Job ID = 3805909 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,317,381 reads read : 66,634,762 reads written : 33,317,381 reads 0-length : 33,317,381 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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:32:25 33317381 reads; of these: 33317381 (100.00%) were unpaired; of these: 1801457 (5.41%) aligned 0 times 24764586 (74.33%) aligned exactly 1 time 6751338 (20.26%) aligned >1 times 94.59% overall alignment rate Time searching: 00:32:30 Overall time: 00:32:30 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_sort_core] merging from 16 files... [bam_rmdupse_core] 14199095 / 31515924 = 0.4505 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Mon, 04 Nov 2019 02:42:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.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 @ Mon, 04 Nov 2019 02:42:48: #1 read tag files... INFO @ Mon, 04 Nov 2019 02:42:48: #1 read treatment tags... INFO @ Mon, 04 Nov 2019 02:42:58: 1000000 INFO @ Mon, 04 Nov 2019 02:43:06: 2000000 INFO @ Mon, 04 Nov 2019 02:43:15: 3000000 INFO @ Mon, 04 Nov 2019 02:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.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 @ Mon, 04 Nov 2019 02:43:18: #1 read tag files... INFO @ Mon, 04 Nov 2019 02:43:18: #1 read treatment tags... INFO @ Mon, 04 Nov 2019 02:43:23: 4000000 INFO @ Mon, 04 Nov 2019 02:43:28: 1000000 INFO @ Mon, 04 Nov 2019 02:43:32: 5000000 INFO @ Mon, 04 Nov 2019 02:43:36: 2000000 INFO @ Mon, 04 Nov 2019 02:43:41: 6000000 INFO @ Mon, 04 Nov 2019 02:43:45: 3000000 BedGraph に変換中... INFO @ Mon, 04 Nov 2019 02:43:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.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 @ Mon, 04 Nov 2019 02:43:48: #1 read tag files... INFO @ Mon, 04 Nov 2019 02:43:48: #1 read treatment tags... INFO @ Mon, 04 Nov 2019 02:43:49: 7000000 INFO @ Mon, 04 Nov 2019 02:43:54: 4000000 INFO @ Mon, 04 Nov 2019 02:43:58: 1000000 INFO @ Mon, 04 Nov 2019 02:43:58: 8000000 INFO @ Mon, 04 Nov 2019 02:44:03: 5000000 INFO @ Mon, 04 Nov 2019 02:44:06: 2000000 INFO @ Mon, 04 Nov 2019 02:44:07: 9000000 INFO @ Mon, 04 Nov 2019 02:44:12: 6000000 INFO @ Mon, 04 Nov 2019 02:44:15: 3000000 INFO @ Mon, 04 Nov 2019 02:44:16: 10000000 INFO @ Mon, 04 Nov 2019 02:44:21: 7000000 INFO @ Mon, 04 Nov 2019 02:44:24: 4000000 INFO @ Mon, 04 Nov 2019 02:44:25: 11000000 INFO @ Mon, 04 Nov 2019 02:44:29: 8000000 INFO @ Mon, 04 Nov 2019 02:44:33: 5000000 INFO @ Mon, 04 Nov 2019 02:44:34: 12000000 INFO @ Mon, 04 Nov 2019 02:44:38: 9000000 INFO @ Mon, 04 Nov 2019 02:44:42: 6000000 INFO @ Mon, 04 Nov 2019 02:44:44: 13000000 INFO @ Mon, 04 Nov 2019 02:44:47: 10000000 INFO @ Mon, 04 Nov 2019 02:44:51: 7000000 INFO @ Mon, 04 Nov 2019 02:44:53: 14000000 INFO @ Mon, 04 Nov 2019 02:44:57: 11000000 INFO @ Mon, 04 Nov 2019 02:45:00: 8000000 INFO @ Mon, 04 Nov 2019 02:45:02: 15000000 INFO @ Mon, 04 Nov 2019 02:45:06: 12000000 INFO @ Mon, 04 Nov 2019 02:45:09: 9000000 INFO @ Mon, 04 Nov 2019 02:45:11: 16000000 INFO @ Mon, 04 Nov 2019 02:45:15: 13000000 INFO @ Mon, 04 Nov 2019 02:45:18: 10000000 INFO @ Mon, 04 Nov 2019 02:45:20: 17000000 INFO @ Mon, 04 Nov 2019 02:45:23: #1 tag size is determined as 75 bps INFO @ Mon, 04 Nov 2019 02:45:23: #1 tag size = 75 INFO @ Mon, 04 Nov 2019 02:45:23: #1 total tags in treatment: 17316829 INFO @ Mon, 04 Nov 2019 02:45:23: #1 user defined the maximum tags... INFO @ Mon, 04 Nov 2019 02:45:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Nov 2019 02:45:24: #1 tags after filtering in treatment: 17316680 INFO @ Mon, 04 Nov 2019 02:45:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 04 Nov 2019 02:45:24: #1 finished! INFO @ Mon, 04 Nov 2019 02:45:24: #2 Build Peak Model... INFO @ Mon, 04 Nov 2019 02:45:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Nov 2019 02:45:24: 14000000 INFO @ Mon, 04 Nov 2019 02:45:27: #2 number of paired peaks: 29083 INFO @ Mon, 04 Nov 2019 02:45:27: start model_add_line... INFO @ Mon, 04 Nov 2019 02:45:27: start X-correlation... INFO @ Mon, 04 Nov 2019 02:45:27: end of X-cor INFO @ Mon, 04 Nov 2019 02:45:27: #2 finished! INFO @ Mon, 04 Nov 2019 02:45:27: #2 predicted fragment length is 192 bps INFO @ Mon, 04 Nov 2019 02:45:27: #2 alternative fragment length(s) may be 192 bps INFO @ Mon, 04 Nov 2019 02:45:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.05_model.r INFO @ Mon, 04 Nov 2019 02:45:27: #3 Call peaks... INFO @ Mon, 04 Nov 2019 02:45:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 04 Nov 2019 02:45:27: 11000000 INFO @ Mon, 04 Nov 2019 