Job ID = 1295813 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,898,068 reads read : 15,898,068 reads written : 15,898,068 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: 00:05:10 15898068 reads; of these: 15898068 (100.00%) were unpaired; of these: 936566 (5.89%) aligned 0 times 13121132 (82.53%) aligned exactly 1 time 1840370 (11.58%) aligned >1 times 94.11% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 9408288 / 14961502 = 0.6288 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 15:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.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 15:56:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:56:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.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 15:56:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:56:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.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 15:56:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:56:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:56:46: 1000000 INFO @ Mon, 03 Jun 2019 15:56:46: 1000000 INFO @ Mon, 03 Jun 2019 15:56:47: 1000000 INFO @ Mon, 03 Jun 2019 15:56:54: 2000000 INFO @ Mon, 03 Jun 2019 15:56:55: 2000000 INFO @ Mon, 03 Jun 2019 15:56:56: 2000000 INFO @ Mon, 03 Jun 2019 15:57:02: 3000000 INFO @ Mon, 03 Jun 2019 15:57:02: 3000000 INFO @ Mon, 03 Jun 2019 15:57:05: 3000000 INFO @ Mon, 03 Jun 2019 15:57:10: 4000000 INFO @ Mon, 03 Jun 2019 15:57:10: 4000000 INFO @ Mon, 03 Jun 2019 15:57:13: 4000000 INFO @ Mon, 03 Jun 2019 15:57:17: 5000000 INFO @ Mon, 03 Jun 2019 15:57:18: 5000000 INFO @ Mon, 03 Jun 2019 15:57:21: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:57:21: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:57:21: #1 total tags in treatment: 5553214 INFO @ Mon, 03 Jun 2019 15:57:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:57:21: #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 15:57:21: #1 tags after filtering in treatment: 5553214 INFO @ Mon, 03 Jun 2019 15:57:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:57:21: #1 finished! INFO @ Mon, 03 Jun 2019 15:57:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:57:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:57:22: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:57:22: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:57:22: #1 total tags in treatment: 5553214 INFO @ Mon, 03 Jun 2019 15:57:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:57:22: #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 15:57:22: 5000000 INFO @ Mon, 03 Jun 2019 15:57:22: #1 tags after filtering in treatment: 5553214 INFO @ Mon, 03 Jun 2019 15:57:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:57:22: #1 finished! INFO @ Mon, 03 Jun 2019 15:57:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:57:22: #2 number of paired peaks: 6572 INFO @ Mon, 03 Jun 2019 15:57:22: start model_add_line... INFO @ Mon, 03 Jun 2019 15:57:23: start X-correlation... INFO @ Mon, 03 Jun 2019 15:57:23: end of X-cor INFO @ Mon, 03 Jun 2019 15:57:23: #2 finished! INFO @ Mon, 03 Jun 2019 15:57:23: #2 predicted fragment length is 300 bps INFO @ Mon, 03 Jun 2019 15:57:23: #2 alternative fragment length(s) may be 300 bps INFO @ Mon, 03 Jun 2019 15:57:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.05_model.r INFO @ Mon, 03 Jun 2019 15:57:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:57:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:57:23: #2 number of paired peaks: 6572 INFO @ Mon, 03 Jun 2019 15:57:23: start model_add_line... INFO @ Mon, 03 Jun 2019 15:57:23: start X-correlation... INFO @ Mon, 03 Jun 2019 15:57:23: end of X-cor INFO @ Mon, 03 Jun 2019 15:57:23: #2 finished! INFO @ Mon, 03 Jun 2019 15:57:23: #2 predicted fragment length is 300 bps INFO @ Mon, 03 Jun 2019 15:57:23: #2 alternative fragment length(s) may be 300 bps INFO @ Mon, 03 Jun 2019 15:57:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.10_model.r INFO @ Mon, 03 Jun 2019 15:57:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:57:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:57:27: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:57:27: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:57:27: #1 total tags in treatment: 5553214 INFO @ Mon, 03 Jun 2019 15:57:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:57:27: #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 15:57:27: #1 tags after filtering in treatment: 5553214 INFO @ Mon, 03 Jun 2019 15:57:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:57:27: #1 finished! INFO @ Mon, 03 Jun 2019 15:57:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:57:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:57:28: #2 number of paired peaks: 6572 INFO @ Mon, 03 Jun 2019 15:57:28: start model_add_line... INFO @ Mon, 03 Jun 2019 15:57:28: start X-correlation... INFO @ Mon, 03 Jun 2019 15:57:28: end of X-cor INFO @ Mon, 03 Jun 2019 15:57:28: #2 finished! INFO @ Mon, 03 Jun 2019 15:57:28: #2 predicted fragment length is 300 bps INFO @ Mon, 03 Jun 2019 15:57:28: #2 alternative fragment length(s) may be 300 bps INFO @ Mon, 03 Jun 2019 15:57:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.20_model.r INFO @ Mon, 03 Jun 2019 15:57:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:57:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:57:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:57:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.05_summits.bed INFO @ Mon, 03 Jun 2019 15:57:54: Done! INFO @ Mon, 03 Jun 2019 15:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.10_summits.bed INFO @ Mon, 03 Jun 2019 15:57:54: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8162 records, 4 fields): 13 millis pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6808 records, 4 fields): 14 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:57:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:57:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:57:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563531/SRX4563531.20_summits.bed INFO @ Mon, 03 Jun 2019 15:57:59: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5208 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。