Job ID = 1293304 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,945,648 reads read : 9,945,648 reads written : 9,945,648 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: 00:01:58 9945648 reads; of these: 9945648 (100.00%) were unpaired; of these: 699172 (7.03%) aligned 0 times 8681576 (87.29%) aligned exactly 1 time 564900 (5.68%) aligned >1 times 92.97% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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_rmdupse_core] 1628952 / 9246476 = 0.1762 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 @ Sun, 02 Jun 2019 22:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.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 @ Sun, 02 Jun 2019 22:55:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:55:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.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 @ Sun, 02 Jun 2019 22:55:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:55:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.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 @ Sun, 02 Jun 2019 22:55:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:55:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:55:33: 1000000 INFO @ Sun, 02 Jun 2019 22:55:34: 1000000 INFO @ Sun, 02 Jun 2019 22:55:34: 1000000 INFO @ Sun, 02 Jun 2019 22:55:39: 2000000 INFO @ Sun, 02 Jun 2019 22:55:42: 2000000 INFO @ Sun, 02 Jun 2019 22:55:42: 2000000 INFO @ Sun, 02 Jun 2019 22:55:46: 3000000 INFO @ Sun, 02 Jun 2019 22:55:50: 3000000 INFO @ Sun, 02 Jun 2019 22:55:50: 3000000 INFO @ Sun, 02 Jun 2019 22:55:53: 4000000 INFO @ Sun, 02 Jun 2019 22:55:58: 4000000 INFO @ Sun, 02 Jun 2019 22:55:58: 4000000 INFO @ Sun, 02 Jun 2019 22:56:00: 5000000 INFO @ Sun, 02 Jun 2019 22:56:06: 5000000 INFO @ Sun, 02 Jun 2019 22:56:06: 6000000 INFO @ Sun, 02 Jun 2019 22:56:06: 5000000 INFO @ Sun, 02 Jun 2019 22:56:13: 7000000 INFO @ Sun, 02 Jun 2019 22:56:14: 6000000 INFO @ Sun, 02 Jun 2019 22:56:14: 6000000 INFO @ Sun, 02 Jun 2019 22:56:17: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:56:17: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:56:17: #1 total tags in treatment: 7617524 INFO @ Sun, 02 Jun 2019 22:56:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:56:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:56:17: #1 tags after filtering in treatment: 7617524 INFO @ Sun, 02 Jun 2019 22:56:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:56:17: #1 finished! INFO @ Sun, 02 Jun 2019 22:56:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:56:19: #2 number of paired peaks: 6497 INFO @ Sun, 02 Jun 2019 22:56:19: start model_add_line... INFO @ Sun, 02 Jun 2019 22:56:19: start X-correlation... INFO @ Sun, 02 Jun 2019 22:56:19: end of X-cor INFO @ Sun, 02 Jun 2019 22:56:19: #2 finished! INFO @ Sun, 02 Jun 2019 22:56:19: #2 predicted fragment length is 103 bps INFO @ Sun, 02 Jun 2019 22:56:19: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 02 Jun 2019 22:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.10_model.r INFO @ Sun, 02 Jun 2019 22:56:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:56:22: 7000000 INFO @ Sun, 02 Jun 2019 22:56:22: 7000000 INFO @ Sun, 02 Jun 2019 22:56:27: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:56:27: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:56:27: #1 total tags in treatment: 7617524 INFO @ Sun, 02 Jun 2019 22:56:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:56:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:56:27: #1 tags after filtering in treatment: 7617524 INFO @ Sun, 02 Jun 2019 22:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:56:27: #1 finished! INFO @ Sun, 02 Jun 2019 22:56:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:56:27: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:56:27: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:56:27: #1 total tags in treatment: 7617524 INFO @ Sun, 02 Jun 2019 22:56:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:56:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:56:27: #1 tags after filtering in treatment: 7617524 INFO @ Sun, 02 Jun 2019 22:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:56:27: #1 finished! INFO @ Sun, 02 Jun 2019 22:56:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:56:28: #2 number of paired peaks: 6497 INFO @ Sun, 02 Jun 2019 22:56:28: start model_add_line... INFO @ Sun, 02 Jun 2019 22:56:28: start X-correlation... INFO @ Sun, 02 Jun 2019 22:56:28: end of X-cor INFO @ Sun, 02 Jun 2019 22:56:28: #2 finished! INFO @ Sun, 02 Jun 2019 22:56:28: #2 predicted fragment length is 103 bps INFO @ Sun, 02 Jun 2019 22:56:28: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 02 Jun 2019 22:56:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.05_model.r INFO @ Sun, 02 Jun 2019 22:56:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:56:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:56:29: #2 number of paired peaks: 6497 INFO @ Sun, 02 Jun 2019 22:56:29: start model_add_line... INFO @ Sun, 02 Jun 2019 22:56:29: start X-correlation... INFO @ Sun, 02 Jun 2019 22:56:29: end of X-cor INFO @ Sun, 02 Jun 2019 22:56:29: #2 finished! INFO @ Sun, 02 Jun 2019 22:56:29: #2 predicted fragment length is 103 bps INFO @ Sun, 02 Jun 2019 22:56:29: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 02 Jun 2019 22:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.20_model.r INFO @ Sun, 02 Jun 2019 22:56:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:56:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:56:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:56:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:56:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:56:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:56:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.10_summits.bed INFO @ Sun, 02 Jun 2019 22:56:57: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (6892 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:57:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:57:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:57:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.05_summits.bed INFO @ Sun, 02 Jun 2019 22:57:07: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (9580 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:57:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:57:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:57:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX101804/ERX101804.20_summits.bed INFO @ Sun, 02 Jun 2019 22:57:07: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4253 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。