Job ID = 1295124 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,029,411 reads read : 26,029,411 reads written : 26,029,411 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:09:51 26029411 reads; of these: 26029411 (100.00%) were unpaired; of these: 1706343 (6.56%) aligned 0 times 17244369 (66.25%) aligned exactly 1 time 7078699 (27.20%) aligned >1 times 93.44% overall alignment rate Time searching: 00:09:51 Overall time: 00:09:51 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] 6374646 / 24323068 = 0.2621 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, 03 Jun 2019 12:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.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, 03 Jun 2019 12:31:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:31:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.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, 03 Jun 2019 12:31:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:31:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.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, 03 Jun 2019 12:31:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:31:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:31:16: 1000000 INFO @ Mon, 03 Jun 2019 12:31:17: 1000000 INFO @ Mon, 03 Jun 2019 12:31:17: 1000000 INFO @ Mon, 03 Jun 2019 12:31:22: 2000000 INFO @ Mon, 03 Jun 2019 12:31:25: 2000000 INFO @ Mon, 03 Jun 2019 12:31:25: 2000000 INFO @ Mon, 03 Jun 2019 12:31:29: 3000000 INFO @ Mon, 03 Jun 2019 12:31:32: 3000000 INFO @ Mon, 03 Jun 2019 12:31:32: 3000000 INFO @ Mon, 03 Jun 2019 12:31:35: 4000000 INFO @ Mon, 03 Jun 2019 12:31:39: 4000000 INFO @ Mon, 03 Jun 2019 12:31:40: 4000000 INFO @ Mon, 03 Jun 2019 12:31:42: 5000000 INFO @ Mon, 03 Jun 2019 12:31:47: 5000000 INFO @ Mon, 03 Jun 2019 12:31:47: 5000000 INFO @ Mon, 03 Jun 2019 12:31:48: 6000000 INFO @ Mon, 03 Jun 2019 12:31:55: 6000000 INFO @ Mon, 03 Jun 2019 12:31:55: 6000000 INFO @ Mon, 03 Jun 2019 12:31:55: 7000000 INFO @ Mon, 03 Jun 2019 12:32:01: 8000000 INFO @ Mon, 03 Jun 2019 12:32:02: 7000000 INFO @ Mon, 03 Jun 2019 12:32:02: 7000000 INFO @ Mon, 03 Jun 2019 12:32:08: 9000000 INFO @ Mon, 03 Jun 2019 12:32:09: 8000000 INFO @ Mon, 03 Jun 2019 12:32:09: 8000000 INFO @ Mon, 03 Jun 2019 12:32:14: 10000000 INFO @ Mon, 03 Jun 2019 12:32:17: 9000000 INFO @ Mon, 03 Jun 2019 12:32:17: 9000000 INFO @ Mon, 03 Jun 2019 12:32:21: 11000000 INFO @ Mon, 03 Jun 2019 12:32:25: 10000000 INFO @ Mon, 03 Jun 2019 12:32:25: 10000000 INFO @ Mon, 03 Jun 2019 12:32:28: 12000000 INFO @ Mon, 03 Jun 2019 12:32:33: 11000000 INFO @ Mon, 03 Jun 2019 12:32:33: 11000000 INFO @ Mon, 03 Jun 2019 12:32:34: 13000000 INFO @ Mon, 03 Jun 2019 12:32:40: 12000000 INFO @ Mon, 03 Jun 2019 12:32:40: 12000000 INFO @ Mon, 03 Jun 2019 12:32:41: 14000000 INFO @ Mon, 03 Jun 2019 12:32:46: 13000000 INFO @ Mon, 03 Jun 2019 12:32:47: 13000000 INFO @ Mon, 03 Jun 2019 12:32:48: 15000000 INFO @ Mon, 03 Jun 2019 12:32:53: 14000000 INFO @ Mon, 03 Jun 2019 12:32:54: 14000000 INFO @ Mon, 03 Jun 2019 12:32:55: 16000000 INFO @ Mon, 03 Jun 2019 12:33:00: 15000000 INFO @ Mon, 03 Jun 2019 12:33:01: 15000000 INFO @ Mon, 03 Jun 2019 12:33:02: 17000000 INFO @ Mon, 03 Jun 2019 12:33:07: 16000000 INFO @ Mon, 03 Jun 2019 12:33:07: 16000000 INFO @ Mon, 03 Jun 2019 12:33:09: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:33:09: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:33:09: #1 total tags in treatment: 17948422 INFO @ Mon, 03 Jun 2019 12:33:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:33:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:33:09: #1 tags after filtering in treatment: 17948422 INFO @ Mon, 03 Jun 2019 12:33:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:33:09: #1 finished! INFO @ Mon, 03 Jun 2019 12:33:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:33:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:33:12: #2 number of paired peaks: 3922 INFO @ Mon, 03 Jun 2019 12:33:12: start model_add_line... INFO @ Mon, 03 Jun 2019 12:33:12: start X-correlation... INFO @ Mon, 03 Jun 2019 12:33:12: end of X-cor INFO @ Mon, 03 Jun 