Job ID = 2003569 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,130,848 reads read : 5,130,848 reads written : 5,130,848 spots read : 3,066,932 reads read : 3,066,932 reads written : 3,066,932 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:12 8197780 reads; of these: 8197780 (100.00%) were unpaired; of these: 1546887 (18.87%) aligned 0 times 5154428 (62.88%) aligned exactly 1 time 1496465 (18.25%) aligned >1 times 81.13% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 1852286 / 6650893 = 0.2785 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 @ Fri, 05 Jul 2019 12:38:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:38:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:38:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:38:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:16: 1000000 INFO @ Fri, 05 Jul 2019 12:38:16: 1000000 INFO @ Fri, 05 Jul 2019 12:38:17: 1000000 INFO @ Fri, 05 Jul 2019 12:38:25: 2000000 INFO @ Fri, 05 Jul 2019 12:38:27: 2000000 INFO @ Fri, 05 Jul 2019 12:38:28: 2000000 INFO @ Fri, 05 Jul 2019 12:38:34: 3000000 INFO @ Fri, 05 Jul 2019 12:38:38: 3000000 INFO @ Fri, 05 Jul 2019 12:38:38: 3000000 INFO @ Fri, 05 Jul 2019 12:38:44: 4000000 INFO @ Fri, 05 Jul 2019 12:38:49: 4000000 INFO @ Fri, 05 Jul 2019 12:38:49: 4000000 INFO @ Fri, 05 Jul 2019 12:38:51: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:38:51: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:38:51: #1 total tags in treatment: 4798607 INFO @ Fri, 05 Jul 2019 12:38:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:38:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:38:52: #1 tags after filtering in treatment: 4798316 INFO @ Fri, 05 Jul 2019 12:38:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:38:52: #1 finished! INFO @ Fri, 05 Jul 2019 12:38:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:38:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:38:55: #2 number of paired peaks: 40293 INFO @ Fri, 05 Jul 2019 12:38:55: start model_add_line... INFO @ Fri, 05 Jul 2019 12:38:55: start X-correlation... INFO @ Fri, 05 Jul 2019 12:38:55: end of X-cor INFO @ Fri, 05 Jul 2019 12:38:55: #2 finished! INFO @ Fri, 05 Jul 2019 12:38:55: #2 predicted fragment length is 238 bps INFO @ Fri, 05 Jul 2019 12:38:55: #2 alternative fragment length(s) may be 238 bps INFO @ Fri, 05 Jul 2019 12:38:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.10_model.r INFO @ Fri, 05 Jul 2019 12:38:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:38:58: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:38:58: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:38:58: #1 total tags in treatment: 4798607 INFO @ Fri, 05 Jul 2019 12:38:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:38:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:38:58: #1 tags after filtering in treatment: 4798316 INFO @ Fri, 05 Jul 2019 12:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:38:58: #1 finished! INFO @ Fri, 05 Jul 2019 12:38:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:38:58: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:38:58: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:38:58: #1 total tags in treatment: 4798607 INFO @ Fri, 05 Jul 2019 12:38:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:38:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:38:58: #1 tags after filtering in treatment: 4798316 INFO @ Fri, 05 Jul 2019 12:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:38:58: #1 finished! INFO @ Fri, 05 Jul 2019 12:38:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:39:01: #2 number of paired peaks: 40293 INFO @ Fri, 05 Jul 2019 12:39:01: start model_add_line... INFO @ Fri, 05 Jul 2019 12:39:01: start X-correlation... INFO @ Fri, 05 Jul 2019 12:39:01: end of X-cor INFO @ Fri, 05 Jul 2019 12:39:01: #2 finished! INFO @ Fri, 05 Jul 2019 12:39:01: #2 predicted fragment length is 238 bps INFO @ Fri, 05 Jul 2019 12:39:01: #2 alternative fragment length(s) may be 238 bps INFO @ Fri, 05 Jul 2019 12:39:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.20_model.r INFO @ Fri, 05 Jul 2019 12:39:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:39:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:39:01: #2 number of paired peaks: 40293 INFO @ Fri, 05 Jul 2019 12:39:01: start model_add_line... INFO @ Fri, 05 Jul 2019 12:39:01: start X-correlation... INFO @ Fri, 05 Jul 2019 12:39:01: end of X-cor INFO @ Fri, 05 Jul 2019 12:39:01: #2 finished! INFO @ Fri, 05 Jul 2019 12:39:01: #2 predicted fragment length is 238 bps INFO @ Fri, 05 Jul 2019 12:39:01: #2 alternative fragment length(s) may be 238 bps INFO @ Fri, 05 Jul 2019 12:39:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.05_model.r INFO @ Fri, 05 Jul 2019 12:39:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:39:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:39:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:39:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:39:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:39:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:39:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:39:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.10_summits.bed INFO @ Fri, 05 Jul 2019 12:39:22: Done! pass1 - making usageList (57 chroms): 6 millis pass2 - checking and writing primary data (8275 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:39:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:39:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:39:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.20_summits.bed INFO @ Fri, 05 Jul 2019 12:39:27: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (2536 records, 4 fields): 15 millis INFO @ Fri, 05 Jul 2019 12:39:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.05_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:39:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:39:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204150/SRX204150.05_summits.bed INFO @ Fri, 05 Jul 2019 12:39:29: Done! pass1 - making usageList (94 chroms): 7 millis pass2 - checking and writing primary data (15673 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。