Job ID = 2590322 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,901,603 reads read : 17,901,603 reads written : 17,901,603 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: 00:06:26 17901603 reads; of these: 17901603 (100.00%) were unpaired; of these: 902985 (5.04%) aligned 0 times 12928678 (72.22%) aligned exactly 1 time 4069940 (22.74%) aligned >1 times 94.96% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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] 4441245 / 16998618 = 0.2613 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 20:59:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.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 20:59:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:59:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:59:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.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 20:59:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:59:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:59:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.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 20:59:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:59:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:00:02: 1000000 INFO @ Mon, 12 Aug 2019 21:00:05: 1000000 INFO @ Mon, 12 Aug 2019 21:00:05: 1000000 INFO @ Mon, 12 Aug 2019 21:00:11: 2000000 INFO @ Mon, 12 Aug 2019 21:00:13: 2000000 INFO @ Mon, 12 Aug 2019 21:00:15: 2000000 INFO @ Mon, 12 Aug 2019 21:00:19: 3000000 INFO @ Mon, 12 Aug 2019 21:00:22: 3000000 INFO @ Mon, 12 Aug 2019 21:00:24: 3000000 INFO @ Mon, 12 Aug 2019 21:00:27: 4000000 INFO @ Mon, 12 Aug 2019 21:00:29: 4000000 INFO @ Mon, 12 Aug 2019 21:00:34: 4000000 INFO @ Mon, 12 Aug 2019 21:00:35: 5000000 INFO @ Mon, 12 Aug 2019 21:00:37: 5000000 INFO @ Mon, 12 Aug 2019 21:00:42: 6000000 INFO @ Mon, 12 Aug 2019 21:00:43: 5000000 INFO @ Mon, 12 Aug 2019 21:00:44: 6000000 INFO @ Mon, 12 Aug 2019 21:00:49: 7000000 INFO @ Mon, 12 Aug 2019 21:00:52: 7000000 INFO @ Mon, 12 Aug 2019 21:00:52: 6000000 INFO @ Mon, 12 Aug 2019 21:00:57: 8000000 INFO @ Mon, 12 Aug 2019 21:00:59: 8000000 INFO @ Mon, 12 Aug 2019 21:01:02: 7000000 INFO @ Mon, 12 Aug 2019 21:01:04: 9000000 INFO @ Mon, 12 Aug 2019 21:01:06: 9000000 INFO @ Mon, 12 Aug 2019 21:01:11: 8000000 INFO @ Mon, 12 Aug 2019 21:01:12: 10000000 INFO @ Mon, 12 Aug 2019 21:01:14: 10000000 INFO @ Mon, 12 Aug 2019 21:01:19: 11000000 INFO @ Mon, 12 Aug 2019 21:01:20: 9000000 INFO @ Mon, 12 Aug 2019 21:01:21: 11000000 INFO @ Mon, 12 Aug 2019 21:01:27: 12000000 INFO @ Mon, 12 Aug 2019 21:01:29: 12000000 INFO @ Mon, 12 Aug 2019 21:01:30: 10000000 INFO @ Mon, 12 Aug 2019 21:01:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:01:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:01:31: #1 total tags in treatment: 12557373 INFO @ Mon, 12 Aug 2019 21:01:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:01:31: #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 21:01:31: #1 tags after filtering in treatment: 12557373 INFO @ Mon, 12 Aug 2019 21:01:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:01:31: #1 finished! INFO @ Mon, 12 Aug 2019 21:01:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:01:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:01:33: #2 number of paired peaks: 6218 INFO @ Mon, 12 Aug 2019 21:01:33: start model_add_line... INFO @ Mon, 12 Aug 2019 21:01:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:01:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:01:33: #1 total tags in treatment: 12557373 INFO @ Mon, 12 Aug 2019 21:01:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:01:33: #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 21:01:33: start X-correlation... INFO @ Mon, 12 Aug 2019 21:01:33: end of X-cor INFO @ Mon, 12 Aug 2019 21:01:33: #2 finished! INFO @ Mon, 12 Aug 2019 21:01:33: #2 predicted fragment length is 208 bps INFO @ Mon, 12 Aug 2019 21:01:33: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 12 Aug 2019 21:01:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.05_model.r INFO @ Mon, 12 Aug 2019 21:01:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:01:34: #1 tags after filtering in treatment: 12557373 INFO @ Mon, 12 Aug 2019 21:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:01:34: #1 finished! INFO @ Mon, 12 Aug 2019 21:01:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:01:35: #2 number of paired peaks: 6218 INFO @ Mon, 12 Aug 2019 21:01:35: start model_add_line... INFO @ Mon, 12 Aug 2019 21:01:36: start X-correlation... INFO @ Mon, 12 Aug 2019 21:01:36: end of X-cor INFO @ Mon, 12 Aug 2019 21:01:36: #2 finished! INFO @ Mon, 12 Aug 2019 21:01:36: #2 predicted fragment length is 208 bps INFO @ Mon, 12 Aug 2019 21:01:36: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 12 Aug 2019 21:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.20_model.r INFO @ Mon, 12 Aug 2019 21:01:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:01:39: 11000000 INFO @ Mon, 12 Aug 2019 21:01:49: 12000000 INFO @ Mon, 12 Aug 2019 21:01:54: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:01:54: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:01:54: #1 total tags in treatment: 12557373 INFO @ Mon, 12 Aug 2019 21:01:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:01:54: #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 21:01:54: #1 tags after filtering in treatment: 12557373 INFO @ Mon, 12 Aug 2019 21:01:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:01:54: #1 finished! INFO @ Mon, 12 Aug 2019 21:01:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:01:56: #2 number of paired peaks: 6218 INFO @ Mon, 12 Aug 2019 21:01:56: start model_add_line... INFO @ Mon, 12 Aug 2019 21:01:56: start X-correlation... INFO @ Mon, 12 Aug 2019 21:01:56: end of X-cor INFO @ Mon, 12 Aug 2019 21:01:56: #2 finished! INFO @ Mon, 12 Aug 2019 21:01:56: #2 predicted fragment length is 208 bps INFO @ Mon, 12 Aug 2019 21:01:56: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 12 Aug 2019 21:01:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.10_model.r INFO @ Mon, 12 Aug 2019 21:01:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:01:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:02:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:02:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:02:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:02:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:02:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.05_summits.bed INFO @ Mon, 12 Aug 2019 21:02:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9202 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:02:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:02:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:02:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.20_summits.bed INFO @ Mon, 12 Aug 2019 21:02:40: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6058 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:02:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331428/SRX331428.10_summits.bed INFO @ Mon, 12 Aug 2019 21:03:01: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7776 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。