Job ID = 1294139 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,599,246 reads read : 22,599,246 reads written : 22,599,246 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: 00:07:31 22599246 reads; of these: 22599246 (100.00%) were unpaired; of these: 2729839 (12.08%) aligned 0 times 15426430 (68.26%) aligned exactly 1 time 4442977 (19.66%) aligned >1 times 87.92% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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 12 files... [bam_rmdupse_core] 7427726 / 19869407 = 0.3738 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 05:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.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 05:15:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:15:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.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 05:15:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:15:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.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 05:15:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:15:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:15:31: 1000000 INFO @ Mon, 03 Jun 2019 05:15:31: 1000000 INFO @ Mon, 03 Jun 2019 05:15:31: 1000000 INFO @ Mon, 03 Jun 2019 05:15:37: 2000000 INFO @ Mon, 03 Jun 2019 05:15:37: 2000000 INFO @ Mon, 03 Jun 2019 05:15:38: 2000000 INFO @ Mon, 03 Jun 2019 05:15:44: 3000000 INFO @ Mon, 03 Jun 2019 05:15:44: 3000000 INFO @ Mon, 03 Jun 2019 05:15:45: 3000000 INFO @ Mon, 03 Jun 2019 05:15:50: 4000000 INFO @ Mon, 03 Jun 2019 05:15:51: 4000000 INFO @ Mon, 03 Jun 2019 05:15:52: 4000000 INFO @ Mon, 03 Jun 2019 05:15:57: 5000000 INFO @ Mon, 03 Jun 2019 05:15:57: 5000000 INFO @ Mon, 03 Jun 2019 05:15:59: 5000000 INFO @ Mon, 03 Jun 2019 05:16:03: 6000000 INFO @ Mon, 03 Jun 2019 05:16:04: 6000000 INFO @ Mon, 03 Jun 2019 05:16:06: 6000000 INFO @ Mon, 03 Jun 2019 05:16:10: 7000000 INFO @ Mon, 03 Jun 2019 05:16:10: 7000000 INFO @ Mon, 03 Jun 2019 05:16:13: 7000000 INFO @ Mon, 03 Jun 2019 05:16:16: 8000000 INFO @ Mon, 03 Jun 2019 05:16:17: 8000000 INFO @ Mon, 03 Jun 2019 05:16:20: 8000000 INFO @ Mon, 03 Jun 2019 05:16:23: 9000000 INFO @ Mon, 03 Jun 2019 05:16:23: 9000000 INFO @ Mon, 03 Jun 2019 05:16:27: 9000000 INFO @ Mon, 03 Jun 2019 05:16:30: 10000000 INFO @ Mon, 03 Jun 2019 05:16:30: 10000000 INFO @ Mon, 03 Jun 2019 05:16:34: 10000000 INFO @ Mon, 03 Jun 2019 05:16:36: 11000000 INFO @ Mon, 03 Jun 2019 05:16:37: 11000000 INFO @ Mon, 03 Jun 2019 05:16:42: 11000000 INFO @ Mon, 03 Jun 2019 05:16:43: 12000000 INFO @ Mon, 03 Jun 2019 05:16:44: 12000000 INFO @ Mon, 03 Jun 2019 05:16:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:16:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:16:46: #1 total tags in treatment: 12441681 INFO @ Mon, 03 Jun 2019 05:16:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:16:46: #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 05:16:46: #1 tags after filtering in treatment: 12441681 INFO @ Mon, 03 Jun 2019 05:16:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:16:46: #1 finished! INFO @ Mon, 03 Jun 2019 05:16:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:16:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:16:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:16:47: #1 total tags in treatment: 12441681 INFO @ Mon, 03 Jun 2019 05:16:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:16:47: #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 05:16:47: #1 tags after filtering in treatment: 12441681 INFO @ Mon, 03 Jun 2019 05:16:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:16:47: #1 finished! INFO @ Mon, 03 Jun 2019 05:16:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:16:48: #2 number of paired peaks: 5380 INFO @ Mon, 03 Jun 2019 05:16:48: start model_add_line... INFO @ Mon, 03 Jun 2019 05:16:48: start X-correlation... INFO @ Mon, 03 Jun 2019 05:16:48: end of X-cor INFO @ Mon, 03 Jun 2019 05:16:48: #2 finished! INFO @ Mon, 03 Jun 2019 05:16:48: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 05:16:48: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 05:16:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.10_model.r INFO @ Mon, 03 Jun 2019 05:16:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:16:49: 12000000 INFO @ Mon, 03 Jun 2019 05:16:49: #2 number of paired peaks: 5380 INFO @ Mon, 03 Jun 2019 05:16:49: start model_add_line... INFO @ Mon, 03 Jun 2019 05:16:49: start X-correlation... INFO @ Mon, 03 Jun 2019 05:16:49: end of X-cor INFO @ Mon, 03 Jun 2019 05:16:49: #2 finished! INFO @ Mon, 03 Jun 2019 05:16:49: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 05:16:49: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 05:16:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.20_model.r INFO @ Mon, 03 Jun 2019 05:16:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:16:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:16:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:16:52: #1 total tags in treatment: 12441681 INFO @ Mon, 03 Jun 2019 05:16:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:16:52: #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 05:16:52: #1 tags after filtering in treatment: 12441681 INFO @ Mon, 03 Jun 2019 05:16:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:16:52: #1 finished! INFO @ Mon, 03 Jun 2019 05:16:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:16:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:16:54: #2 number of paired peaks: 5380 INFO @ Mon, 03 Jun 2019 05:16:54: start model_add_line... INFO @ Mon, 03 Jun 2019 05:16:54: start X-correlation... INFO @ Mon, 03 Jun 2019 05:16:54: end of X-cor INFO @ Mon, 03 Jun 2019 05:16:54: #2 finished! INFO @ Mon, 03 Jun 2019 05:16:54: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 05:16:54: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 03 Jun 2019 05:16:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.05_model.r INFO @ Mon, 03 Jun 2019 05:16:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:17:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:17:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:17:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:17:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:17:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:17:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.20_summits.bed INFO @ Mon, 03 Jun 2019 05:17:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6320 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:17:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:17:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:17:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.10_summits.bed INFO @ Mon, 03 Jun 2019 05:17:54: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8413 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:17:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:17:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:17:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193317/SRX193317.05_summits.bed INFO @ Mon, 03 Jun 2019 05:17:56: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10462 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。