Job ID = 1294375 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,214,168 reads read : 7,214,168 reads written : 7,214,168 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: 00:04:01 7214168 reads; of these: 7214168 (100.00%) were unpaired; of these: 979031 (13.57%) aligned 0 times 4169016 (57.79%) aligned exactly 1 time 2066121 (28.64%) aligned >1 times 86.43% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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_rmdupse_core] 1289382 / 6235137 = 0.2068 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 07:06:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.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 07:06:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.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 07:06:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:06:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:06:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:06:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:06:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.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 07:06:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:06:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:06:20: 1000000 INFO @ Mon, 03 Jun 2019 07:06:22: 1000000 INFO @ Mon, 03 Jun 2019 07:06:22: 1000000 INFO @ Mon, 03 Jun 2019 07:06:29: 2000000 INFO @ Mon, 03 Jun 2019 07:06:31: 2000000 INFO @ Mon, 03 Jun 2019 07:06:31: 2000000 INFO @ Mon, 03 Jun 2019 07:06:37: 3000000 INFO @ Mon, 03 Jun 2019 07:06:40: 3000000 INFO @ Mon, 03 Jun 2019 07:06:40: 3000000 INFO @ Mon, 03 Jun 2019 07:06:45: 4000000 INFO @ Mon, 03 Jun 2019 07:06:49: 4000000 INFO @ Mon, 03 Jun 2019 07:06:49: 4000000 INFO @ Mon, 03 Jun 2019 07:06:52: #1 tag size is determined as 71 bps INFO @ Mon, 03 Jun 2019 07:06:52: #1 tag size = 71 INFO @ Mon, 03 Jun 2019 07:06:52: #1 total tags in treatment: 4945755 INFO @ Mon, 03 Jun 2019 07:06:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:06:52: #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 07:06:52: #1 tags after filtering in treatment: 4945755 INFO @ Mon, 03 Jun 2019 07:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:06:52: #1 finished! INFO @ Mon, 03 Jun 2019 07:06:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:06:53: #2 number of paired peaks: 2190 INFO @ Mon, 03 Jun 2019 07:06:53: start model_add_line... INFO @ Mon, 03 Jun 2019 07:06:53: start X-correlation... INFO @ Mon, 03 Jun 2019 07:06:53: end of X-cor INFO @ Mon, 03 Jun 2019 07:06:53: #2 finished! INFO @ Mon, 03 Jun 2019 07:06:53: #2 predicted fragment length is 195 bps INFO @ Mon, 03 Jun 2019 07:06:53: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 03 Jun 2019 07:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.20_model.r INFO @ Mon, 03 Jun 2019 07:06:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:06:57: #1 tag size is determined as 71 bps INFO @ Mon, 03 Jun 2019 07:06:57: #1 tag size = 71 INFO @ Mon, 03 Jun 2019 07:06:57: #1 total tags in treatment: 4945755 INFO @ Mon, 03 Jun 2019 07:06:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:06:57: #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 07:06:57: #1 tags after filtering in treatment: 4945755 INFO @ Mon, 03 Jun 2019 07:06:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:06:57: #1 finished! INFO @ Mon, 03 Jun 2019 07:06:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:06:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:06:57: #1 tag size is determined as 71 bps INFO @ Mon, 03 Jun 2019 07:06:57: #1 tag size = 71 INFO @ Mon, 03 Jun 2019 07:06:57: #1 total tags in treatment: 4945755 INFO @ Mon, 03 Jun 2019 07:06:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:06:57: #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 07:06:57: #1 tags after filtering in treatment: 4945755 INFO @ Mon, 03 Jun 2019 07:06:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:06:57: #1 finished! INFO @ Mon, 03 Jun 2019 07:06:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:06:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:06:58: #2 number of paired peaks: 2190 INFO @ Mon, 03 Jun 2019 07:06:58: start model_add_line... INFO @ Mon, 03 Jun 2019 07:06:58: start X-correlation... INFO @ Mon, 03 Jun 2019 07:06:58: end of X-cor INFO @ Mon, 03 Jun 2019 07:06:58: #2 finished! INFO @ Mon, 03 Jun 2019 07:06:58: #2 predicted fragment length is 195 bps INFO @ Mon, 03 Jun 2019 07:06:58: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 03 Jun 2019 07:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.05_model.r INFO @ Mon, 03 Jun 2019 07:06:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:06:58: #2 number of paired peaks: 2190 INFO @ Mon, 03 Jun 2019 07:06:58: start model_add_line... INFO @ Mon, 03 Jun 2019 07:06:58: start X-correlation... INFO @ Mon, 03 Jun 2019 07:06:58: end of X-cor INFO @ Mon, 03 Jun 2019 07:06:58: #2 finished! INFO @ Mon, 03 Jun 2019 07:06:58: #2 predicted fragment length is 195 bps INFO @ Mon, 03 Jun 2019 07:06:58: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 03 Jun 2019 07:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.10_model.r INFO @ Mon, 03 Jun 2019 07:06:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:07:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:07:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:07:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.20_summits.bed INFO @ Mon, 03 Jun 2019 07:07:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1837 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.05_summits.bed INFO @ Mon, 03 Jun 2019 07:07:22: Done! INFO @ Mon, 03 Jun 2019 07:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX273675/SRX273675.10_summits.bed pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3554 records, 4 fields): 7 millis INFO @ Mon, 03 Jun 2019 07:07:22: Done! CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2613 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。