Job ID = 1294093 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,657,102 reads read : 10,657,102 reads written : 10,657,102 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: 00:00:01 Multiseed full-index search: 00:01:45 10657102 reads; of these: 10657102 (100.00%) were unpaired; of these: 109047 (1.02%) aligned 0 times 10359758 (97.21%) aligned exactly 1 time 188297 (1.77%) aligned >1 times 98.98% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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] 3472948 / 10548055 = 0.3293 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 04:54:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.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 04:54:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:54:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:54:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.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 04:54:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:54:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:54:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.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 04:54:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:54:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:54:52: 1000000 INFO @ Mon, 03 Jun 2019 04:54:52: 1000000 INFO @ Mon, 03 Jun 2019 04:54:53: 1000000 INFO @ Mon, 03 Jun 2019 04:54:58: 2000000 INFO @ Mon, 03 Jun 2019 04:54:59: 2000000 INFO @ Mon, 03 Jun 2019 04:55:01: 2000000 INFO @ Mon, 03 Jun 2019 04:55:04: 3000000 INFO @ Mon, 03 Jun 2019 04:55:06: 3000000 INFO @ Mon, 03 Jun 2019 04:55:09: 3000000 INFO @ Mon, 03 Jun 2019 04:55:11: 4000000 INFO @ Mon, 03 Jun 2019 04:55:13: 4000000 INFO @ Mon, 03 Jun 2019 04:55:17: 4000000 INFO @ Mon, 03 Jun 2019 04:55:17: 5000000 INFO @ Mon, 03 Jun 2019 04:55:20: 5000000 INFO @ Mon, 03 Jun 2019 04:55:24: 6000000 INFO @ Mon, 03 Jun 2019 04:55:25: 5000000 INFO @ Mon, 03 Jun 2019 04:55:27: 6000000 INFO @ Mon, 03 Jun 2019 04:55:30: 7000000 INFO @ Mon, 03 Jun 2019 04:55:31: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 04:55:31: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 04:55:31: #1 total tags in treatment: 7075107 INFO @ Mon, 03 Jun 2019 04:55:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:55:31: #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 04:55:31: #1 tags after filtering in treatment: 7075107 INFO @ Mon, 03 Jun 2019 04:55:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:55:31: #1 finished! INFO @ Mon, 03 Jun 2019 04:55:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:55:31: #2 number of paired peaks: 1071 INFO @ Mon, 03 Jun 2019 04:55:31: start model_add_line... INFO @ Mon, 03 Jun 2019 04:55:31: start X-correlation... INFO @ Mon, 03 Jun 2019 04:55:31: end of X-cor INFO @ Mon, 03 Jun 2019 04:55:31: #2 finished! INFO @ Mon, 03 Jun 2019 04:55:31: #2 predicted fragment length is 100 bps INFO @ Mon, 03 Jun 2019 04:55:31: #2 alternative fragment length(s) may be 100 bps INFO @ Mon, 03 Jun 2019 04:55:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.10_model.r INFO @ Mon, 03 Jun 2019 04:55:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:55:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:55:32: 6000000 INFO @ Mon, 03 Jun 2019 04:55:33: 7000000 INFO @ Mon, 03 Jun 2019 04:55:34: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 04:55:34: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 04:55:34: #1 total tags in treatment: 7075107 INFO @ Mon, 03 Jun 2019 04:55:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:55:34: #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 04:55:34: #1 tags after filtering in treatment: 7075107 INFO @ Mon, 03 Jun 2019 04:55:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:55:34: #1 finished! INFO @ Mon, 03 Jun 2019 04:55:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:55:35: #2 number of paired peaks: 1071 INFO @ Mon, 03 Jun 2019 04:55:35: start model_add_line... INFO @ Mon, 03 Jun 2019 04:55:35: start X-correlation... INFO @ Mon, 03 Jun 2019 04:55:35: end of X-cor INFO @ Mon, 03 Jun 2019 04:55:35: #2 finished! INFO @ Mon, 03 Jun 2019 04:55:35: #2 predicted fragment length is 100 bps INFO @ Mon, 03 Jun 2019 04:55:35: #2 alternative fragment length(s) may be 100 bps INFO @ Mon, 03 Jun 2019 04:55:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.20_model.r INFO @ Mon, 03 Jun 2019 04:55:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:55:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:55:40: 7000000 INFO @ Mon, 03 Jun 2019 04:55:41: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 04:55:41: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 04:55:41: #1 total tags in treatment: 7075107 INFO @ Mon, 03 Jun 2019 04:55:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:55:41: #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 04:55:41: #1 tags after filtering in treatment: 7075107 INFO @ Mon, 03 Jun 2019 04:55:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:55:41: #1 finished! INFO @ Mon, 03 Jun 2019 04:55:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:55:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:55:41: #2 number of paired peaks: 1071 INFO @ Mon, 03 Jun 2019 04:55:41: start model_add_line... INFO @ Mon, 03 Jun 2019 04:55:41: start X-correlation... INFO @ Mon, 03 Jun 2019 04:55:41: end of X-cor INFO @ Mon, 03 Jun 2019 04:55:41: #2 finished! INFO @ Mon, 03 Jun 2019 04:55:41: #2 predicted fragment length is 100 bps INFO @ Mon, 03 Jun 2019 04:55:41: #2 alternative fragment length(s) may be 100 bps INFO @ Mon, 03 Jun 2019 04:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.05_model.r INFO @ Mon, 03 Jun 2019 04:55:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:55:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:55:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:56:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:56:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:56:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:56:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.10_summits.bed INFO @ Mon, 03 Jun 2019 04:56:04: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3835 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:56:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:56:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:56:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.20_summits.bed INFO @ Mon, 03 Jun 2019 04:56:07: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1712 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:56:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:56:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:56:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183882/SRX183882.05_summits.bed INFO @ Mon, 03 Jun 2019 04:56:13: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (8525 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。