: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:06:10: # Command line: callpeak -t SRX3856383.bam -f BAM -g 12100000 -n SRX3856383.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856383.05 # format = BAM # ChIP-seq file = ['SRX3856383.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 18:06:10: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:06:10: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:06:10: # Command line: callpeak -t SRX3856383.bam -f BAM -g 12100000 -n SRX3856383.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856383.10 # format = BAM # ChIP-seq file = ['SRX3856383.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 18:06:10: #1 read tag files... INFO @ Mon, 05 Nov 2018 18:06:10: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 18:06:18: 1000000 INFO @ Mon, 05 Nov 2018 18:06:19: 1000000 INFO @ Mon, 05 Nov 2018 18:06:20: 1000000 INFO @ Mon, 05 Nov 2018 18:06:27: 2000000 INFO @ Mon, 05 Nov 2018 18:06:28: 2000000 INFO @ Mon, 05 Nov 2018 18:06:31: 2000000 INFO @ Mon, 05 Nov 2018 18:06:35: 3000000 INFO @ Mon, 05 Nov 2018 18:06:38: 3000000 INFO @ Mon, 05 Nov 2018 18:06:42: 3000000 INFO @ Mon, 05 Nov 2018 18:06:44: 4000000 INFO @ Mon, 05 Nov 2018 18:06:47: 4000000 INFO @ Mon, 05 Nov 2018 18:06:52: 4000000 INFO @ Mon, 05 Nov 2018 18:06:53: 5000000 INFO @ Mon, 05 Nov 2018 18:06:56: 5000000 INFO @ Mon, 05 Nov 2018 18:07:01: 6000000 INFO @ Mon, 05 Nov 2018 18:07:03: 5000000 INFO @ Mon, 05 Nov 2018 18:07:05: 6000000 INFO @ Mon, 05 Nov 2018 18:07:10: 7000000 INFO @ Mon, 05 Nov 2018 18:07:12: 6000000 INFO @ Mon, 05 Nov 2018 18:07:13: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:07:13: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:07:13: #1 total tags in treatment: 7339826 INFO @ Mon, 05 Nov 2018 18:07:13: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:07:13: #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 18:07:13: #1 tags after filtering in treatment: 7339826 INFO @ Mon, 05 Nov 2018 18:07:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:07:13: #1 finished! INFO @ Mon, 05 Nov 2018 18:07:13: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:07:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:07:14: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:07:14: 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 18:07:14: Process for pairing-model is terminated! cat: SRX3856383.20_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 `SRX3856383.20_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 `SRX3856383.20_*.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 `SRX3856383.20_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 18:07:14: 7000000 INFO @ Mon, 05 Nov 2018 18:07:17: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:07:17: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:07:17: #1 total tags in treatment: 7339826 INFO @ Mon, 05 Nov 2018 18:07:17: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:07:17: #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 18:07:17: #1 tags after filtering in treatment: 7339826 INFO @ Mon, 05 Nov 2018 18:07:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:07:17: #1 finished! INFO @ Mon, 05 Nov 2018 18:07:17: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:07:18: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:07:18: 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 18:07:18: Process for pairing-model is terminated! cat: SRX3856383.10_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 `SRX3856383.10_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 `SRX3856383.10_*.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 `SRX3856383.10_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 18:07:20: 7000000 INFO @ Mon, 05 Nov 2018 18:07:23: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:07:23: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:07:23: #1 total tags in treatment: 7339826 INFO @ Mon, 05 Nov 2018 18:07:23: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:07:23: #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 18:07:23: #1 tags after filtering in treatment: 7339826 INFO @ Mon, 05 Nov 2018 18:07:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:07:23: #1 finished! INFO @ Mon, 05 Nov 2018 18:07:23: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:07:23: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:07:23: 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 18:07:23: Process for pairing-model is terminated! cat: SRX3856383.05_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 `SRX3856383.05_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 `SRX3856383.05_*.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 `SRX3856383.05_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。