Job ID = 1307952 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,599,381 reads read : 35,198,762 reads written : 17,599,381 reads 0-length : 17,599,381 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: 00:06:41 17599381 reads; of these: 17599381 (100.00%) were unpaired; of these: 2612201 (14.84%) aligned 0 times 13085517 (74.35%) aligned exactly 1 time 1901663 (10.81%) aligned >1 times 85.16% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 8747382 / 14987180 = 0.5837 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 22:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.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 22:52:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.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 22:52:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.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 22:52:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:53:01: 1000000 INFO @ Mon, 03 Jun 2019 22:53:02: 1000000 INFO @ Mon, 03 Jun 2019 22:53:03: 1000000 INFO @ Mon, 03 Jun 2019 22:53:09: 2000000 INFO @ Mon, 03 Jun 2019 22:53:11: 2000000 INFO @ Mon, 03 Jun 2019 22:53:12: 2000000 INFO @ Mon, 03 Jun 2019 22:53:17: 3000000 INFO @ Mon, 03 Jun 2019 22:53:19: 3000000 INFO @ Mon, 03 Jun 2019 22:53:22: 3000000 INFO @ Mon, 03 Jun 2019 22:53:24: 4000000 INFO @ Mon, 03 Jun 2019 22:53:27: 4000000 INFO @ Mon, 03 Jun 2019 22:53:31: 4000000 INFO @ Mon, 03 Jun 2019 22:53:32: 5000000 INFO @ Mon, 03 Jun 2019 22:53:35: 5000000 INFO @ Mon, 03 Jun 2019 22:53:39: 6000000 INFO @ Mon, 03 Jun 2019 22:53:40: 5000000 INFO @ Mon, 03 Jun 2019 22:53:41: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:53:41: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:53:41: #1 total tags in treatment: 6239798 INFO @ Mon, 03 Jun 2019 22:53:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:53:41: #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 22:53:41: #1 tags after filtering in treatment: 6239798 INFO @ Mon, 03 Jun 2019 22:53:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:53:41: #1 finished! INFO @ Mon, 03 Jun 2019 22:53:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:53:42: #2 number of paired peaks: 8512 INFO @ Mon, 03 Jun 2019 22:53:42: start model_add_line... INFO @ Mon, 03 Jun 2019 22:53:43: start X-correlation... INFO @ Mon, 03 Jun 2019 22:53:43: 6000000 INFO @ Mon, 03 Jun 2019 22:53:43: end of X-cor INFO @ Mon, 03 Jun 2019 22:53:43: #2 finished! INFO @ Mon, 03 Jun 2019 22:53:43: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 22:53:43: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 03 Jun 2019 22:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.05_model.r INFO @ Mon, 03 Jun 2019 22:53:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:53:45: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:53:45: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:53:45: #1 total tags in treatment: 6239798 INFO @ Mon, 03 Jun 2019 22:53:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:53:45: #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 22:53:45: #1 tags after filtering in treatment: 6239798 INFO @ Mon, 03 Jun 2019 22:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:53:45: #1 finished! INFO @ Mon, 03 Jun 2019 22:53:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:53:46: #2 number of paired peaks: 8512 INFO @ Mon, 03 Jun 2019 22:53:46: start model_add_line... INFO @ Mon, 03 Jun 2019 22:53:46: start X-correlation... INFO @ Mon, 03 Jun 2019 22:53:46: end of X-cor INFO @ Mon, 03 Jun 2019 22:53:46: #2 finished! INFO @ Mon, 03 Jun 2019 22:53:46: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 22:53:46: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 03 Jun 2019 22:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.20_model.r INFO @ Mon, 03 Jun 2019 22:53:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:53:48: 6000000 INFO @ Mon, 03 Jun 2019 22:53:50: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:53:50: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:53:50: #1 total tags in treatment: 6239798 INFO @ Mon, 03 Jun 2019 22:53:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:53:50: #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 22:53:50: #1 tags after filtering in treatment: 6239798 INFO @ Mon, 03 Jun 2019 22:53:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:53:50: #1 finished! INFO @ Mon, 03 Jun 2019 22:53:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:53:52: #2 number of paired peaks: 8512 INFO @ Mon, 03 Jun 2019 22:53:52: start model_add_line... INFO @ Mon, 03 Jun 2019 22:53:52: start X-correlation... INFO @ Mon, 03 Jun 2019 22:53:52: end of X-cor INFO @ Mon, 03 Jun 2019 22:53:52: #2 finished! INFO @ Mon, 03 Jun 2019 22:53:52: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 22:53:52: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 03 Jun 2019 22:53:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.10_model.r INFO @ Mon, 03 Jun 2019 22:53:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:53:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:54:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:54:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:54:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.05_summits.bed INFO @ Mon, 03 Jun 2019 22:54:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8093 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:54:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:54:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:54:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.20_summits.bed INFO @ Mon, 03 Jun 2019 22:54:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5624 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:54:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:54:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:54:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343125/SRX5343125.10_summits.bed INFO @ Mon, 03 Jun 2019 22:54:22: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7193 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。