Job ID = 1291781 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,696,870 reads read : 35,393,740 reads written : 17,696,870 reads 0-length : 17,696,870 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: 00:06:42 17696870 reads; of these: 17696870 (100.00%) were unpaired; of these: 2159963 (12.21%) aligned 0 times 13455759 (76.03%) aligned exactly 1 time 2081148 (11.76%) aligned >1 times 87.79% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4064895 / 15536907 = 0.2616 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 16:44:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.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 16:44:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:44:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:44:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.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 16:44:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:44:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:44:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.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 16:44:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:44:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:45:02: 1000000 INFO @ Sun, 02 Jun 2019 16:45:03: 1000000 INFO @ Sun, 02 Jun 2019 16:45:07: 1000000 INFO @ Sun, 02 Jun 2019 16:45:12: 2000000 INFO @ Sun, 02 Jun 2019 16:45:14: 2000000 INFO @ Sun, 02 Jun 2019 16:45:21: 2000000 INFO @ Sun, 02 Jun 2019 16:45:22: 3000000 INFO @ Sun, 02 Jun 2019 16:45:25: 3000000 INFO @ Sun, 02 Jun 2019 16:45:33: 4000000 INFO @ Sun, 02 Jun 2019 16:45:35: 3000000 INFO @ Sun, 02 Jun 2019 16:45:36: 4000000 INFO @ Sun, 02 Jun 2019 16:45:43: 5000000 INFO @ Sun, 02 Jun 2019 16:45:46: 5000000 INFO @ Sun, 02 Jun 2019 16:45:49: 4000000 INFO @ Sun, 02 Jun 2019 16:45:54: 6000000 INFO @ Sun, 02 Jun 2019 16:45:56: 6000000 INFO @ Sun, 02 Jun 2019 16:46:02: 5000000 INFO @ Sun, 02 Jun 2019 16:46:05: 7000000 INFO @ Sun, 02 Jun 2019 16:46:06: 7000000 INFO @ Sun, 02 Jun 2019 16:46:16: 6000000 INFO @ Sun, 02 Jun 2019 16:46:16: 8000000 INFO @ Sun, 02 Jun 2019 16:46:16: 8000000 INFO @ Sun, 02 Jun 2019 16:46:25: 7000000 INFO @ Sun, 02 Jun 2019 16:46:27: 9000000 INFO @ Sun, 02 Jun 2019 16:46:27: 9000000 INFO @ Sun, 02 Jun 2019 16:46:33: 8000000 INFO @ Sun, 02 Jun 2019 16:46:37: 10000000 INFO @ Sun, 02 Jun 2019 16:46:39: 10000000 INFO @ Sun, 02 Jun 2019 16:46:42: 9000000 INFO @ Sun, 02 Jun 2019 16:46:48: 11000000 INFO @ Sun, 02 Jun 2019 16:46:50: 11000000 INFO @ Sun, 02 Jun 2019 16:46:51: 10000000 INFO @ Sun, 02 Jun 2019 16:46:53: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:46:53: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:46:53: #1 total tags in treatment: 11472012 INFO @ Sun, 02 Jun 2019 16:46:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:46:53: #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 16:46:53: #1 tags after filtering in treatment: 11472012 INFO @ Sun, 02 Jun 2019 16:46:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:46:53: #1 finished! INFO @ Sun, 02 Jun 2019 16:46:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:46:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:46:54: #2 number of paired peaks: 3240 INFO @ Sun, 02 Jun 2019 16:46:54: start model_add_line... INFO @ Sun, 02 Jun 2019 16:46:54: start X-correlation... INFO @ Sun, 02 Jun 2019 16:46:54: end of X-cor INFO @ Sun, 02 Jun 2019 16:46:54: #2 finished! INFO @ Sun, 02 Jun 2019 16:46:54: #2 predicted fragment length is 229 bps INFO @ Sun, 02 Jun 2019 16:46:54: #2 alternative fragment length(s) may be 4,229 bps INFO @ Sun, 02 Jun 2019 16:46:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.20_model.r INFO @ Sun, 02 Jun 2019 16:46:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:46:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:46:55: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:46:55: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:46:55: #1 total tags in treatment: 11472012 INFO @ Sun, 02 Jun 2019 16:46:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:46:55: #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 16:46:55: #1 tags after filtering in treatment: 11472012 INFO @ Sun, 02 Jun 2019 16:46:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:46:55: #1 finished! INFO @ Sun, 02 Jun 2019 16:46:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:46:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:46:57: #2 number of paired peaks: 3240 INFO @ Sun, 02 Jun 2019 16:46:57: start model_add_line... INFO @ Sun, 02 Jun 2019 16:46:57: start X-correlation... INFO @ Sun, 02 Jun 2019 16:46:57: end of X-cor INFO @ Sun, 02 Jun 2019 16:46:57: #2 finished! INFO @ Sun, 02 Jun 2019 16:46:57: #2 predicted fragment length is 229 bps INFO @ Sun, 02 Jun 2019 16:46:57: #2 alternative fragment length(s) may be 4,229 bps INFO @ Sun, 02 Jun 2019 16:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.10_model.r INFO @ Sun, 02 Jun 2019 16:46:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:46:59: 11000000 INFO @ Sun, 02 Jun 2019 16:47:03: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:47:03: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:47:03: #1 total tags in treatment: 11472012 INFO @ Sun, 02 Jun 2019 16:47:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:03: #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 16:47:03: #1 tags after filtering in treatment: 11472012 INFO @ Sun, 02 Jun 2019 16:47:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:03: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:05: #2 number of paired peaks: 3240 INFO @ Sun, 02 Jun 2019 16:47:05: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:05: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:05: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:05: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:05: #2 predicted fragment length is 229 bps INFO @ Sun, 02 Jun 2019 16:47:05: #2 alternative fragment length(s) may be 4,229 bps INFO @ Sun, 02 Jun 2019 16:47:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.05_model.r INFO @ Sun, 02 Jun 2019 16:47:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.20_summits.bed INFO @ Sun, 02 Jun 2019 16:47:50: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (2969 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:47:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.10_summits.bed INFO @ Sun, 02 Jun 2019 16:47:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3902 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543052/SRX2543052.05_summits.bed INFO @ Sun, 02 Jun 2019 16:48:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4879 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。