Job ID = 11634684 sra ファイルのダウンロード中... Completed: 291451K bytes transferred in 5 seconds (440835K 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 13235232 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4092964/SRR7175392.sra Written 13235232 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4092964/SRR7175392.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: 00:02:13 13235232 reads; of these: 13235232 (100.00%) were unpaired; of these: 549133 (4.15%) aligned 0 times 10001259 (75.57%) aligned exactly 1 time 2684840 (20.29%) aligned >1 times 95.85% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 4323680 / 12686099 = 0.3408 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 @ Fri, 15 Feb 2019 10:30:11: # Command line: callpeak -t SRX4092964.bam -f BAM -g 12100000 -n SRX4092964.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4092964.20 # format = BAM # ChIP-seq file = ['SRX4092964.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 @ Fri, 15 Feb 2019 10:30:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:30:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:30:11: # Command line: callpeak -t SRX4092964.bam -f BAM -g 12100000 -n SRX4092964.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4092964.05 # format = BAM # ChIP-seq file = ['SRX4092964.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 @ Fri, 15 Feb 2019 10:30:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:30:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:30:11: # Command line: callpeak -t SRX4092964.bam -f BAM -g 12100000 -n SRX4092964.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4092964.10 # format = BAM # ChIP-seq file = ['SRX4092964.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 @ Fri, 15 Feb 2019 10:30:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:30:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:30:17: 1000000 INFO @ Fri, 15 Feb 2019 10:30:17: 1000000 INFO @ Fri, 15 Feb 2019 10:30:17: 1000000 INFO @ Fri, 15 Feb 2019 10:30:23: 2000000 INFO @ Fri, 15 Feb 2019 10:30:24: 2000000 INFO @ Fri, 15 Feb 2019 10:30:24: 2000000 INFO @ Fri, 15 Feb 2019 10:30:29: 3000000 INFO @ Fri, 15 Feb 2019 10:30:30: 3000000 INFO @ Fri, 15 Feb 2019 10:30:30: 3000000 INFO @ Fri, 15 Feb 2019 10:30:35: 4000000 INFO @ Fri, 15 Feb 2019 10:30:36: 4000000 INFO @ Fri, 15 Feb 2019 10:30:36: 4000000 INFO @ Fri, 15 Feb 2019 10:30:42: 5000000 INFO @ Fri, 15 Feb 2019 10:30:42: 5000000 INFO @ Fri, 15 Feb 2019 10:30:43: 5000000 INFO @ Fri, 15 Feb 2019 10:30:48: 6000000 INFO @ Fri, 15 Feb 2019 10:30:48: 6000000 INFO @ Fri, 15 Feb 2019 10:30:49: 6000000 INFO @ Fri, 15 Feb 2019 10:30:54: 7000000 INFO @ Fri, 15 Feb 2019 10:30:55: 7000000 INFO @ Fri, 15 Feb 2019 10:30:56: 7000000 INFO @ Fri, 15 Feb 2019 10:31:00: 8000000 INFO @ Fri, 15 Feb 2019 10:31:01: 8000000 INFO @ Fri, 15 Feb 2019 10:31:02: 8000000 INFO @ Fri, 15 Feb 2019 10:31:02: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:31:02: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:31:02: #1 total tags in treatment: 8362419 INFO @ Fri, 15 Feb 2019 10:31:02: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:31:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:31:03: #1 tags after filtering in treatment: 8362419 INFO @ Fri, 15 Feb 2019 10:31:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:31:03: #1 finished! INFO @ Fri, 15 Feb 2019 10:31:03: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:31:03: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:31:03: 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 @ Fri, 15 Feb 2019 10:31:03: Process for pairing-model is terminated! cat: SRX4092964.10_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4092964.10_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 `SRX4092964.10_*.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 `SRX4092964.10_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 @ Fri, 15 Feb 2019 10:31:03: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:31:03: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:31:03: #1 total tags in treatment: 8362419 INFO @ Fri, 15 Feb 2019 10:31:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:31:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:31:04: #1 tags after filtering in treatment: 8362419 INFO @ Fri, 15 Feb 2019 10:31:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:31:04: #1 finished! INFO @ Fri, 15 Feb 2019 10:31:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:31:04: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:31:04: 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 @ Fri, 15 Feb 2019 10:31:04: Process for pairing-model is terminated! cat: SRX4092964.05_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4092964.05_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 `SRX4092964.05_*.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 `SRX4092964.05_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 @ Fri, 15 Feb 2019 10:31:04: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:31:04: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:31:04: #1 total tags in treatment: 8362419 INFO @ Fri, 15 Feb 2019 10:31:04: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:31:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:31:04: #1 tags after filtering in treatment: 8362419 INFO @ Fri, 15 Feb 2019 10:31:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:31:04: #1 finished! INFO @ Fri, 15 Feb 2019 10:31:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:31:05: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:31:05: 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 @ Fri, 15 Feb 2019 10:31:05: Process for pairing-model is terminated! cat: SRX4092964.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4092964.20_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 `SRX4092964.20_*.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 `SRX4092964.20_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。