Job ID = 1293809 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,240,947 reads read : 24,240,947 reads written : 24,240,947 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: 00:06:08 24240947 reads; of these: 24240947 (100.00%) were unpaired; of these: 1880250 (7.76%) aligned 0 times 19405025 (80.05%) aligned exactly 1 time 2955672 (12.19%) aligned >1 times 92.24% overall alignment rate Time searching: 00:06:08 Overall time: 00:06:08 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 12 files... [bam_rmdupse_core] 13290215 / 22360697 = 0.5944 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 02:51:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.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 02:51:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:51:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:51:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.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 02:51:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:51:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:51:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.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 02:51:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:51:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:51:53: 1000000 INFO @ Mon, 03 Jun 2019 02:51:54: 1000000 INFO @ Mon, 03 Jun 2019 02:51:54: 1000000 INFO @ Mon, 03 Jun 2019 02:52:01: 2000000 INFO @ Mon, 03 Jun 2019 02:52:04: 2000000 INFO @ Mon, 03 Jun 2019 02:52:04: 2000000 INFO @ Mon, 03 Jun 2019 02:52:08: 3000000 INFO @ Mon, 03 Jun 2019 02:52:14: 3000000 INFO @ Mon, 03 Jun 2019 02:52:15: 3000000 INFO @ Mon, 03 Jun 2019 02:52:16: 4000000 INFO @ Mon, 03 Jun 2019 02:52:23: 5000000 INFO @ Mon, 03 Jun 2019 02:52:24: 4000000 INFO @ Mon, 03 Jun 2019 02:52:24: 4000000 INFO @ Mon, 03 Jun 2019 02:52:30: 6000000 INFO @ Mon, 03 Jun 2019 02:52:33: 5000000 INFO @ Mon, 03 Jun 2019 02:52:34: 5000000 INFO @ Mon, 03 Jun 2019 02:52:38: 7000000 INFO @ Mon, 03 Jun 2019 02:52:43: 6000000 INFO @ Mon, 03 Jun 2019 02:52:43: 6000000 INFO @ Mon, 03 Jun 2019 02:52:45: 8000000 INFO @ Mon, 03 Jun 2019 02:52:52: 9000000 INFO @ Mon, 03 Jun 2019 02:52:52: 7000000 INFO @ Mon, 03 Jun 2019 02:52:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:52:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:52:53: #1 total tags in treatment: 9070482 INFO @ Mon, 03 Jun 2019 02:52:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:52:53: #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 02:52:53: #1 tags after filtering in treatment: 9070482 INFO @ Mon, 03 Jun 2019 02:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:52:53: #1 finished! INFO @ Mon, 03 Jun 2019 02:52:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:52:53: 7000000 INFO @ Mon, 03 Jun 2019 02:52:54: #2 number of paired peaks: 2660 INFO @ Mon, 03 Jun 2019 02:52:54: start model_add_line... INFO @ Mon, 03 Jun 2019 02:52:54: start X-correlation... INFO @ Mon, 03 Jun 2019 02:52:54: end of X-cor INFO @ Mon, 03 Jun 2019 02:52:54: #2 finished! INFO @ Mon, 03 Jun 2019 02:52:54: #2 predicted fragment length is 200 bps INFO @ Mon, 03 Jun 2019 02:52:54: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 03 Jun 2019 02:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.05_model.r INFO @ Mon, 03 Jun 2019 02:52:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:53:02: 8000000 INFO @ Mon, 03 Jun 2019 02:53:03: 8000000 INFO @ Mon, 03 Jun 2019 02:53:11: 9000000 INFO @ Mon, 03 Jun 2019 02:53:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:53:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:53:12: #1 total tags in treatment: 9070482 INFO @ Mon, 03 Jun 2019 02:53:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:53:12: #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 02:53:12: #1 tags after filtering in treatment: 9070482 INFO @ Mon, 03 Jun 2019 02:53:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:53:12: #1 finished! INFO @ Mon, 03 Jun 2019 02:53:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:53:12: 9000000 INFO @ Mon, 03 Jun 2019 02:53:13: #2 number of paired peaks: 2660 INFO @ Mon, 03 Jun 2019 02:53:13: start model_add_line... INFO @ Mon, 03 Jun 2019 02:53:13: start X-correlation... INFO @ Mon, 03 Jun 2019 02:53:13: end of X-cor INFO @ Mon, 03 Jun 2019 02:53:13: #2 finished! INFO @ Mon, 03 Jun 2019 02:53:13: #2 predicted fragment length is 200 bps INFO @ Mon, 03 Jun 2019 02:53:13: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 03 Jun 2019 02:53:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.10_model.r INFO @ Mon, 03 Jun 2019 02:53:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:53:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:53:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:53:13: #1 total tags in treatment: 9070482 INFO @ Mon, 03 Jun 2019 02:53:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:53:13: #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 02:53:13: #1 tags after filtering in treatment: 9070482 INFO @ Mon, 03 Jun 2019 02:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:53:13: #1 finished! INFO @ Mon, 03 Jun 2019 02:53:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:53:14: #2 number of paired peaks: 2660 INFO @ Mon, 03 Jun 2019 02:53:14: start model_add_line... INFO @ Mon, 03 Jun 2019 02:53:15: start X-correlation... INFO @ Mon, 03 Jun 2019 02:53:15: end of X-cor INFO @ Mon, 03 Jun 2019 02:53:15: #2 finished! INFO @ Mon, 03 Jun 2019 02:53:15: #2 predicted fragment length is 200 bps INFO @ Mon, 03 Jun 2019 02:53:15: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 03 Jun 2019 02:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.20_model.r INFO @ Mon, 03 Jun 2019 02:53:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:53:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:53:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.05_summits.bed INFO @ Mon, 03 Jun 2019 02:53:39: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5762 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:53:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:53:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:53:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:53:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:53:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.10_summits.bed INFO @ Mon, 03 Jun 2019 02:53:58: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4177 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:54:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:54:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:54:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134709/SRX1134709.20_summits.bed INFO @ Mon, 03 Jun 2019 02:54:00: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2889 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。