Job ID = 4288951 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,045,351 reads read : 44,090,702 reads written : 22,045,351 reads 0-length : 22,045,351 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:48 22045351 reads; of these: 22045351 (100.00%) were unpaired; of these: 1233111 (5.59%) aligned 0 times 17881300 (81.11%) aligned exactly 1 time 2930940 (13.30%) aligned >1 times 94.41% overall alignment rate Time searching: 00:25:52 Overall time: 00:25:52 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 12 files... [bam_rmdupse_core] 2847939 / 20812240 = 0.1368 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:34:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.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 @ Tue, 10 Dec 2019 13:34:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:34:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:34:45: 1000000 INFO @ Tue, 10 Dec 2019 13:34:59: 2000000 INFO @ Tue, 10 Dec 2019 13:35:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.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 @ Tue, 10 Dec 2019 13:35:00: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:35:00: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:35:13: 3000000 INFO @ Tue, 10 Dec 2019 13:35:15: 1000000 INFO @ Tue, 10 Dec 2019 13:35:27: 4000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:35:28: 2000000 INFO @ Tue, 10 Dec 2019 13:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.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 @ Tue, 10 Dec 2019 13:35:30: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:35:30: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:35:41: 5000000 INFO @ Tue, 10 Dec 2019 13:35:42: 3000000 INFO @ Tue, 10 Dec 2019 13:35:44: 1000000 INFO @ Tue, 10 Dec 2019 13:35:55: 6000000 INFO @ Tue, 10 Dec 2019 13:35:57: 4000000 INFO @ Tue, 10 Dec 2019 13:35:58: 2000000 INFO @ Tue, 10 Dec 2019 13:36:09: 7000000 INFO @ Tue, 10 Dec 2019 13:36:11: 3000000 INFO @ Tue, 10 Dec 2019 13:36:13: 5000000 INFO @ Tue, 10 Dec 2019 13:36:23: 8000000 INFO @ Tue, 10 Dec 2019 13:36:25: 4000000 INFO @ Tue, 10 Dec 2019 13:36:28: 6000000 INFO @ Tue, 10 Dec 2019 13:36:38: 9000000 INFO @ Tue, 10 Dec 2019 13:36:38: 5000000 INFO @ Tue, 10 Dec 2019 13:36:43: 7000000 INFO @ Tue, 10 Dec 2019 13:36:52: 6000000 INFO @ Tue, 10 Dec 2019 13:36:52: 10000000 INFO @ Tue, 10 Dec 2019 13:36:58: 8000000 INFO @ Tue, 10 Dec 2019 13:37:05: 7000000 INFO @ Tue, 10 Dec 2019 13:37:07: 11000000 INFO @ Tue, 10 Dec 2019 13:37:13: 9000000 INFO @ Tue, 10 Dec 2019 13:37:19: 8000000 INFO @ Tue, 10 Dec 2019 13:37:20: 12000000 INFO @ Tue, 10 Dec 2019 13:37:29: 10000000 INFO @ Tue, 10 Dec 2019 13:37:32: 9000000 INFO @ Tue, 10 Dec 2019 13:37:34: 13000000 INFO @ Tue, 10 Dec 2019 13:37:44: 11000000 INFO @ Tue, 10 Dec 2019 13:37:46: 10000000 INFO @ Tue, 10 Dec 2019 13:37:48: 14000000 INFO @ Tue, 10 Dec 2019 13:37:58: 12000000 INFO @ Tue, 10 Dec 2019 13:37:59: 11000000 INFO @ Tue, 10 Dec 2019 13:38:02: 15000000 INFO @ Tue, 10 Dec 2019 13:38:12: 12000000 INFO @ Tue, 10 Dec 2019 13:38:13: 13000000 INFO @ Tue, 10 Dec 2019 13:38:16: 16000000 INFO @ Tue, 10 Dec 2019 13:38:25: 13000000 INFO @ Tue, 10 Dec 2019 13:38:28: 14000000 INFO @ Tue, 10 Dec 2019 13:38:30: 17000000 INFO @ Tue, 10 Dec 2019 13:38:38: 14000000 INFO @ Tue, 10 Dec 2019 13:38:42: 15000000 INFO @ Tue, 10 Dec 2019 13:38:43: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:38:43: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:38:43: #1 total tags in treatment: 17964301 INFO @ Tue, 10 Dec 2019 13:38:43: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:38:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:38:44: #1 tags after filtering in treatment: 17964102 INFO @ Tue, 10 Dec 2019 13:38:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:38:44: #1 finished! INFO @ Tue, 10 Dec 2019 13:38:44: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:38:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:38:48: #2 number of paired peaks: 66253 INFO @ Tue, 10 Dec 2019 13:38:48: start model_add_line... INFO @ Tue, 10 Dec 2019 13:38:49: start X-correlation... INFO @ Tue, 10 Dec 2019 13:38:49: end of X-cor INFO @ Tue, 10 Dec 2019 13:38:49: #2 finished! INFO @ Tue, 10 Dec 2019 13:38:49: #2 