Job ID = 11293706 sra ファイルのダウンロード中... Completed: 190538K bytes transferred in 9 seconds (160175K 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 5088228 spots for /home/okishinya/chipatlas/results/dm3/SRX4375866/SRR7506520.sra Written 5088228 spots for /home/okishinya/chipatlas/results/dm3/SRX4375866/SRR7506520.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: 00:02:07 5088228 reads; of these: 5088228 (100.00%) were unpaired; of these: 1086676 (21.36%) aligned 0 times 2710499 (53.27%) aligned exactly 1 time 1291053 (25.37%) aligned >1 times 78.64% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 2008573 / 4001552 = 0.5019 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 @ Sun, 04 Nov 2018 17:51:09: # Command line: callpeak -t SRX4375866.bam -f BAM -g dm -n SRX4375866.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375866.05 # format = BAM # ChIP-seq file = ['SRX4375866.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 @ Sun, 04 Nov 2018 17:51:09: # Command line: callpeak -t SRX4375866.bam -f BAM -g dm -n SRX4375866.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375866.10 # format = BAM # ChIP-seq file = ['SRX4375866.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 @ Sun, 04 Nov 2018 17:51:09: # Command line: callpeak -t SRX4375866.bam -f BAM -g dm -n SRX4375866.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375866.20 # format = BAM # ChIP-seq file = ['SRX4375866.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 @ Sun, 04 Nov 2018 17:51:09: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:51:09: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:51:09: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:51:09: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:51:09: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:51:09: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:51:16: 1000000 INFO @ Sun, 04 Nov 2018 17:51:16: 1000000 INFO @ Sun, 04 Nov 2018 17:51:16: 1000000 INFO @ Sun, 04 Nov 2018 17:51:22: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:51:22: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:51:22: #1 total tags in treatment: 1992979 INFO @ Sun, 04 Nov 2018 17:51:22: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:51:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:51:22: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:51:22: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:51:22: #1 total tags in treatment: 1992979 INFO @ Sun, 04 Nov 2018 17:51:22: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:51:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:51:22: #1 tags after filtering in treatment: 1992979 INFO @ Sun, 04 Nov 2018 17:51:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:51:22: #1 finished! INFO @ Sun, 04 Nov 2018 17:51:22: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:51:22: #1 tags after filtering in treatment: 1992979 INFO @ Sun, 04 Nov 2018 17:51:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:51:22: #1 finished! INFO @ Sun, 04 Nov 2018 17:51:22: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:51:23: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:51:23: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:51:23: #1 total tags in treatment: 1992979 INFO @ Sun, 04 Nov 2018 17:51:23: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:51:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:51:23: #1 tags after filtering in treatment: 1992979 INFO @ Sun, 04 Nov 2018 17:51:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:51:23: #1 finished! INFO @ Sun, 04 Nov 2018 17:51:23: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:51:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:51:23: #2 number of paired peaks: 1145 INFO @ Sun, 04 Nov 2018 17:51:23: start model_add_line... INFO @ Sun, 04 Nov 2018 17:51:23: #2 number of paired peaks: 1145 INFO @ Sun, 04 Nov 2018 17:51:23: start model_add_line... INFO @ Sun, 04 Nov 2018 17:51:23: start X-correlation... INFO @ Sun, 04 Nov 2018 17:51:23: start X-correlation... INFO @ Sun, 04 Nov 2018 17:51:23: #2 number of paired peaks: 1145 INFO @ Sun, 04 Nov 2018 17:51:23: start model_add_line... INFO @ Sun, 04 Nov 2018 17:51:23: start X-correlation... INFO @ Sun, 04 Nov 2018 17:51:23: end of X-cor INFO @ Sun, 04 Nov 2018 17:51:23: end of X-cor INFO @ Sun, 04 Nov 2018 17:51:23: end of X-cor INFO @ Sun, 04 Nov 2018 17:51:23: #2 finished! INFO @ Sun, 04 Nov 2018 17:51:23: #2 finished! INFO @ Sun, 04 Nov 2018 17:51:23: #2 finished! INFO @ Sun, 04 Nov 2018 17:51:23: #2 predicted fragment length is 55 bps INFO @ Sun, 04 Nov 2018 17:51:23: #2 predicted fragment length is 55 bps INFO @ Sun, 04 Nov 2018 17:51:23: #2 predicted fragment length is 55 bps INFO @ Sun, 04 Nov 2018 17:51:23: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 04 Nov 2018 17:51:23: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 04 Nov 2018 17:51:23: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 04 Nov 2018 17:51:23: #2.2 Generate R script for model : SRX4375866.10_model.r INFO @ Sun, 04 Nov 2018 17:51:23: #2.2 Generate R script for model : SRX4375866.05_model.r INFO @ Sun, 04 Nov 2018 17:51:23: #2.2 Generate R script for model : SRX4375866.20_model.r WARNING @ Sun, 04 Nov 2018 17:51:23: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:51:23: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 04 Nov 2018 17:51:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:51:23: #3 Call peaks... WARNING @ Sun, 04 Nov 2018 17:51:23: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:51:23: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 04 Nov 2018 17:51:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:51:23: #3 Call peaks... WARNING @ Sun, 04 Nov 2018 17:51:23: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:51:23: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 04 Nov 2018 17:51:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:51:23: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:51:28: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:51:28: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:51:28: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:51:31: #4 Write output xls file... SRX4375866.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:51:31: #4 Write peak in narrowPeak format file... SRX4375866.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:51:31: #4 Write summits bed file... SRX4375866.05_summits.bed INFO @ Sun, 04 Nov 2018 17:51:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1363 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:51:31: #4 Write output xls file... SRX4375866.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:51:31: #4 Write peak in narrowPeak format file... SRX4375866.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:51:31: #4 Write summits bed file... SRX4375866.20_summits.bed INFO @ Sun, 04 Nov 2018 17:51:31: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (714 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:51:31: #4 Write output xls file... SRX4375866.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:51:31: #4 Write peak in narrowPeak format file... SRX4375866.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:51:31: #4 Write summits bed file... SRX4375866.10_summits.bed INFO @ Sun, 04 Nov 2018 17:51:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (961 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。