Job ID = 1292342 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,418,283 reads read : 10,418,283 reads written : 10,418,283 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: 00:02:09 10418283 reads; of these: 10418283 (100.00%) were unpaired; of these: 623475 (5.98%) aligned 0 times 8165746 (78.38%) aligned exactly 1 time 1629062 (15.64%) aligned >1 times 94.02% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1880022 / 9794808 = 0.1919 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 @ Sun, 02 Jun 2019 18:01:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 18:01:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 18:01:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 18:01:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:40: 1000000 INFO @ Sun, 02 Jun 2019 18:01:40: 1000000 INFO @ Sun, 02 Jun 2019 18:01:41: 1000000 INFO @ Sun, 02 Jun 2019 18:01:47: 2000000 INFO @ Sun, 02 Jun 2019 18:01:47: 2000000 INFO @ Sun, 02 Jun 2019 18:01:49: 2000000 INFO @ Sun, 02 Jun 2019 18:01:54: 3000000 INFO @ Sun, 02 Jun 2019 18:01:54: 3000000 INFO @ Sun, 02 Jun 2019 18:01:57: 3000000 INFO @ Sun, 02 Jun 2019 18:02:01: 4000000 INFO @ Sun, 02 Jun 2019 18:02:01: 4000000 INFO @ Sun, 02 Jun 2019 18:02:04: 4000000 INFO @ Sun, 02 Jun 2019 18:02:08: 5000000 INFO @ Sun, 02 Jun 2019 18:02:09: 5000000 INFO @ Sun, 02 Jun 2019 18:02:12: 5000000 INFO @ Sun, 02 Jun 2019 18:02:15: 6000000 INFO @ Sun, 02 Jun 2019 18:02:16: 6000000 INFO @ Sun, 02 Jun 2019 18:02:20: 6000000 INFO @ Sun, 02 Jun 2019 18:02:23: 7000000 INFO @ Sun, 02 Jun 2019 18:02:23: 7000000 INFO @ Sun, 02 Jun 2019 18:02:28: 7000000 INFO @ Sun, 02 Jun 2019 18:02:29: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:02:29: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:02:29: #1 total tags in treatment: 7914786 INFO @ Sun, 02 Jun 2019 18:02:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:02:29: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:02:29: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:02:29: #1 total tags in treatment: 7914786 INFO @ Sun, 02 Jun 2019 18:02:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:02:29: #1 tags after filtering in treatment: 7914786 INFO @ Sun, 02 Jun 2019 18:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:02:29: #1 finished! INFO @ Sun, 02 Jun 2019 18:02:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:02:29: #1 tags after filtering in treatment: 7914786 INFO @ Sun, 02 Jun 2019 18:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:02:29: #1 finished! INFO @ Sun, 02 Jun 2019 18:02:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:02:30: #2 number of paired peaks: 1271 INFO @ Sun, 02 Jun 2019 18:02:30: start model_add_line... INFO @ Sun, 02 Jun 2019 18:02:30: start X-correlation... INFO @ Sun, 02 Jun 2019 18:02:30: end of X-cor INFO @ Sun, 02 Jun 2019 18:02:30: #2 finished! INFO @ Sun, 02 Jun 2019 18:02:30: #2 predicted fragment length is 145 bps INFO @ Sun, 02 Jun 2019 18:02:30: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 02 Jun 2019 18:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.20_model.r INFO @ Sun, 02 Jun 2019 18:02:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:02:30: #2 number of paired peaks: 1271 INFO @ Sun, 02 Jun 2019 18:02:30: start model_add_line... INFO @ Sun, 02 Jun 2019 18:02:30: start X-correlation... INFO @ Sun, 02 Jun 2019 18:02:30: end of X-cor INFO @ Sun, 02 Jun 2019 18:02:30: #2 finished! INFO @ Sun, 02 Jun 2019 18:02:30: #2 predicted fragment length is 145 bps INFO @ Sun, 02 Jun 2019 18:02:30: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 02 Jun 2019 18:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.05_model.r INFO @ Sun, 02 Jun 2019 18:02:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:02:35: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:02:35: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:02:35: #1 total tags in treatment: 7914786 INFO @ Sun, 02 Jun 2019 18:02:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:02:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:02:35: #1 tags after filtering in treatment: 7914786 INFO @ Sun, 02 Jun 2019 18:02:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:02:35: #1 finished! INFO @ Sun, 02 Jun 2019 18:02:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:02:36: #2 number of paired peaks: 1271 INFO @ Sun, 02 Jun 2019 18:02:36: start model_add_line... INFO @ Sun, 02 Jun 2019 18:02:36: start X-correlation... INFO @ Sun, 02 Jun 2019 18:02:36: end of X-cor INFO @ Sun, 02 Jun 2019 18:02:36: #2 finished! INFO @ Sun, 02 Jun 2019 18:02:36: #2 predicted fragment length is 145 bps INFO @ Sun, 02 Jun 2019 18:02:36: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 02 Jun 2019 18:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.10_model.r INFO @ Sun, 02 Jun 2019 18:02:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:02:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:02:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:03:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:03:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:03:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:03:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.05_summits.bed INFO @ Sun, 02 Jun 2019 18:03:06: Done! INFO @ Sun, 02 Jun 2019 18:03:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:03:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:03:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.20_summits.bed pass1 - making usageList (7 chroms): 2 millis INFO @ Sun, 02 Jun 2019 18:03:06: Done! pass2 - checking and writing primary data (5340 records, 4 fields): 8 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2663 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX335102/SRX335102.10_summits.bed INFO @ Sun, 02 Jun 2019 18:03:12: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3946 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。