Job ID = 1295058 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,433,944 reads read : 12,433,944 reads written : 12,433,944 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: 00:03:37 12433944 reads; of these: 12433944 (100.00%) were unpaired; of these: 1476080 (11.87%) aligned 0 times 9533155 (76.67%) aligned exactly 1 time 1424709 (11.46%) aligned >1 times 88.13% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 2621443 / 10957864 = 0.2392 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 11:40:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.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 11:40:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:40:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:40:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.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 11:40:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:40:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:40:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.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 11:40:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:40:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:40:14: 1000000 INFO @ Mon, 03 Jun 2019 11:40:17: 1000000 INFO @ Mon, 03 Jun 2019 11:40:17: 1000000 INFO @ Mon, 03 Jun 2019 11:40:23: 2000000 INFO @ Mon, 03 Jun 2019 11:40:27: 2000000 INFO @ Mon, 03 Jun 2019 11:40:28: 2000000 INFO @ Mon, 03 Jun 2019 11:40:31: 3000000 INFO @ Mon, 03 Jun 2019 11:40:37: 3000000 INFO @ Mon, 03 Jun 2019 11:40:38: 3000000 INFO @ Mon, 03 Jun 2019 11:40:39: 4000000 INFO @ Mon, 03 Jun 2019 11:40:47: 4000000 INFO @ Mon, 03 Jun 2019 11:40:47: 5000000 INFO @ Mon, 03 Jun 2019 11:40:49: 4000000 INFO @ Mon, 03 Jun 2019 11:40:55: 6000000 INFO @ Mon, 03 Jun 2019 11:40:57: 5000000 INFO @ Mon, 03 Jun 2019 11:41:00: 5000000 INFO @ Mon, 03 Jun 2019 11:41:04: 7000000 INFO @ Mon, 03 Jun 2019 11:41:09: 6000000 INFO @ Mon, 03 Jun 2019 11:41:12: 6000000 INFO @ Mon, 03 Jun 2019 11:41:12: 8000000 INFO @ Mon, 03 Jun 2019 11:41:15: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:41:15: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:41:15: #1 total tags in treatment: 8336421 INFO @ Mon, 03 Jun 2019 11:41:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:41:15: #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 11:41:15: #1 tags after filtering in treatment: 8336421 INFO @ Mon, 03 Jun 2019 11:41:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:41:15: #1 finished! INFO @ Mon, 03 Jun 2019 11:41:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:41:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:41:16: #2 number of paired peaks: 6823 INFO @ Mon, 03 Jun 2019 11:41:16: start model_add_line... INFO @ Mon, 03 Jun 2019 11:41:16: start X-correlation... INFO @ Mon, 03 Jun 2019 11:41:17: end of X-cor INFO @ Mon, 03 Jun 2019 11:41:17: #2 finished! INFO @ Mon, 03 Jun 2019 11:41:17: #2 predicted fragment length is 303 bps INFO @ Mon, 03 Jun 2019 11:41:17: #2 alternative fragment length(s) may be 303 bps INFO @ Mon, 03 Jun 2019 11:41:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.10_model.r INFO @ Mon, 03 Jun 2019 11:41:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:41:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:41:19: 7000000 INFO @ Mon, 03 Jun 2019 11:41:23: 7000000 INFO @ Mon, 03 Jun 2019 11:41:30: 8000000 INFO @ Mon, 03 Jun 2019 11:41:33: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:41:33: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:41:33: #1 total tags in treatment: 8336421 INFO @ Mon, 03 Jun 2019 11:41:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:41:33: #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 11:41:33: #1 tags after filtering in treatment: 8336421 INFO @ Mon, 03 Jun 2019 11:41:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:41:33: #1 finished! INFO @ Mon, 03 Jun 2019 11:41:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:41:34: 8000000 INFO @ Mon, 03 Jun 2019 11:41:35: #2 number of paired peaks: 6823 INFO @ Mon, 03 Jun 2019 11:41:35: start model_add_line... INFO @ Mon, 03 Jun 2019 11:41:35: start X-correlation... INFO @ Mon, 03 Jun 2019 11:41:35: end of X-cor INFO @ Mon, 03 Jun 2019 11:41:35: #2 finished! INFO @ Mon, 03 Jun 2019 11:41:35: #2 predicted fragment length is 303 bps INFO @ Mon, 03 Jun 2019 11:41:35: #2 alternative fragment length(s) may be 303 bps INFO @ Mon, 03 Jun 2019 11:41:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.05_model.r INFO @ Mon, 03 Jun 2019 11:41:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:41:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:41:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:41:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:41:38: #1 total tags in treatment: 8336421 INFO @ Mon, 03 Jun 2019 11:41:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:41:38: #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 11:41:38: #1 tags after filtering in treatment: 8336421 INFO @ Mon, 03 Jun 2019 11:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:41:38: #1 finished! INFO @ Mon, 03 Jun 2019 11:41:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:41:39: #2 number of paired peaks: 6823 INFO @ Mon, 03 Jun 2019 11:41:39: start model_add_line... INFO @ Mon, 03 Jun 2019 11:41:39: start X-correlation... INFO @ Mon, 03 Jun 2019 11:41:39: end of X-cor INFO @ Mon, 03 Jun 2019 11:41:39: #2 finished! INFO @ Mon, 03 Jun 2019 11:41:39: #2 predicted fragment length is 303 bps INFO @ Mon, 03 Jun 2019 11:41:39: #2 alternative fragment length(s) may be 303 bps INFO @ Mon, 03 Jun 2019 11:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.20_model.r INFO @ Mon, 03 Jun 2019 11:41:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:41:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:42:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:42:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:42:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.10_summits.bed INFO @ Mon, 03 Jun 2019 11:42:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7358 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:42:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:42:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:42:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:42:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:42:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.05_summits.bed INFO @ Mon, 03 Jun 2019 11:42:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8953 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:42:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:42:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:42:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167252/SRX3167252.20_summits.bed INFO @ Mon, 03 Jun 2019 11:42:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5790 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。