Job ID = 1293641 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,170,982 reads read : 24,170,982 reads written : 24,170,982 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: 00:15:32 24170982 reads; of these: 24170982 (100.00%) were unpaired; of these: 2210114 (9.14%) aligned 0 times 15878097 (65.69%) aligned exactly 1 time 6082771 (25.17%) aligned >1 times 90.86% overall alignment rate Time searching: 00:15:32 Overall time: 00:15:32 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] 8744621 / 21960868 = 0.3982 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 01:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.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 01:44:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:44:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.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 01:44:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:44:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.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 01:44:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:44:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:44:27: 1000000 INFO @ Mon, 03 Jun 2019 01:44:28: 1000000 INFO @ Mon, 03 Jun 2019 01:44:28: 1000000 INFO @ Mon, 03 Jun 2019 01:44:39: 2000000 INFO @ Mon, 03 Jun 2019 01:44:40: 2000000 INFO @ Mon, 03 Jun 2019 01:44:40: 2000000 INFO @ Mon, 03 Jun 2019 01:44:50: 3000000 INFO @ Mon, 03 Jun 2019 01:44:52: 3000000 INFO @ Mon, 03 Jun 2019 01:44:52: 3000000 INFO @ Mon, 03 Jun 2019 01:45:02: 4000000 INFO @ Mon, 03 Jun 2019 01:45:03: 4000000 INFO @ Mon, 03 Jun 2019 01:45:04: 4000000 INFO @ Mon, 03 Jun 2019 01:45:14: 5000000 INFO @ Mon, 03 Jun 2019 01:45:15: 5000000 INFO @ Mon, 03 Jun 2019 01:45:16: 5000000 INFO @ Mon, 03 Jun 2019 01:45:25: 6000000 INFO @ Mon, 03 Jun 2019 01:45:27: 6000000 INFO @ Mon, 03 Jun 2019 01:45:28: 6000000 INFO @ Mon, 03 Jun 2019 01:45:37: 7000000 INFO @ Mon, 03 Jun 2019 01:45:39: 7000000 INFO @ Mon, 03 Jun 2019 01:45:40: 7000000 INFO @ Mon, 03 Jun 2019 01:45:48: 8000000 INFO @ Mon, 03 Jun 2019 01:45:50: 8000000 INFO @ Mon, 03 Jun 2019 01:45:51: 8000000 INFO @ Mon, 03 Jun 2019 01:45:58: 9000000 INFO @ Mon, 03 Jun 2019 01:46:02: 9000000 INFO @ Mon, 03 Jun 2019 01:46:02: 9000000 INFO @ Mon, 03 Jun 2019 01:46:10: 10000000 INFO @ Mon, 03 Jun 2019 01:46:14: 10000000 INFO @ Mon, 03 Jun 2019 01:46:14: 10000000 INFO @ Mon, 03 Jun 2019 01:46:21: 11000000 INFO @ Mon, 03 Jun 2019 01:46:25: 11000000 INFO @ Mon, 03 Jun 2019 01:46:25: 11000000 INFO @ Mon, 03 Jun 2019 01:46:31: 12000000 INFO @ Mon, 03 Jun 2019 01:46:36: 12000000 INFO @ Mon, 03 Jun 2019 01:46:37: 12000000 INFO @ Mon, 03 Jun 2019 01:46:42: 13000000 INFO @ Mon, 03 Jun 2019 01:46:45: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:46:45: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:46:45: #1 total tags in treatment: 13216247 INFO @ Mon, 03 Jun 2019 01:46:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:46:45: #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 01:46:46: #1 tags after filtering in treatment: 13216247 INFO @ Mon, 03 Jun 2019 01:46:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:46:46: #1 finished! INFO @ Mon, 03 Jun 2019 01:46:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:46:48: #2 number of paired peaks: 2819 INFO @ Mon, 03 Jun 2019 01:46:48: start model_add_line... INFO @ Mon, 03 Jun 2019 01:46:48: start X-correlation... INFO @ Mon, 03 Jun 2019 01:46:48: end of X-cor INFO @ Mon, 03 Jun 2019 01:46:48: #2 finished! INFO @ Mon, 03 Jun 2019 01:46:48: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 01:46:48: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 01:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.05_model.r INFO @ Mon, 03 Jun 2019 01:46:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:46:49: 13000000 INFO @ Mon, 03 Jun 2019 01:46:49: 13000000 INFO @ Mon, 03 Jun 2019 01:46:51: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:46:51: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:46:51: #1 total tags in treatment: 13216247 INFO @ Mon, 03 Jun 2019 01:46:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:46:51: #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 01:46:52: #1 tags after filtering in treatment: 13216247 INFO @ Mon, 03 Jun 2019 01:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:46:52: #1 finished! INFO @ Mon, 03 Jun 2019 01:46:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:46:52: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:46:52: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:46:52: #1 total tags in treatment: 13216247 INFO @ Mon, 03 Jun 2019 01:46:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:46:52: #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 01:46:52: #1 tags after filtering in treatment: 13216247 INFO @ Mon, 03 Jun 2019 01:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:46:52: #1 finished! INFO @ Mon, 03 Jun 2019 01:46:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:46:54: #2 number of paired peaks: 2819 INFO @ Mon, 03 Jun 2019 01:46:54: start model_add_line... INFO @ Mon, 03 Jun 2019 01:46:54: start X-correlation... INFO @ Mon, 03 Jun 2019 01:46:54: end of X-cor INFO @ Mon, 03 Jun 2019 01:46:54: #2 finished! INFO @ Mon, 03 Jun 2019 01:46:54: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 01:46:54: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 01:46:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.10_model.r INFO @ Mon, 03 Jun 2019 01:46:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:46:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:46:54: #2 number of paired peaks: 2819 INFO @ Mon, 03 Jun 2019 01:46:54: start model_add_line... INFO @ Mon, 03 Jun 2019 01:46:55: start X-correlation... INFO @ Mon, 03 Jun 2019 01:46:55: end of X-cor INFO @ Mon, 03 Jun 2019 01:46:55: #2 finished! INFO @ Mon, 03 Jun 2019 01:46:55: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 01:46:55: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 01:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.20_model.r INFO @ Mon, 03 Jun 2019 01:46:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:46:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:47:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:47:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:47:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:48:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:48:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:48:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.05_summits.bed INFO @ Mon, 03 Jun 2019 01:48:24: Done! pass1 - making usageList (15 chroms): 10 millis pass2 - checking and writing primary data (17340 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:48:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:48:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.10_summits.bed INFO @ Mon, 03 Jun 2019 01:48:27: Done! pass1 - making usageList (15 chroms): 9 millis pass2 - checking and writing primary data (11884 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:48:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:48:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:48:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032414/SRX1032414.20_summits.bed INFO @ Mon, 03 Jun 2019 01:48:28: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7491 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。