Job ID = 10924635 sra ファイルのダウンロード中... Completed: 235952K bytes transferred in 5 seconds (343305K 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 8397617 spots for /home/okishinya/chipatlas/results/dm3/SRX994747/SRR1973465.sra Written 8397617 spots for /home/okishinya/chipatlas/results/dm3/SRX994747/SRR1973465.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: 00:00:01 Multiseed full-index search: 00:04:19 8397617 reads; of these: 8397617 (100.00%) were unpaired; of these: 349300 (4.16%) aligned 0 times 6017054 (71.65%) aligned exactly 1 time 2031263 (24.19%) aligned >1 times 95.84% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 1362067 / 8048317 = 0.1692 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, 06 Aug 2018 10:33:00: # Command line: callpeak -t SRX994747.bam -f BAM -g dm -n SRX994747.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX994747.10 # format = BAM # ChIP-seq file = ['SRX994747.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 @ Mon, 06 Aug 2018 10:33:00: # Command line: callpeak -t SRX994747.bam -f BAM -g dm -n SRX994747.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX994747.20 # format = BAM # ChIP-seq file = ['SRX994747.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 @ Mon, 06 Aug 2018 10:33:00: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:33:00: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:33:00: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:33:00: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:33:00: # Command line: callpeak -t SRX994747.bam -f BAM -g dm -n SRX994747.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX994747.05 # format = BAM # ChIP-seq file = ['SRX994747.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 @ Mon, 06 Aug 2018 10:33:00: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:33:00: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:33:07: 1000000 INFO @ Mon, 06 Aug 2018 10:33:07: 1000000 INFO @ Mon, 06 Aug 2018 10:33:07: 1000000 INFO @ Mon, 06 Aug 2018 10:33:14: 2000000 INFO @ Mon, 06 Aug 2018 10:33:14: 2000000 INFO @ Mon, 06 Aug 2018 10:33:14: 2000000 INFO @ Mon, 06 Aug 2018 10:33:20: 3000000 INFO @ Mon, 06 Aug 2018 10:33:21: 3000000 INFO @ Mon, 06 Aug 2018 10:33:21: 3000000 INFO @ Mon, 06 Aug 2018 10:33:27: 4000000 INFO @ Mon, 06 Aug 2018 10:33:27: 4000000 INFO @ Mon, 06 Aug 2018 10:33:28: 4000000 INFO @ Mon, 06 Aug 2018 10:33:33: 5000000 INFO @ Mon, 06 Aug 2018 10:33:34: 5000000 INFO @ Mon, 06 Aug 2018 10:33:35: 5000000 INFO @ Mon, 06 Aug 2018 10:33:40: 6000000 INFO @ Mon, 06 Aug 2018 10:33:41: 6000000 INFO @ Mon, 06 Aug 2018 10:33:41: 6000000 INFO @ Mon, 06 Aug 2018 10:33:45: #1 tag size is determined as 75 bps INFO @ Mon, 06 Aug 2018 10:33:45: #1 tag size = 75 INFO @ Mon, 06 Aug 2018 10:33:45: #1 total tags in treatment: 6686250 INFO @ Mon, 06 Aug 2018 10:33:45: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:33:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:33:45: #1 tags after filtering in treatment: 6686250 INFO @ Mon, 06 Aug 2018 10:33:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:33:45: #1 finished! INFO @ Mon, 06 Aug 2018 10:33:45: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:33:45: #1 tag size is determined as 75 bps INFO @ Mon, 06 Aug 2018 10:33:45: #1 tag size = 75 INFO @ Mon, 06 Aug 2018 10:33:45: #1 total tags in treatment: 6686250 INFO @ Mon, 06 Aug 2018 10:33:45: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:33:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:33:46: #1 tags after filtering in treatment: 6686250 INFO @ Mon, 06 Aug 2018 10:33:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:33:46: #1 finished! INFO @ Mon, 06 Aug 2018 10:33:46: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:33:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:33:46: #2 number of paired peaks: 1259 INFO @ Mon, 06 Aug 2018 10:33:46: start model_add_line... INFO @ Mon, 06 Aug 2018 10:33:46: start X-correlation... INFO @ Mon, 06 Aug 2018 10:33:46: end of X-cor INFO @ Mon, 06 Aug 2018 10:33:46: #2 finished! INFO @ Mon, 06 Aug 2018 10:33:46: #2 predicted fragment length is 126 bps INFO @ Mon, 06 Aug 