Job ID = 4178266 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,322,666 reads read : 19,322,666 reads written : 19,322,666 rm: cannot remove ‘[DSE]RR*’: 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: 00:03:15 19322666 reads; of these: 19322666 (100.00%) were unpaired; of these: 7280568 (37.68%) aligned 0 times 9643685 (49.91%) aligned exactly 1 time 2398413 (12.41%) aligned >1 times 62.32% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 2245453 / 12042098 = 0.1865 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:32:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.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 @ Thu, 05 Dec 2019 12:32:14: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:32:14: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:32:21: 1000000 INFO @ Thu, 05 Dec 2019 12:32:28: 2000000 INFO @ Thu, 05 Dec 2019 12:32:35: 3000000 INFO @ Thu, 05 Dec 2019 12:32:42: 4000000 INFO @ Thu, 05 Dec 2019 12:32:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.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 @ Thu, 05 Dec 2019 12:32:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:32:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:32:49: 5000000 INFO @ Thu, 05 Dec 2019 12:32:51: 1000000 INFO @ Thu, 05 Dec 2019 12:32:57: 6000000 INFO @ Thu, 05 Dec 2019 12:32:58: 2000000 INFO @ Thu, 05 Dec 2019 12:33:04: 7000000 INFO @ Thu, 05 Dec 2019 12:33:05: 3000000 INFO @ Thu, 05 Dec 2019 12:33:11: 8000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:33:13: 4000000 INFO @ Thu, 05 Dec 2019 12:33:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.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 @ Thu, 05 Dec 2019 12:33:14: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:33:14: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:33:18: 9000000 INFO @ Thu, 05 Dec 2019 12:33:20: 5000000 INFO @ Thu, 05 Dec 2019 12:33:21: 1000000 INFO @ Thu, 05 Dec 2019 12:33:24: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:33:24: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:33:24: #1 total tags in treatment: 9796645 INFO @ Thu, 05 Dec 2019 12:33:24: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:33:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:33:25: #1 tags after filtering in treatment: 9796645 INFO @ Thu, 05 Dec 2019 12:33:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:33:25: #1 finished! INFO @ Thu, 05 Dec 2019 12:33:25: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:33:26: #2 number of paired peaks: 1890 INFO @ Thu, 05 Dec 2019 12:33:26: start model_add_line... INFO @ Thu, 05 Dec 2019 12:33:26: start X-correlation... INFO @ Thu, 05 Dec 2019 12:33:26: end of X-cor INFO @ Thu, 05 Dec 2019 12:33:26: #2 finished! INFO @ Thu, 05 Dec 2019 12:33:26: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Dec 2019 12:33:26: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 05 Dec 2019 12:33:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.05_model.r INFO @ Thu, 05 Dec 2019 12:33:26: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:33:27: 6000000 INFO @ Thu, 05 Dec 2019 12:33:28: 2000000 INFO @ Thu, 05 Dec 2019 12:33:35: 7000000 INFO @ Thu, 05 Dec 2019 12:33:36: 3000000 INFO @ Thu, 05 Dec 2019 12:33:42: 8000000 INFO @ Thu, 05 Dec 2019 12:33:43: 4000000 INFO @ Thu, 05 Dec 2019 12:33:49: 9000000 INFO @ Thu, 05 Dec 2019 12:33:50: 5000000 INFO @ Thu, 05 Dec 2019 12:33:56: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:33:56: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:33:56: #1 total tags in treatment: 9796645 INFO @ Thu, 05 Dec 2019 12:33:56: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:33:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:33:56: #1 tags after filtering in treatment: 9796645 INFO @ Thu, 05 Dec 2019 12:33:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:33:56: #1 finished! INFO @ Thu, 05 Dec 2019 12:33:56: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:33:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:33:57: #2 number of paired peaks: 1890 INFO @ Thu, 05 Dec 2019 12:33:57: start model_add_line... INFO @ Thu, 05 Dec 2019 12:33:57: start X-correlation... INFO @ Thu, 05 Dec 2019 12:33:57: end of X-cor INFO @ Thu, 05 Dec 2019 12:33:57: #2 finished! INFO @ Thu, 05 Dec 2019 12:33:57: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Dec 2019 12:33:57: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 05 Dec 2019 12:33:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.10_model.r INFO @ Thu, 05 Dec 2019 12:33:57: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:33:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:33:57: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:33:57: 6000000 INFO @ Thu, 05 Dec 2019 12:34:05: 7000000 INFO @ Thu, 05 Dec 2019 12:34:12: 8000000 INFO @ Thu, 05 Dec 2019 12:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:34:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.05_summits.bed INFO @ Thu, 05 Dec 2019 12:34:15: Done! INFO @ Thu, 05 Dec 2019 12:34:19: 9000000 pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (8496 records, 4 fields): 222 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:34:26: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:34:26: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:34:26: #1 total tags in treatment: 9796645 INFO @ Thu, 05 Dec 2019 12:34:26: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:34:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:34:26: #1 tags after filtering in treatment: 9796645 INFO @ Thu, 05 Dec 2019 12:34:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:34:26: #1 finished! INFO @ Thu, 05 Dec 2019 12:34:26: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:34:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:34:27: #2 number of paired peaks: 1890 INFO @ Thu, 05 Dec 2019 12:34:27: start model_add_line... INFO @ Thu, 05 Dec 2019 12:34:27: start X-correlation... INFO @ Thu, 05 Dec 2019 12:34:27: end of X-cor INFO @ Thu, 05 Dec 2019 12:34:27: #2 finished! INFO @ Thu, 05 Dec 2019 12:34:27: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Dec 2019 12:34:27: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 05 Dec 2019 12:34:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.20_model.r INFO @ Thu, 05 Dec 2019 12:34:27: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:34:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:34:30: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:34:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:34:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:34:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.10_summits.bed INFO @ Thu, 05 Dec 2019 12:34:44: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (5087 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:34:58: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:35:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:35:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:35:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107865/SRX4107865.20_summits.bed INFO @ Thu, 05 Dec 2019 12:35:13: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2521 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。