02:45:33: 15000000 INFO @ Mon, 04 Nov 2019 02:45:36: 12000000 INFO @ Mon, 04 Nov 2019 02:45:41: 16000000 INFO @ Mon, 04 Nov 2019 02:45:45: 13000000 INFO @ Mon, 04 Nov 2019 02:45:50: 17000000 INFO @ Mon, 04 Nov 2019 02:45:53: #1 tag size is determined as 75 bps INFO @ Mon, 04 Nov 2019 02:45:53: #1 tag size = 75 INFO @ Mon, 04 Nov 2019 02:45:53: #1 total tags in treatment: 17316829 INFO @ Mon, 04 Nov 2019 02:45:53: #1 user defined the maximum tags... INFO @ Mon, 04 Nov 2019 02:45:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Nov 2019 02:45:54: #1 tags after filtering in treatment: 17316680 INFO @ Mon, 04 Nov 2019 02:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 04 Nov 2019 02:45:54: #1 finished! INFO @ Mon, 04 Nov 2019 02:45:54: #2 Build Peak Model... INFO @ Mon, 04 Nov 2019 02:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Nov 2019 02:45:54: 14000000 INFO @ Mon, 04 Nov 2019 02:45:57: #2 number of paired peaks: 29083 INFO @ Mon, 04 Nov 2019 02:45:57: start model_add_line... INFO @ Mon, 04 Nov 2019 02:45:57: start X-correlation... INFO @ Mon, 04 Nov 2019 02:45:57: end of X-cor INFO @ Mon, 04 Nov 2019 02:45:57: #2 finished! INFO @ Mon, 04 Nov 2019 02:45:57: #2 predicted fragment length is 192 bps INFO @ Mon, 04 Nov 2019 02:45:57: #2 alternative fragment length(s) may be 192 bps INFO @ Mon, 04 Nov 2019 02:45:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.10_model.r INFO @ Mon, 04 Nov 2019 02:45:57: #3 Call peaks... INFO @ Mon, 04 Nov 2019 02:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 04 Nov 2019 02:46:02: 15000000 INFO @ Mon, 04 Nov 2019 02:46:11: 16000000 INFO @ Mon, 04 Nov 2019 02:46:20: 17000000 INFO @ Mon, 04 Nov 2019 02:46:22: #1 tag size is determined as 75 bps INFO @ Mon, 04 Nov 2019 02:46:22: #1 tag size = 75 INFO @ Mon, 04 Nov 2019 02:46:22: #1 total tags in treatment: 17316829 INFO @ Mon, 04 Nov 2019 02:46:22: #1 user defined the maximum tags... INFO @ Mon, 04 Nov 2019 02:46:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 04 Nov 2019 02:46:23: #1 tags after filtering in treatment: 17316680 INFO @ Mon, 04 Nov 2019 02:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 04 Nov 2019 02:46:23: #1 finished! INFO @ Mon, 04 Nov 2019 02:46:23: #2 Build Peak Model... INFO @ Mon, 04 Nov 2019 02:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 04 Nov 2019 02:46:24: #3 Call peaks for each chromosome... INFO @ Mon, 04 Nov 2019 02:46:26: #2 number of paired peaks: 29083 INFO @ Mon, 04 Nov 2019 02:46:26: start model_add_line... INFO @ Mon, 04 Nov 2019 02:46:26: start X-correlation... INFO @ Mon, 04 Nov 2019 02:46:26: end of X-cor INFO @ Mon, 04 Nov 2019 02:46:26: #2 finished! INFO @ Mon, 04 Nov 2019 02:46:26: #2 predicted fragment length is 192 bps INFO @ Mon, 04 Nov 2019 02:46:26: #2 alternative fragment length(s) may be 192 bps INFO @ Mon, 04 Nov 2019 02:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.20_model.r INFO @ Mon, 04 Nov 2019 02:46:26: #3 Call peaks... INFO @ Mon, 04 Nov 2019 02:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 04 Nov 2019 02:46:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.05_peaks.xls INFO @ Mon, 04 Nov 2019 02:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.05_peaks.narrowPeak INFO @ Mon, 04 Nov 2019 02:46:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.05_summits.bed INFO @ Mon, 04 Nov 2019 02:46:52: Done! pass1 - making usageList (96 chroms): 5 millis pass2 - checking and writing primary data (10440 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Mon, 04 Nov 2019 02:46:53: #3 Call peaks for each chromosome... INFO @ Mon, 04 Nov 2019 02:47:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.10_peaks.xls INFO @ Mon, 04 Nov 2019 02:47:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.10_peaks.narrowPeak INFO @ Mon, 04 Nov 2019 02:47:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.10_summits.bed INFO @ Mon, 04 Nov 2019 02:47:21: Done! pass1 - making usageList (57 chroms): 4 millis pass2 - checking and writing primary data (3966 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 04 Nov 2019 02:47:22: #3 Call peaks for each chromosome... INFO @ Mon, 04 Nov 2019 02:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.20_peaks.xls INFO @ Mon, 04 Nov 2019 02:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.20_peaks.narrowPeak INFO @ Mon, 04 Nov 2019 02:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4098375/SRX4098375.20_summits.bed INFO @ Mon, 04 Nov 2019 02:47:50: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (1622 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。