Job ID = 1295221 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,583,449 reads read : 13,583,449 reads written : 13,583,449 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: 00:03:08 13583449 reads; of these: 13583449 (100.00%) were unpaired; of these: 678635 (5.00%) aligned 0 times 12236147 (90.08%) aligned exactly 1 time 668667 (4.92%) aligned >1 times 95.00% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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] 1754664 / 12904814 = 0.1360 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 12:57:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.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 12:57:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:57:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:57:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.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 12:57:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:57:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:57:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.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 12:57:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:57:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:57:30: 1000000 INFO @ Mon, 03 Jun 2019 12:57:31: 1000000 INFO @ Mon, 03 Jun 2019 12:57:34: 1000000 INFO @ Mon, 03 Jun 2019 12:57:40: 2000000 INFO @ Mon, 03 Jun 2019 12:57:42: 2000000 INFO @ Mon, 03 Jun 2019 12:57:46: 2000000 INFO @ Mon, 03 Jun 2019 12:57:50: 3000000 INFO @ Mon, 03 Jun 2019 12:57:52: 3000000 INFO @ Mon, 03 Jun 2019 12:57:58: 3000000 INFO @ Mon, 03 Jun 2019 12:57:59: 4000000 INFO @ Mon, 03 Jun 2019 12:58:03: 4000000 INFO @ Mon, 03 Jun 2019 12:58:09: 5000000 INFO @ Mon, 03 Jun 2019 12:58:11: 4000000 INFO @ Mon, 03 Jun 2019 12:58:14: 5000000 INFO @ Mon, 03 Jun 2019 12:58:19: 6000000 INFO @ Mon, 03 Jun 2019 12:58:23: 5000000 INFO @ Mon, 03 Jun 2019 12:58:25: 6000000 INFO @ Mon, 03 Jun 2019 12:58:29: 7000000 INFO @ Mon, 03 Jun 2019 12:58:35: 6000000 INFO @ Mon, 03 Jun 2019 12:58:36: 7000000 INFO @ Mon, 03 Jun 2019 12:58:39: 8000000 INFO @ Mon, 03 Jun 2019 12:58:46: 8000000 INFO @ Mon, 03 Jun 2019 12:58:46: 7000000 INFO @ Mon, 03 Jun 2019 12:58:49: 9000000 INFO @ Mon, 03 Jun 2019 12:58:56: 9000000 INFO @ Mon, 03 Jun 2019 12:58:57: 8000000 INFO @ Mon, 03 Jun 2019 12:58:59: 10000000 INFO @ Mon, 03 Jun 2019 12:59:07: 10000000 INFO @ Mon, 03 Jun 2019 12:59:09: 9000000 INFO @ Mon, 03 Jun 2019 12:59:09: 11000000 INFO @ Mon, 03 Jun 2019 12:59:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:59:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:59:11: #1 total tags in treatment: 11150150 INFO @ Mon, 03 Jun 2019 12:59:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:59:11: #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 12:59:11: #1 tags after filtering in treatment: 11150150 INFO @ Mon, 03 Jun 2019 12:59:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:59:11: #1 finished! INFO @ Mon, 03 Jun 2019 12:59:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:59:13: #2 number of paired peaks: 5290 INFO @ Mon, 03 Jun 2019 12:59:13: start model_add_line... INFO @ Mon, 03 Jun 2019 12:59:13: start X-correlation... INFO @ Mon, 03 Jun 2019 12:59:13: end of X-cor INFO @ Mon, 03 Jun 2019 12:59:13: #2 finished! INFO @ Mon, 03 Jun 2019 12:59:13: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 12:59:13: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 03 Jun 2019 12:59:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.10_model.r INFO @ Mon, 03 Jun 2019 12:59:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:59:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:59:16: 11000000 INFO @ Mon, 03 Jun 2019 12:59:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:59:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:59:18: #1 total tags in treatment: 11150150 INFO @ Mon, 03 Jun 2019 12:59:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:59:18: #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 12:59:18: #1 tags after filtering in treatment: 11150150 INFO @ Mon, 03 Jun 2019 12:59:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:59:18: #1 finished! INFO @ Mon, 03 Jun 2019 12:59:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:59:19: 10000000 INFO @ Mon, 03 Jun 2019 12:59:20: #2 number of paired peaks: 5290 INFO @ Mon, 03 Jun 2019 12:59:20: start model_add_line... INFO @ Mon, 03 Jun 2019 12:59:20: start X-correlation... INFO @ Mon, 03 Jun 2019 12:59:20: end of X-cor INFO @ Mon, 03 Jun 2019 12:59:20: #2 finished! INFO @ Mon, 03 Jun 2019 12:59:20: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 12:59:20: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 03 Jun 2019 12:59:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.20_model.r INFO @ Mon, 03 Jun 2019 12:59:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:59:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:59:30: 11000000 INFO @ Mon, 03 Jun 2019 12:59:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:59:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:59:31: #1 total tags in treatment: 11150150 INFO @ Mon, 03 Jun 2019 12:59:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:59:31: #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 12:59:32: #1 tags after filtering in treatment: 11150150 INFO @ Mon, 03 Jun 2019 12:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:59:32: #1 finished! INFO @ Mon, 03 Jun 2019 12:59:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:59:33: #2 number of paired peaks: 5290 INFO @ Mon, 03 Jun 2019 12:59:33: start model_add_line... INFO @ Mon, 03 Jun 2019 12:59:33: start X-correlation... INFO @ Mon, 03 Jun 2019 12:59:33: end of X-cor INFO @ Mon, 03 Jun 2019 12:59:33: #2 finished! INFO @ Mon, 03 Jun 2019 12:59:33: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 12:59:33: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 03 Jun 2019 12:59:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.05_model.r INFO @ Mon, 03 Jun 2019 12:59:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:59:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:59:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:00:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:00:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:00:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.10_summits.bed INFO @ Mon, 03 Jun 2019 13:00:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4321 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:00:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.20_summits.bed INFO @ Mon, 03 Jun 2019 13:00:16: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2208 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:00:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:00:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331396/SRX331396.05_summits.bed INFO @ Mon, 03 Jun 2019 13:00:31: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (6592 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。