Job ID = 1307957 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,836,618 reads read : 41,673,236 reads written : 20,836,618 reads 0-length : 20,836,618 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: 00:06:44 20836618 reads; of these: 20836618 (100.00%) were unpaired; of these: 3259248 (15.64%) aligned 0 times 15290713 (73.38%) aligned exactly 1 time 2286657 (10.97%) aligned >1 times 84.36% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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] 10947166 / 17577370 = 0.6228 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 22:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.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 22:52:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.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 22:52:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.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 22:52:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:44: 1000000 INFO @ Mon, 03 Jun 2019 22:52:44: 1000000 INFO @ Mon, 03 Jun 2019 22:52:45: 1000000 INFO @ Mon, 03 Jun 2019 22:52:52: 2000000 INFO @ Mon, 03 Jun 2019 22:52:53: 2000000 INFO @ Mon, 03 Jun 2019 22:52:54: 2000000 INFO @ Mon, 03 Jun 2019 22:53:00: 3000000 INFO @ Mon, 03 Jun 2019 22:53:01: 3000000 INFO @ Mon, 03 Jun 2019 22:53:02: 3000000 INFO @ Mon, 03 Jun 2019 22:53:07: 4000000 INFO @ Mon, 03 Jun 2019 22:53:08: 4000000 INFO @ Mon, 03 Jun 2019 22:53:11: 4000000 INFO @ Mon, 03 Jun 2019 22:53:15: 5000000 INFO @ Mon, 03 Jun 2019 22:53:16: 5000000 INFO @ Mon, 03 Jun 2019 22:53:19: 5000000 INFO @ Mon, 03 Jun 2019 22:53:22: 6000000 INFO @ Mon, 03 Jun 2019 22:53:23: 6000000 INFO @ Mon, 03 Jun 2019 22:53:27: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:53:27: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:53:27: #1 total tags in treatment: 6630204 INFO @ Mon, 03 Jun 2019 22:53:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:53:27: #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 22:53:27: 6000000 INFO @ Mon, 03 Jun 2019 22:53:27: #1 tags after filtering in treatment: 6630204 INFO @ Mon, 03 Jun 2019 22:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:53:27: #1 finished! INFO @ Mon, 03 Jun 2019 22:53:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:53:28: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:53:28: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:53:28: #1 total tags in treatment: 6630204 INFO @ Mon, 03 Jun 2019 22:53:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:53:28: #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 22:53:28: #1 tags after filtering in treatment: 6630204 INFO @ Mon, 03 Jun 2019 22:53:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:53:28: #1 finished! INFO @ Mon, 03 Jun 2019 22:53:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:53:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:53:29: #2 number of paired peaks: 8583 INFO @ Mon, 03 Jun 2019 22:53:29: start model_add_line... INFO @ Mon, 03 Jun 2019 22:53:29: start X-correlation... INFO @ Mon, 03 Jun 2019 22:53:29: end of X-cor INFO @ Mon, 03 Jun 2019 22:53:29: #2 finished! INFO @ Mon, 03 Jun 2019 22:53:29: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 22:53:29: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 03 Jun 2019 22:53:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.10_model.r INFO @ Mon, 03 Jun 2019 22:53:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:53:29: #2 number of paired peaks: 8583 INFO @ Mon, 03 Jun 2019 22:53:29: start model_add_line... INFO @ Mon, 03 Jun 2019 22:53:30: start X-correlation... INFO @ Mon, 03 Jun 2019 22:53:30: end of X-cor INFO @ Mon, 03 Jun 2019 22:53:30: #2 finished! INFO @ Mon, 03 Jun 2019 22:53:30: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 22:53:30: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 03 Jun 2019 22:53:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.20_model.r INFO @ Mon, 03 Jun 2019 22:53:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:53:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:53:32: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:53:32: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:53:32: #1 total tags in treatment: 6630204 INFO @ Mon, 03 Jun 2019 22:53:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:53:32: #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 22:53:33: #1 tags after filtering in treatment: 6630204 INFO @ Mon, 03 Jun 2019 22:53:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:53:33: #1 finished! INFO @ Mon, 03 Jun 2019 22:53:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:53:34: #2 number of paired peaks: 8583 INFO @ Mon, 03 Jun 2019 22:53:34: start model_add_line... INFO @ Mon, 03 Jun 2019 22:53:34: start X-correlation... INFO @ Mon, 03 Jun 2019 22:53:34: end of X-cor INFO @ Mon, 03 Jun 2019 22:53:34: #2 finished! INFO @ Mon, 03 Jun 2019 22:53:34: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 22:53:34: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 03 Jun 2019 22:53:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.05_model.r INFO @ Mon, 03 Jun 2019 22:53:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:53:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:53:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:53:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:53:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:54:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.10_summits.bed INFO @ Mon, 03 Jun 2019 22:54:01: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7327 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:54:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.20_summits.bed INFO @ Mon, 03 Jun 2019 22:54:01: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5809 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:54:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:54:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:54:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343126/SRX5343126.05_summits.bed INFO @ Mon, 03 Jun 2019 22:54:06: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8188 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。