Job ID = 11162546 sra ファイルのダウンロード中... Completed: 300744K bytes transferred in 27 seconds (91013K 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 6894671 spots for /home/okishinya/chipatlas/results/rn6/SRX4292396/SRR7421570.sra Written 6894671 spots for /home/okishinya/chipatlas/results/rn6/SRX4292396/SRR7421570.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: 00:00:02 Time loading forward index: 00:00:04 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:09:33 6894671 reads; of these: 6894671 (100.00%) were unpaired; of these: 214651 (3.11%) aligned 0 times 4966895 (72.04%) aligned exactly 1 time 1713125 (24.85%) aligned >1 times 96.89% overall alignment rate Time searching: 00:09:42 Overall time: 00:09:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 113296 / 6680020 = 0.0170 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, 05 Sep 2018 10:01:33: # Command line: callpeak -t SRX4292396.bam -f BAM -g 2.15e9 -n SRX4292396.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4292396.05 # format = BAM # ChIP-seq file = ['SRX4292396.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 05 Sep 2018 10:01:33: # Command line: callpeak -t SRX4292396.bam -f BAM -g 2.15e9 -n SRX4292396.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4292396.10 # format = BAM # ChIP-seq file = ['SRX4292396.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 05 Sep 2018 10:01:33: # Command line: callpeak -t SRX4292396.bam -f BAM -g 2.15e9 -n SRX4292396.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4292396.20 # format = BAM # ChIP-seq file = ['SRX4292396.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 05 Sep 2018 10:01:33: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:01:33: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:01:33: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:01:33: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:01:33: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:01:33: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:01:41: 1000000 INFO @ Wed, 05 Sep 2018 10:01:41: 1000000 INFO @ Wed, 05 Sep 2018 10:01:41: 1000000 INFO @ Wed, 05 Sep 2018 10:01:49: 2000000 INFO @ Wed, 05 Sep 2018 10:01:49: 2000000 INFO @ Wed, 05 Sep 2018 10:01:50: 2000000 INFO @ Wed, 05 Sep 2018 10:01:57: 3000000 INFO @ Wed, 05 Sep 2018 10:01:57: 3000000 INFO @ Wed, 05 Sep 2018 10:01:58: 3000000 INFO @ Wed, 05 Sep 2018 10:02:05: 4000000 INFO @ Wed, 05 Sep 2018 10:02:06: 4000000 INFO @ Wed, 05 Sep 2018 10:02:06: 4000000 INFO @ Wed, 05 Sep 2018 10:02:13: 5000000 INFO @ Wed, 05 Sep 2018 10:02:13: 5000000 INFO @ Wed, 05 Sep 2018 10:02:14: 5000000 INFO @ Wed, 05 Sep 2018 10:02:21: 6000000 INFO @ Wed, 05 Sep 2018 10:02:21: 6000000 INFO @ Wed, 05 Sep 2018 10:02:22: 6000000 INFO @ Wed, 05 Sep 2018 10:02:26: #1 tag size is determined as 75 bps INFO @ Wed, 05 Sep 2018 10:02:26: #1 tag size = 75 INFO @ Wed, 05 Sep 2018 10:02:26: #1 total tags in treatment: 6566724 INFO @ Wed, 05 Sep 2018 10:02:26: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:02:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:02:26: #1 tag size is determined as 75 bps INFO @ Wed, 05 Sep 2018 10:02:26: #1 tag size = 75 INFO @ Wed, 05 Sep 2018 10:02:26: #1 total tags in treatment: 6566724 INFO @ Wed, 05 Sep 2018 10:02:26: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:02:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:02:26: #1 tags after filtering in treatment: 6566445 INFO @ Wed, 05 Sep 2018 10:02:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 05 Sep 2018 10:02:26: #1 finished! INFO @ Wed, 05 Sep 2018 10:02:26: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:02:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:02:26: #1 tag size is determined as 75 bps INFO @ Wed, 05 Sep 2018 10:02:26: #1 tag size = 75 INFO @ Wed, 05 Sep 2018 10:02:26: #1 total tags in treatment: 6566724 INFO @ Wed, 05 Sep 2018 10:02:26: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:02:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:02:26: #1 tags after filtering in treatment: 6566445 INFO @ Wed, 05 Sep 2018 10:02:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 05 Sep 2018 10:02:26: #1 finished! INFO @ Wed, 05 Sep 2018 10:02:26: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:02:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:02:27: #1 tags after filtering in treatment: 6566445 INFO @ Wed, 05 Sep 2018 