Job ID = 11171387 sra ファイルのダウンロード中... Completed: 64912K bytes transferred in 3 seconds (136199K 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 3803721 spots for /home/okishinya/chipatlas/results/dm3/SRX4315036/SRR7444497.sra Written 3803721 spots for /home/okishinya/chipatlas/results/dm3/SRX4315036/SRR7444497.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: 00:01:38 3803721 reads; of these: 3803721 (100.00%) were unpaired; of these: 1030 (0.03%) aligned 0 times 3240969 (85.21%) aligned exactly 1 time 561722 (14.77%) aligned >1 times 99.97% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2076770 / 3802691 = 0.5461 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 @ Sat, 08 Sep 2018 14:07:49: # Command line: callpeak -t SRX4315036.bam -f BAM -g dm -n SRX4315036.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4315036.10 # format = BAM # ChIP-seq file = ['SRX4315036.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 08 Sep 2018 14:07:49: # Command line: callpeak -t SRX4315036.bam -f BAM -g dm -n SRX4315036.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4315036.20 # format = BAM # ChIP-seq file = ['SRX4315036.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 08 Sep 2018 14:07:49: # Command line: callpeak -t SRX4315036.bam -f BAM -g dm -n SRX4315036.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4315036.05 # format = BAM # ChIP-seq file = ['SRX4315036.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 08 Sep 2018 14:07:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:07:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:07:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:07:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:07:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:07:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:07:56: 1000000 INFO @ Sat, 08 Sep 2018 14:07:56: 1000000 INFO @ Sat, 08 Sep 2018 14:07:56: 1000000 INFO @ Sat, 08 Sep 2018 14:08:01: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:08:01: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:08:01: #1 total tags in treatment: 1725921 INFO @ Sat, 08 Sep 2018 14:08:01: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:08:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:08:01: #1 tags after filtering in treatment: 1725921 INFO @ Sat, 08 Sep 2018 14:08:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:08:01: #1 finished! INFO @ Sat, 08 Sep 2018 14:08:01: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:08:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:08:01: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:08:01: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:08:01: #1 total tags in treatment: 1725921 INFO @ Sat, 08 Sep 2018 14:08:01: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:08:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:08:01: #2 number of paired peaks: 1872 INFO @ Sat, 08 Sep 2018 14:08:01: start model_add_line... INFO @ Sat, 08 Sep 2018 14:08:01: start X-correlation... INFO @ Sat, 08 Sep 2018 14:08:01: end of X-cor INFO @ Sat, 08 Sep 2018 14:08:01: #2 finished! INFO @ Sat, 08 Sep 2018 14:08:01: #2 predicted fragment length is 118 bps INFO @ Sat, 08 Sep 2018 14:08:01: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 08 Sep 2018 14:08:01: #2.2 Generate R script for model : SRX4315036.05_model.r INFO @ Sat, 08 Sep 2018 14:08:01: #1 tags after filtering in treatment: 1725921 INFO @ Sat, 08 Sep 2018 14:08:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:08:01: #1 finished! INFO @ Sat, 08 Sep 2018 14:08:01: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:08:01: #2 looking for paired plus/minus strand peaks... WARNING @ Sat, 08 Sep 2018 14:08:01: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:08:01: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sat, 08 Sep 2018 14:08:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:08:01: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:08:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:08:01: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:08:01: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:08:01: #1 total tags in treatment: 1725921 INFO @ Sat, 08 Sep 2018 14:08:01: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:08:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:08:01: #1 tags after filtering in treatment: 1725921 INFO @ Sat, 08 Sep 2018 14:08:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:08:01: #1 finished! INFO @ Sat, 08 Sep 2018 14:08:01: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:08:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:08:01: #2 number of paired peaks: 1872 INFO @ Sat, 08 Sep 2018 14:08:01: start model_add_line... INFO @ Sat, 08 Sep 2018 14:08:01: start X-correlation... INFO @ Sat, 08 Sep 2018 14:08:01: end of X-cor INFO @ Sat, 08 Sep 2018 14:08:01: #2 finished! INFO @ Sat, 08 Sep 2018 14:08:01: #2 predicted fragment length is 118 bps INFO @ Sat, 08 Sep 2018 14:08:01: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 08 Sep 2018 14:08:01: #2.2 Generate R script for model : SRX4315036.20_model.r INFO @ Sat, 08 Sep 2018 14:08:01: #2 number of paired peaks: 1872 INFO @ Sat, 08 Sep 2018 14:08:01: start model_add_line... INFO @ Sat, 08 Sep 2018 14:08:01: start X-correlation... INFO @ Sat, 08 Sep 2018 14:08:01: end of X-cor INFO @ Sat, 08 Sep 2018 14:08:01: #2 finished! INFO @ Sat, 08 Sep 2018 14:08:01: #2 predicted fragment length is 118 bps INFO @ Sat, 08 Sep 2018 14:08:01: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 08 Sep 2018 14:08:01: #2.2 Generate R script for model : SRX4315036.10_model.r WARNING @ Sat, 08 Sep 2018 14:08:01: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:08:01: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sat, 08 Sep 2018 14:08:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:08:01: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:08:01: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 08 Sep 2018 14:08:01: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:08:01: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sat, 08 Sep 2018 14:08:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:08:01: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:08:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:08:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:08:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:08:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:08:08: #4 Write output xls file... SRX4315036.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:08:08: #4 Write peak in narrowPeak format file... SRX4315036.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:08:08: #4 Write summits bed file... SRX4315036.05_summits.bed INFO @ Sat, 08 Sep 2018 14:08:08: Done! INFO @ Sat, 08 Sep 2018 14:08:08: #4 Write output xls file... SRX4315036.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:08:08: #4 Write peak in narrowPeak format file... SRX4315036.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:08:08: #4 Write summits bed file... SRX4315036.10_summits.bed INFO @ Sat, 08 Sep 2018 14:08:08: Done! INFO @ Sat, 08 Sep 2018 14:08:08: #4 Write output xls file... SRX4315036.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:08:08: #4 Write peak in narrowPeak format file... SRX4315036.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:08:08: #4 Write summits bed file... SRX4315036.20_summits.bed INFO @ Sat, 08 Sep 2018 14:08:08: Done! pass1 - making usageList (15 chroms): 18 millis pass1 - making usageList (13 chroms): 23 millis pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1005 records, 4 fields): 51 millis pass2 - checking and writing primary data (350 records, 4 fields): 6 millis pass2 - checking and writing primary data (2431 records, 4 fields): 58 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。