2019 12:33:12: #2 finished! INFO @ Mon, 03 Jun 2019 12:33:12: #2 predicted fragment length is 203 bps INFO @ Mon, 03 Jun 2019 12:33:12: #2 alternative fragment length(s) may be 203 bps INFO @ Mon, 03 Jun 2019 12:33:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.05_model.r INFO @ Mon, 03 Jun 2019 12:33:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:33:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:33:14: 17000000 INFO @ Mon, 03 Jun 2019 12:33:14: 17000000 INFO @ Mon, 03 Jun 2019 12:33:20: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:33:20: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:33:20: #1 total tags in treatment: 17948422 INFO @ Mon, 03 Jun 2019 12:33:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:33:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:33:20: #1 tags after filtering in treatment: 17948422 INFO @ Mon, 03 Jun 2019 12:33:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:33:20: #1 finished! INFO @ Mon, 03 Jun 2019 12:33:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:33:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:33:20: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:33:20: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:33:20: #1 total tags in treatment: 17948422 INFO @ Mon, 03 Jun 2019 12:33:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:33:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:33:21: #1 tags after filtering in treatment: 17948422 INFO @ Mon, 03 Jun 2019 12:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:33:21: #1 finished! INFO @ Mon, 03 Jun 2019 12:33:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:33:22: #2 number of paired peaks: 3922 INFO @ Mon, 03 Jun 2019 12:33:22: start model_add_line... INFO @ Mon, 03 Jun 2019 12:33:23: start X-correlation... INFO @ Mon, 03 Jun 2019 12:33:23: end of X-cor INFO @ Mon, 03 Jun 2019 12:33:23: #2 finished! INFO @ Mon, 03 Jun 2019 12:33:23: #2 predicted fragment length is 203 bps INFO @ Mon, 03 Jun 2019 12:33:23: #2 alternative fragment length(s) may be 203 bps INFO @ Mon, 03 Jun 2019 12:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.20_model.r INFO @ Mon, 03 Jun 2019 12:33:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:33:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:33:23: #2 number of paired peaks: 3922 INFO @ Mon, 03 Jun 2019 12:33:23: start model_add_line... INFO @ Mon, 03 Jun 2019 12:33:23: start X-correlation... INFO @ Mon, 03 Jun 2019 12:33:23: end of X-cor INFO @ Mon, 03 Jun 2019 12:33:23: #2 finished! INFO @ Mon, 03 Jun 2019 12:33:23: #2 predicted fragment length is 203 bps INFO @ Mon, 03 Jun 2019 12:33:23: #2 alternative fragment length(s) may be 203 bps INFO @ Mon, 03 Jun 2019 12:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.10_model.r INFO @ Mon, 03 Jun 2019 12:33:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:33:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:34:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:34:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:34:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:34:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:34:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:34:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.05_summits.bed INFO @ Mon, 03 Jun 2019 12:34:35: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10779 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:34:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:34:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:34:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.20_summits.bed INFO @ Mon, 03 Jun 2019 12:34:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6518 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:34:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:34:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:34:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326967/SRX326967.10_summits.bed INFO @ Mon, 03 Jun 2019 12:34:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8641 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。