Job ID = 1294159 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,836,328 reads read : 22,836,328 reads written : 22,836,328 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: 00:06:32 22836328 reads; of these: 22836328 (100.00%) were unpaired; of these: 837040 (3.67%) aligned 0 times 18411394 (80.62%) aligned exactly 1 time 3587894 (15.71%) aligned >1 times 96.33% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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] 3953867 / 21999288 = 0.1797 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 05:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.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 05:24:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:24:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.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 05:24:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:24:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.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 05:24:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:24:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:24:26: 1000000 INFO @ Mon, 03 Jun 2019 05:24:26: 1000000 INFO @ Mon, 03 Jun 2019 05:24:27: 1000000 INFO @ Mon, 03 Jun 2019 05:24:35: 2000000 INFO @ Mon, 03 Jun 2019 05:24:36: 2000000 INFO @ Mon, 03 Jun 2019 05:24:38: 2000000 INFO @ Mon, 03 Jun 2019 05:24:44: 3000000 INFO @ Mon, 03 Jun 2019 05:24:45: 3000000 INFO @ Mon, 03 Jun 2019 05:24:48: 3000000 INFO @ Mon, 03 Jun 2019 05:24:54: 4000000 INFO @ Mon, 03 Jun 2019 05:24:55: 4000000 INFO @ Mon, 03 Jun 2019 05:24:59: 4000000 INFO @ Mon, 03 Jun 2019 05:25:03: 5000000 INFO @ Mon, 03 Jun 2019 05:25:04: 5000000 INFO @ Mon, 03 Jun 2019 05:25:09: 5000000 INFO @ Mon, 03 Jun 2019 05:25:12: 6000000 INFO @ Mon, 03 Jun 2019 05:25:14: 6000000 INFO @ Mon, 03 Jun 2019 05:25:19: 6000000 INFO @ Mon, 03 Jun 2019 05:25:21: 7000000 INFO @ Mon, 03 Jun 2019 05:25:23: 7000000 INFO @ Mon, 03 Jun 2019 05:25:28: 7000000 INFO @ Mon, 03 Jun 2019 05:25:30: 8000000 INFO @ Mon, 03 Jun 2019 05:25:32: 8000000 INFO @ Mon, 03 Jun 2019 05:25:38: 8000000 INFO @ Mon, 03 Jun 2019 05:25:40: 9000000 INFO @ Mon, 03 Jun 2019 05:25:41: 9000000 INFO @ Mon, 03 Jun 2019 05:25:48: 9000000 INFO @ Mon, 03 Jun 2019 05:25:49: 10000000 INFO @ Mon, 03 Jun 2019 05:25:50: 10000000 INFO @ Mon, 03 Jun 2019 05:25:57: 10000000 INFO @ Mon, 03 Jun 2019 05:25:58: 11000000 INFO @ Mon, 03 Jun 2019 05:26:00: 11000000 INFO @ Mon, 03 Jun 2019 05:26:07: 12000000 INFO @ Mon, 03 Jun 2019 05:26:07: 11000000 INFO @ Mon, 03 Jun 2019 05:26:09: 12000000 INFO @ Mon, 03 Jun 2019 05:26:17: 13000000 INFO @ Mon, 03 Jun 2019 05:26:17: 12000000 INFO @ Mon, 03 Jun 2019 05:26:18: 13000000 INFO @ Mon, 03 Jun 2019 05:26:26: 14000000 INFO @ Mon, 03 Jun 2019 05:26:27: 13000000 INFO @ Mon, 03 Jun 2019 05:26:27: 14000000 INFO @ Mon, 03 Jun 2019 05:26:35: 15000000 INFO @ Mon, 03 Jun 2019 05:26:37: 15000000 INFO @ Mon, 03 Jun 2019 05:26:37: 14000000 INFO @ Mon, 03 Jun 2019 05:26:44: 16000000 INFO @ Mon, 03 Jun 2019 05:26:46: 16000000 INFO @ Mon, 03 Jun 2019 05:26:46: 15000000 INFO @ Mon, 03 Jun 2019 05:26:54: 17000000 INFO @ Mon, 03 Jun 2019 05:26:55: 17000000 INFO @ Mon, 03 Jun 2019 05:26:56: 16000000 INFO @ Mon, 03 Jun 2019 05:27:04: 18000000 INFO @ Mon, 03 Jun 2019 05:27:04: 18000000 INFO @ Mon, 03 Jun 2019 05:27:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:27:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:27:04: #1 total tags in treatment: 18045421 INFO @ Mon, 03 Jun 2019 05:27:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:27:04: #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 05:27:04: #1 tags after filtering in treatment: 18045421 INFO @ Mon, 03 Jun 2019 05:27:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:27:04: #1 finished! INFO @ Mon, 03 Jun 2019 05:27:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:27:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:27:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:27:05: #1 total tags in treatment: 18045421 INFO @ Mon, 03 Jun 2019 05:27:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:27:05: #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 05:27:05: #1 tags after filtering in treatment: 18045421 INFO @ Mon, 03 Jun 2019 05:27:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:27:05: #1 finished! INFO @ Mon, 03 Jun 2019 05:27:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:27:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:27:06: 17000000 INFO @ Mon, 03 Jun 2019 05:27:06: #2 number of paired peaks: 2937 INFO @ Mon, 03 Jun 2019 05:27:06: start model_add_line... INFO @ Mon, 03 Jun 2019 05:27:07: start X-correlation... INFO @ Mon, 03 Jun 2019 05:27:07: end of X-cor INFO @ Mon, 03 Jun 2019 05:27:07: #2 finished! INFO @ Mon, 03 Jun 2019 05:27:07: #2 predicted fragment length is 127 bps INFO @ Mon, 03 Jun 2019 05:27:07: #2 alternative fragment length(s) may be 3,116,127 bps INFO @ Mon, 03 Jun 2019 05:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.05_model.r INFO @ Mon, 03 Jun 2019 05:27:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:27:07: #2 number of paired peaks: 2937 INFO @ Mon, 03 Jun 2019 05:27:07: start model_add_line... INFO @ Mon, 03 Jun 2019 05:27:07: start X-correlation... INFO @ Mon, 03 Jun 2019 05:27:07: end of X-cor INFO @ Mon, 03 Jun 2019 05:27:07: #2 finished! INFO @ Mon, 03 Jun 2019 05:27:07: #2 predicted fragment length is 127 bps INFO @ Mon, 03 Jun 2019 05:27:07: #2 alternative fragment length(s) may be 3,116,127 bps INFO @ Mon, 03 Jun 2019 05:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.10_model.r INFO @ Mon, 03 Jun 2019 05:27:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:27:15: 18000000 INFO @ Mon, 03 Jun 2019 05:27:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:27:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:27:16: #1 total tags in treatment: 18045421 INFO @ Mon, 03 Jun 2019 05:27:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:27:16: #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 05:27:16: #1 tags after filtering in treatment: 18045421 INFO @ Mon, 03 Jun 2019 05:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:27:16: #1 finished! INFO @ Mon, 03 Jun 2019 05:27:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:27:18: #2 number of paired peaks: 2937 INFO @ Mon, 03 Jun 2019 05:27:18: start model_add_line... INFO @ Mon, 03 Jun 2019 05:27:19: start X-correlation... INFO @ Mon, 03 Jun 2019 05:27:19: end of X-cor INFO @ Mon, 03 Jun 2019 05:27:19: #2 finished! INFO @ Mon, 03 Jun 2019 05:27:19: #2 predicted fragment length is 127 bps INFO @ Mon, 03 Jun 2019 05:27:19: #2 alternative fragment length(s) may be 3,116,127 bps INFO @ Mon, 03 Jun 2019 05:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.20_model.r INFO @ Mon, 03 Jun 2019 05:27:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:27:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:27:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:28:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:28:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.10_summits.bed INFO @ Mon, 03 Jun 2019 05:28:23: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6126 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:28:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:28:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.05_summits.bed INFO @ Mon, 03 Jun 2019 05:28:24: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (12656 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:28:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:28:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:28:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193335/SRX193335.20_summits.bed INFO @ Mon, 03 Jun 2019 05:28:37: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1840 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。