Job ID = 2590305 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,875,574 reads read : 16,875,574 reads written : 16,875,574 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: 00:06:49 16875574 reads; of these: 16875574 (100.00%) were unpaired; of these: 668943 (3.96%) aligned 0 times 11748490 (69.62%) aligned exactly 1 time 4458141 (26.42%) aligned >1 times 96.04% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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] 3667791 / 16206631 = 0.2263 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 20:51:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.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 20:51:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.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 20:51:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.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 20:51:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:52:00: 1000000 INFO @ Mon, 12 Aug 2019 20:52:01: 1000000 INFO @ Mon, 12 Aug 2019 20:52:03: 1000000 INFO @ Mon, 12 Aug 2019 20:52:08: 2000000 INFO @ Mon, 12 Aug 2019 20:52:09: 2000000 INFO @ Mon, 12 Aug 2019 20:52:13: 2000000 INFO @ Mon, 12 Aug 2019 20:52:17: 3000000 INFO @ Mon, 12 Aug 2019 20:52:19: 3000000 INFO @ Mon, 12 Aug 2019 20:52:23: 3000000 INFO @ Mon, 12 Aug 2019 20:52:26: 4000000 INFO @ Mon, 12 Aug 2019 20:52:29: 4000000 INFO @ Mon, 12 Aug 2019 20:52:33: 4000000 INFO @ Mon, 12 Aug 2019 20:52:35: 5000000 INFO @ Mon, 12 Aug 2019 20:52:39: 5000000 INFO @ Mon, 12 Aug 2019 20:52:43: 6000000 INFO @ Mon, 12 Aug 2019 20:52:44: 5000000 INFO @ Mon, 12 Aug 2019 20:52:50: 6000000 INFO @ Mon, 12 Aug 2019 20:52:52: 7000000 INFO @ Mon, 12 Aug 2019 20:52:55: 6000000 INFO @ Mon, 12 Aug 2019 20:53:01: 7000000 INFO @ Mon, 12 Aug 2019 20:53:01: 8000000 INFO @ Mon, 12 Aug 2019 20:53:05: 7000000 INFO @ Mon, 12 Aug 2019 20:53:11: 9000000 INFO @ Mon, 12 Aug 2019 20:53:12: 8000000 INFO @ Mon, 12 Aug 2019 20:53:16: 8000000 INFO @ Mon, 12 Aug 2019 20:53:20: 10000000 INFO @ Mon, 12 Aug 2019 20:53:23: 9000000 INFO @ Mon, 12 Aug 2019 20:53:27: 9000000 INFO @ Mon, 12 Aug 2019 20:53:29: 11000000 INFO @ Mon, 12 Aug 2019 20:53:35: 10000000 INFO @ Mon, 12 Aug 2019 20:53:38: 10000000 INFO @ Mon, 12 Aug 2019 20:53:38: 12000000 INFO @ Mon, 12 Aug 2019 20:53:43: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:53:43: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:53:43: #1 total tags in treatment: 12538840 INFO @ Mon, 12 Aug 2019 20:53:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:53:43: #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 20:53:44: #1 tags after filtering in treatment: 12538840 INFO @ Mon, 12 Aug 2019 20:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:53:44: #1 finished! INFO @ Mon, 12 Aug 2019 20:53:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:53:45: #2 number of paired peaks: 4347 INFO @ Mon, 12 Aug 2019 20:53:45: start model_add_line... INFO @ Mon, 12 Aug 2019 20:53:46: start X-correlation... INFO @ Mon, 12 Aug 2019 20:53:46: end of X-cor INFO @ Mon, 12 Aug 2019 20:53:46: #2 finished! INFO @ Mon, 12 Aug 2019 20:53:46: #2 predicted fragment length is 213 bps INFO @ Mon, 12 Aug 2019 20:53:46: #2 alternative fragment length(s) may be 213 bps INFO @ Mon, 12 Aug 2019 20:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.05_model.r INFO @ Mon, 12 Aug 2019 20:53:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:53:46: 11000000 INFO @ Mon, 12 Aug 2019 20:53:49: 11000000 INFO @ Mon, 12 Aug 2019 20:53:57: 12000000 INFO @ Mon, 12 Aug 2019 20:53:59: 12000000 INFO @ Mon, 12 Aug 2019 20:54:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:54:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:54:03: #1 total tags in treatment: 12538840 INFO @ Mon, 12 Aug 2019 20:54:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:54:03: #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 20:54:03: #1 tags after filtering in treatment: 12538840 INFO @ Mon, 12 Aug 2019 20:54:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:54:03: #1 finished! INFO @ Mon, 12 Aug 2019 20:54:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:54:05: #2 number of paired peaks: 4347 INFO @ Mon, 12 Aug 2019 20:54:05: start model_add_line... INFO @ Mon, 12 Aug 2019 20:54:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:54:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:54:05: #1 total tags in treatment: 12538840 INFO @ Mon, 12 Aug 2019 20:54:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:54:05: #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 20:54:05: start X-correlation... INFO @ Mon, 12 Aug 2019 20:54:05: end of X-cor INFO @ Mon, 12 Aug 2019 20:54:05: #2 finished! INFO @ Mon, 12 Aug 2019 20:54:05: #2 predicted fragment length is 213 bps INFO @ Mon, 12 Aug 2019 20:54:05: #2 alternative fragment length(s) may be 213 bps INFO @ Mon, 12 Aug 2019 20:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.20_model.r INFO @ Mon, 12 Aug 2019 20:54:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:54:05: #1 tags after filtering in treatment: 12538840 INFO @ Mon, 12 Aug 2019 20:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:54:05: #1 finished! INFO @ Mon, 12 Aug 2019 20:54:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:54:07: #2 number of paired peaks: 4347 INFO @ Mon, 12 Aug 2019 20:54:07: start model_add_line... INFO @ Mon, 12 Aug 2019 20:54:07: start X-correlation... INFO @ Mon, 12 Aug 2019 20:54:07: end of X-cor INFO @ Mon, 12 Aug 2019 20:54:07: #2 finished! INFO @ Mon, 12 Aug 2019 20:54:07: #2 predicted fragment length is 213 bps INFO @ Mon, 12 Aug 2019 20:54:07: #2 alternative fragment length(s) may be 213 bps INFO @ Mon, 12 Aug 2019 20:54:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.10_model.r INFO @ Mon, 12 Aug 2019 20:54:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:54:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:54:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.05_summits.bed INFO @ Mon, 12 Aug 2019 20:54:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:54:49: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9223 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:54:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:55:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:55:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:55:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.20_summits.bed INFO @ Mon, 12 Aug 2019 20:55:07: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5327 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:55:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:55:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:55:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318800/SRX318800.10_summits.bed INFO @ Mon, 12 Aug 2019 20:55:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7300 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。