2018 10:33:46: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 06 Aug 2018 10:33:46: #2.2 Generate R script for model : SRX994747.20_model.r WARNING @ Mon, 06 Aug 2018 10:33:46: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Aug 2018 10:33:46: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Mon, 06 Aug 2018 10:33:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Aug 2018 10:33:46: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:33:46: #2 number of paired peaks: 1259 INFO @ Mon, 06 Aug 2018 10:33:46: start model_add_line... INFO @ Mon, 06 Aug 2018 10:33:46: #1 tag size is determined as 75 bps INFO @ Mon, 06 Aug 2018 10:33:46: #1 tag size = 75 INFO @ Mon, 06 Aug 2018 10:33:46: #1 total tags in treatment: 6686250 INFO @ Mon, 06 Aug 2018 10:33:46: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:33:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:33:46: start X-correlation... INFO @ Mon, 06 Aug 2018 10:33:46: end of X-cor INFO @ Mon, 06 Aug 2018 10:33:46: #2 finished! INFO @ Mon, 06 Aug 2018 10:33:46: #2 predicted fragment length is 126 bps INFO @ Mon, 06 Aug 2018 10:33:46: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 06 Aug 2018 10:33:46: #2.2 Generate R script for model : SRX994747.05_model.r INFO @ Mon, 06 Aug 2018 10:33:46: #1 tags after filtering in treatment: 6686250 INFO @ Mon, 06 Aug 2018 10:33:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:33:46: #1 finished! INFO @ Mon, 06 Aug 2018 10:33:46: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:33:46: #2 looking for paired plus/minus strand peaks... WARNING @ Mon, 06 Aug 2018 10:33:46: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Aug 2018 10:33:46: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Mon, 06 Aug 2018 10:33:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Aug 2018 10:33:46: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:33:47: #2 number of paired peaks: 1259 INFO @ Mon, 06 Aug 2018 10:33:47: start model_add_line... INFO @ Mon, 06 Aug 2018 10:33:47: start X-correlation... INFO @ Mon, 06 Aug 2018 10:33:47: end of X-cor INFO @ Mon, 06 Aug 2018 10:33:47: #2 finished! INFO @ Mon, 06 Aug 2018 10:33:47: #2 predicted fragment length is 126 bps INFO @ Mon, 06 Aug 2018 10:33:47: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 06 Aug 2018 10:33:47: #2.2 Generate R script for model : SRX994747.10_model.r WARNING @ Mon, 06 Aug 2018 10:33:47: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Aug 2018 10:33:47: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Mon, 06 Aug 2018 10:33:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Aug 2018 10:33:47: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:33:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:34:03: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:34:03: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:34:04: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:34:12: #4 Write output xls file... SRX994747.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:34:12: #4 Write peak in narrowPeak format file... SRX994747.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:34:12: #4 Write summits bed file... SRX994747.20_summits.bed INFO @ Mon, 06 Aug 2018 10:34:12: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (951 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:34:13: #4 Write output xls file... SRX994747.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:34:13: #4 Write peak in narrowPeak format file... SRX994747.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:34:13: #4 Write summits bed file... SRX994747.10_summits.bed INFO @ Mon, 06 Aug 2018 10:34:13: Done! INFO @ Mon, 06 Aug 2018 10:34:13: #4 Write output xls file... SRX994747.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:34:13: #4 Write peak in narrowPeak format file... SRX994747.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:34:13: #4 Write summits bed file... SRX994747.05_summits.bed INFO @ Mon, 06 Aug 2018 10:34:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2609 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1467 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。