Job ID = 10175228 sra ファイルのダウンロード中... Completed: 174110K bytes transferred in 6 seconds (232846K 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... Written 10678664 spots for /home/okishinya/chipatlas/results/dm3/SRX2458931/SRR5140280.sra Written 10678664 spots total 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: 00:04:39 10678664 reads; of these: 10678664 (100.00%) were unpaired; of these: 459607 (4.30%) aligned 0 times 7710146 (72.20%) aligned exactly 1 time 2508911 (23.49%) aligned >1 times 95.70% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6666488 / 10219057 = 0.6524 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 Nov 2017 11:48:33: # Command line: callpeak -t SRX2458931.bam -f BAM -g dm -n SRX2458931.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2458931.05 # format = BAM # ChIP-seq file = ['SRX2458931.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 Nov 2017 11:48:33: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:48:33: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:48:33: # Command line: callpeak -t SRX2458931.bam -f BAM -g dm -n SRX2458931.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2458931.10 # format = BAM # ChIP-seq file = ['SRX2458931.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 Nov 2017 11:48:33: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:48:33: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:48:33: # Command line: callpeak -t SRX2458931.bam -f BAM -g dm -n SRX2458931.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2458931.20 # format = BAM # ChIP-seq file = ['SRX2458931.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 Nov 2017 11:48:33: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:48:33: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:48:40: 1000000 INFO @ Mon, 06 Nov 2017 11:48:40: 1000000 INFO @ Mon, 06 Nov 2017 11:48:40: 1000000 INFO @ Mon, 06 Nov 2017 11:48:48: 2000000 INFO @ Mon, 06 Nov 2017 11:48:48: 2000000 INFO @ Mon, 06 Nov 2017 11:48:48: 2000000 INFO @ Mon, 06 Nov 2017 11:48:56: 3000000 INFO @ Mon, 06 Nov 2017 11:48:56: 3000000 INFO @ Mon, 06 Nov 2017 11:48:56: 3000000 INFO @ Mon, 06 Nov 2017 11:49:00: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:49:00: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:49:00: #1 total tags in treatment: 3552569 INFO @ Mon, 06 Nov 2017 11:49:00: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:49:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:49:00: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:49:00: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:49:00: #1 total tags in treatment: 3552569 INFO @ Mon, 06 Nov 2017 11:49:00: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:49:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:49:00: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:49:00: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:49:00: #1 total tags in treatment: 3552569 INFO @ Mon, 06 Nov 2017 11:49:00: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:49:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:49:00: #1 tags after filtering in treatment: 3552569 INFO @ Mon, 06 Nov 2017 11:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:49:00: #1 finished! INFO @ Mon, 06 Nov 2017 11:49:00: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:49:00: #1 tags after filtering in treatment: 3552569 INFO @ Mon, 06 Nov 2017 11:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:49:00: #1 finished! INFO @ Mon, 06 Nov 2017 11:49:00: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:49:00: #1 tags after filtering in treatment: 3552569 INFO @ Mon, 06 Nov 2017 11:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:49:00: #1 finished! INFO @ Mon, 06 Nov 2017 11:49:00: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:49:01: #2 number of paired peaks: 2686 INFO @ Mon, 06 Nov 2017 11:49:01: start model_add_line... INFO @ Mon, 06 Nov 2017 11:49:01: #2 number of paired peaks: 2686 INFO @ Mon, 06 Nov 2017 11:49:01: start model_add_line... INFO @ Mon, 06 Nov 2017 11:49:01: #2 number of paired peaks: 2686 INFO @ Mon, 06 Nov 2017 11:49:01: start model_add_line... INFO @ Mon, 06 Nov 2017 11:49:01: start X-correlation... INFO @ Mon, 06 Nov 2017 11:49:01: start X-correlation... INFO @ Mon, 06 Nov 2017 11:49:01: end of X-cor INFO @ Mon, 06 Nov 2017 11:49:01: end of X-cor INFO @ Mon, 06 Nov 2017 11:49:01: #2 finished! INFO @ Mon, 06 Nov 2017 11:49:01: #2 finished! INFO @ Mon, 06 Nov 2017 11:49:01: #2 predicted fragment length is 76 bps INFO @ Mon, 06 Nov 2017 11:49:01: #2 predicted fragment length is 76 bps INFO @ Mon, 06 Nov 2017 11:49:01: #2 alternative fragment length(s) may be 76 bps INFO @ Mon, 06 Nov 2017 11:49:01: #2 alternative fragment length(s) may be 76 bps INFO @ Mon, 06 Nov 2017 11:49:01: #2.2 Generate R script for model : SRX2458931.05_model.r INFO @ Mon, 06 Nov 2017 11:49:01: #2.2 Generate R script for model : SRX2458931.10_model.r INFO @ Mon, 06 Nov 2017 11:49:01: start X-correlation... WARNING @ Mon, 06 Nov 2017 11:49:01: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:49:01: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Mon, 06 Nov 2017 11:49:01: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:49:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Mon, 06 Nov 2017 11:49:01: #2 You may need to consider one of the other alternative d(s): 76 INFO @ Mon, 06 Nov 2017 11:49:01: #3 Call peaks... WARNING @ Mon, 06 Nov 2017 11:49:01: #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 Nov 2017 11:49:01: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:49:01: end of X-cor INFO @ Mon, 06 Nov 2017 11:49:01: #2 finished! INFO @ Mon, 06 Nov 2017 11:49:01: #2 predicted fragment length is 76 bps INFO @ Mon, 06 Nov 2017 11:49:01: #2 alternative fragment length(s) may be 76 bps INFO @ Mon, 06 Nov 2017 11:49:01: #2.2 Generate R script for model : SRX2458931.20_model.r WARNING @ Mon, 06 Nov 2017 11:49:01: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:49:01: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Mon, 06 Nov 2017 11:49:01: #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 Nov 2017 11:49:01: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:49:10: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:49:10: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:49:11: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:49:15: #4 Write output xls file... SRX2458931.20_peaks.xls INFO @ Mon, 06 Nov 2017 11:49:15: #4 Write peak in narrowPeak format file... SRX2458931.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:49:15: #4 Write summits bed file... SRX2458931.20_summits.bed INFO @ Mon, 06 Nov 2017 11:49:15: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (640 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:49:15: #4 Write output xls file... SRX2458931.05_peaks.xls INFO @ Mon, 06 Nov 2017 11:49:15: #4 Write peak in narrowPeak format file... SRX2458931.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:49:15: #4 Write summits bed file... SRX2458931.05_summits.bed INFO @ Mon, 06 Nov 2017 11:49:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2400 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:49:16: #4 Write output xls file... SRX2458931.10_peaks.xls INFO @ Mon, 06 Nov 2017 11:49:16: #4 Write peak in narrowPeak format file... SRX2458931.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:49:16: #4 Write summits bed file... SRX2458931.10_summits.bed INFO @ Mon, 06 Nov 2017 11:49:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1262 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。