predicted fragment length is 217 bps INFO @ Tue, 10 Dec 2019 13:38:49: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 10 Dec 2019 13:38:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.05_model.r INFO @ Tue, 10 Dec 2019 13:38:49: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:38:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:38:50: 15000000 INFO @ Tue, 10 Dec 2019 13:38:56: 16000000 INFO @ Tue, 10 Dec 2019 13:39:02: 16000000 INFO @ Tue, 10 Dec 2019 13:39:10: 17000000 INFO @ Tue, 10 Dec 2019 13:39:15: 17000000 INFO @ Tue, 10 Dec 2019 13:39:24: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:39:24: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:39:24: #1 total tags in treatment: 17964301 INFO @ Tue, 10 Dec 2019 13:39:24: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:39:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:39:24: #1 tags after filtering in treatment: 17964102 INFO @ Tue, 10 Dec 2019 13:39:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:39:24: #1 finished! INFO @ Tue, 10 Dec 2019 13:39:24: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:39:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:39:27: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:39:27: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:39:27: #1 total tags in treatment: 17964301 INFO @ Tue, 10 Dec 2019 13:39:27: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:39:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:39:28: #1 tags after filtering in treatment: 17964102 INFO @ Tue, 10 Dec 2019 13:39:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:39:28: #1 finished! INFO @ Tue, 10 Dec 2019 13:39:28: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:39:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:39:29: #2 number of paired peaks: 66253 INFO @ Tue, 10 Dec 2019 13:39:29: start model_add_line... INFO @ Tue, 10 Dec 2019 13:39:29: start X-correlation... INFO @ Tue, 10 Dec 2019 13:39:29: end of X-cor INFO @ Tue, 10 Dec 2019 13:39:29: #2 finished! INFO @ Tue, 10 Dec 2019 13:39:29: #2 predicted fragment length is 217 bps INFO @ Tue, 10 Dec 2019 13:39:29: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 10 Dec 2019 13:39:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.10_model.r INFO @ Tue, 10 Dec 2019 13:39:29: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:39:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:39:33: #2 number of paired peaks: 66253 INFO @ Tue, 10 Dec 2019 13:39:33: start model_add_line... INFO @ Tue, 10 Dec 2019 13:39:33: start X-correlation... INFO @ Tue, 10 Dec 2019 13:39:33: end of X-cor INFO @ Tue, 10 Dec 2019 13:39:33: #2 finished! INFO @ Tue, 10 Dec 2019 13:39:33: #2 predicted fragment length is 217 bps INFO @ Tue, 10 Dec 2019 13:39:33: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 10 Dec 2019 13:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.20_model.r INFO @ Tue, 10 Dec 2019 13:39:33: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:39:51: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:40:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:40:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:40:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.05_summits.bed INFO @ Tue, 10 Dec 2019 13:40:24: Done! pass1 - making usageList (86 chroms): 7 millis pass2 - checking and writing primary data (19104 records, 4 fields): 98 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:40:30: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:40:39: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:41:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:41:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:41:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.10_summits.bed INFO @ Tue, 10 Dec 2019 13:41:02: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (6931 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:41:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:41:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:41:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460577/SRX5460577.20_summits.bed INFO @ Tue, 10 Dec 2019 13:41:25: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (1381 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。