10:02:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 05 Sep 2018 10:02:27: #1 finished! INFO @ Wed, 05 Sep 2018 10:02:27: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:02:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:02:27: #2 number of paired peaks: 4516 INFO @ Wed, 05 Sep 2018 10:02:27: start model_add_line... INFO @ Wed, 05 Sep 2018 10:02:27: start X-correlation... INFO @ Wed, 05 Sep 2018 10:02:27: end of X-cor INFO @ Wed, 05 Sep 2018 10:02:27: #2 finished! INFO @ Wed, 05 Sep 2018 10:02:27: #2 predicted fragment length is 75 bps INFO @ Wed, 05 Sep 2018 10:02:27: #2 alternative fragment length(s) may be 75,227,552 bps INFO @ Wed, 05 Sep 2018 10:02:27: #2.2 Generate R script for model : SRX4292396.05_model.r WARNING @ Wed, 05 Sep 2018 10:02:27: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 05 Sep 2018 10:02:27: #2 You may need to consider one of the other alternative d(s): 75,227,552 WARNING @ Wed, 05 Sep 2018 10:02:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 05 Sep 2018 10:02:27: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:02:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:02:28: #2 number of paired peaks: 4516 INFO @ Wed, 05 Sep 2018 10:02:28: start model_add_line... INFO @ Wed, 05 Sep 2018 10:02:28: start X-correlation... INFO @ Wed, 05 Sep 2018 10:02:28: end of X-cor INFO @ Wed, 05 Sep 2018 10:02:28: #2 finished! INFO @ Wed, 05 Sep 2018 10:02:28: #2 predicted fragment length is 75 bps INFO @ Wed, 05 Sep 2018 10:02:28: #2 alternative fragment length(s) may be 75,227,552 bps INFO @ Wed, 05 Sep 2018 10:02:28: #2.2 Generate R script for model : SRX4292396.10_model.r WARNING @ Wed, 05 Sep 2018 10:02:28: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 05 Sep 2018 10:02:28: #2 You may need to consider one of the other alternative d(s): 75,227,552 WARNING @ Wed, 05 Sep 2018 10:02:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 05 Sep 2018 10:02:28: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:02:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:02:28: #2 number of paired peaks: 4516 INFO @ Wed, 05 Sep 2018 10:02:28: start model_add_line... INFO @ Wed, 05 Sep 2018 10:02:28: start X-correlation... INFO @ Wed, 05 Sep 2018 10:02:28: end of X-cor INFO @ Wed, 05 Sep 2018 10:02:28: #2 finished! INFO @ Wed, 05 Sep 2018 10:02:28: #2 predicted fragment length is 75 bps INFO @ Wed, 05 Sep 2018 10:02:28: #2 alternative fragment length(s) may be 75,227,552 bps INFO @ Wed, 05 Sep 2018 10:02:28: #2.2 Generate R script for model : SRX4292396.20_model.r WARNING @ Wed, 05 Sep 2018 10:02:28: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 05 Sep 2018 10:02:28: #2 You may need to consider one of the other alternative d(s): 75,227,552 WARNING @ Wed, 05 Sep 2018 10:02:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 05 Sep 2018 10:02:28: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:02:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:02:45: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:02:45: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:02:45: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:02:53: #4 Write output xls file... SRX4292396.05_peaks.xls INFO @ Wed, 05 Sep 2018 10:02:53: #4 Write peak in narrowPeak format file... SRX4292396.05_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:02:53: #4 Write summits bed file... SRX4292396.05_summits.bed INFO @ Wed, 05 Sep 2018 10:02:53: Done! INFO @ Wed, 05 Sep 2018 10:02:53: #4 Write output xls file... SRX4292396.20_peaks.xls INFO @ Wed, 05 Sep 2018 10:02:53: #4 Write peak in narrowPeak format file... SRX4292396.20_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:02:53: #4 Write summits bed file... SRX4292396.20_summits.bed INFO @ Wed, 05 Sep 2018 10:02:53: Done! pass1 - making usageList (22 chroms): 2 millis pass2 - checking and writing primary data (183 records, 4 fields): 118 millis pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (583 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Wed, 05 Sep 2018 10:02:53: #4 Write output xls file... SRX4292396.10_peaks.xls INFO @ Wed, 05 Sep 2018 10:02:53: #4 Write peak in narrowPeak format file... SRX4292396.10_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:02:53: #4 Write summits bed file... SRX4292396.10_summits.bed INFO @ Wed, 05 Sep 2018 10:02:53: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (349 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。