Job ID = 2590602 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,317,193 reads read : 34,634,386 reads written : 17,317,193 reads 0-length : 17,317,193 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:05:53 17317193 reads; of these: 17317193 (100.00%) were unpaired; of these: 382772 (2.21%) aligned 0 times 13689809 (79.05%) aligned exactly 1 time 3244612 (18.74%) aligned >1 times 97.79% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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] 5124795 / 16934421 = 0.3026 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, 12 Aug 2019 22:48:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.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, 12 Aug 2019 22:48:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:48:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.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, 12 Aug 2019 22:48:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:48:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:48:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.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, 12 Aug 2019 22:48:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:48:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:48:16: 1000000 INFO @ Mon, 12 Aug 2019 22:48:20: 1000000 INFO @ Mon, 12 Aug 2019 22:48:21: 1000000 INFO @ Mon, 12 Aug 2019 22:48:23: 2000000 INFO @ Mon, 12 Aug 2019 22:48:30: 3000000 INFO @ Mon, 12 Aug 2019 22:48:30: 2000000 INFO @ Mon, 12 Aug 2019 22:48:31: 2000000 INFO @ Mon, 12 Aug 2019 22:48:37: 4000000 INFO @ Mon, 12 Aug 2019 22:48:40: 3000000 INFO @ Mon, 12 Aug 2019 22:48:41: 3000000 INFO @ Mon, 12 Aug 2019 22:48:44: 5000000 INFO @ Mon, 12 Aug 2019 22:48:50: 4000000 INFO @ Mon, 12 Aug 2019 22:48:50: 4000000 INFO @ Mon, 12 Aug 2019 22:48:51: 6000000 INFO @ Mon, 12 Aug 2019 22:48:58: 7000000 INFO @ Mon, 12 Aug 2019 22:48:59: 5000000 INFO @ Mon, 12 Aug 2019 22:49:00: 5000000 INFO @ Mon, 12 Aug 2019 22:49:04: 8000000 INFO @ Mon, 12 Aug 2019 22:49:09: 6000000 INFO @ Mon, 12 Aug 2019 22:49:10: 6000000 INFO @ Mon, 12 Aug 2019 22:49:11: 9000000 INFO @ Mon, 12 Aug 2019 22:49:18: 10000000 INFO @ Mon, 12 Aug 2019 22:49:18: 7000000 INFO @ Mon, 12 Aug 2019 22:49:19: 7000000 INFO @ Mon, 12 Aug 2019 22:49:25: 11000000 INFO @ Mon, 12 Aug 2019 22:49:28: 8000000 INFO @ Mon, 12 Aug 2019 22:49:29: 8000000 INFO @ Mon, 12 Aug 2019 22:49:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:49:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:49:31: #1 total tags in treatment: 11809626 INFO @ Mon, 12 Aug 2019 22:49:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:49:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:49:31: #1 tags after filtering in treatment: 11809626 INFO @ Mon, 12 Aug 2019 22:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:49:31: #1 finished! INFO @ Mon, 12 Aug 2019 22:49:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:49:33: #2 number of paired peaks: 8604 INFO @ Mon, 12 Aug 2019 22:49:33: start model_add_line... INFO @ Mon, 12 Aug 2019 22:49:33: start X-correlation... INFO @ Mon, 12 Aug 2019 22:49:33: end of X-cor INFO @ Mon, 12 Aug 2019 22:49:33: #2 finished! INFO @ Mon, 12 Aug 2019 22:49:33: #2 predicted fragment length is 141 bps INFO @ Mon, 12 Aug 2019 22:49:33: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 12 Aug 2019 22:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.05_model.r INFO @ Mon, 12 Aug 2019 22:49:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:49:38: 9000000 INFO @ Mon, 12 Aug 2019 22:49:39: 9000000 INFO @ Mon, 12 Aug 2019 22:49:48: 10000000 INFO @ Mon, 12 Aug 2019 22:49:48: 10000000 INFO @ Mon, 12 Aug 2019 22:49:57: 11000000 INFO @ Mon, 12 Aug 2019 22:49:58: 11000000 INFO @ Mon, 12 Aug 2019 22:50:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:50:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:50:05: #1 total tags in treatment: 11809626 INFO @ Mon, 12 Aug 2019 22:50:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:50:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:50:05: #1 tags after filtering in treatment: 11809626 INFO @ Mon, 12 Aug 2019 22:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:50:05: #1 finished! INFO @ Mon, 12 Aug 2019 22:50:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:50:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:50:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:50:05: #1 total tags in treatment: 11809626 INFO @ Mon, 12 Aug 2019 22:50:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:50:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:50:06: #1 tags after filtering in treatment: 11809626 INFO @ Mon, 12 Aug 2019 22:50:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:50:06: #1 finished! INFO @ Mon, 12 Aug 2019 22:50:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:50:07: #2 number of paired peaks: 8604 INFO @ Mon, 12 Aug 2019 22:50:07: start model_add_line... INFO @ Mon, 12 Aug 2019 22:50:07: start X-correlation... INFO @ Mon, 12 Aug 2019 22:50:07: end of X-cor INFO @ Mon, 12 Aug 2019 22:50:07: #2 finished! INFO @ Mon, 12 Aug 2019 22:50:07: #2 predicted fragment length is 141 bps INFO @ Mon, 12 Aug 2019 22:50:07: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 12 Aug 2019 22:50:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.10_model.r INFO @ Mon, 12 Aug 2019 22:50:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:50:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:50:08: #2 number of paired peaks: 8604 INFO @ Mon, 12 Aug 2019 22:50:08: start model_add_line... INFO @ Mon, 12 Aug 2019 22:50:08: start X-correlation... INFO @ Mon, 12 Aug 2019 22:50:08: end of X-cor INFO @ Mon, 12 Aug 2019 22:50:08: #2 finished! INFO @ Mon, 12 Aug 2019 22:50:08: #2 predicted fragment length is 141 bps INFO @ Mon, 12 Aug 2019 22:50:08: #2 alternative fragment length(s) may be 141 bps INFO @ Mon, 12 Aug 2019 22:50:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.20_model.r INFO @ Mon, 12 Aug 2019 22:50:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:50:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:50:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:50:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:50:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:50:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.05_summits.bed INFO @ Mon, 12 Aug 2019 22:50:28: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (9083 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:50:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:50:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:51:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.10_summits.bed INFO @ Mon, 12 Aug 2019 22:51:00: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8146 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:51:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:51:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:51:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923186/SRX4923186.20_summits.bed INFO @ Mon, 12 Aug 2019 22:51:01: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6653 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。