Job ID = 2002527 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,532,628 reads read : 27,532,628 reads written : 27,532,628 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR572264.sra.cache’: 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: 00:11:54 27532628 reads; of these: 27532628 (100.00%) were unpaired; of these: 3661869 (13.30%) aligned 0 times 20392785 (74.07%) aligned exactly 1 time 3477974 (12.63%) aligned >1 times 86.70% overall alignment rate Time searching: 00:11:55 Overall time: 00:11:55 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] 6082869 / 23870759 = 0.2548 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 12:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.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 12:01:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:01:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:01:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.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 12:01:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:01:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:01:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.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 12:01:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:01:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:01:52: 1000000 INFO @ Fri, 05 Jul 2019 12:01:53: 1000000 INFO @ Fri, 05 Jul 2019 12:01:55: 1000000 INFO @ Fri, 05 Jul 2019 12:02:00: 2000000 INFO @ Fri, 05 Jul 2019 12:02:02: 2000000 INFO @ Fri, 05 Jul 2019 12:02:04: 2000000 INFO @ Fri, 05 Jul 2019 12:02:09: 3000000 INFO @ Fri, 05 Jul 2019 12:02:11: 3000000 INFO @ Fri, 05 Jul 2019 12:02:13: 3000000 INFO @ Fri, 05 Jul 2019 12:02:17: 4000000 INFO @ Fri, 05 Jul 2019 12:02:21: 4000000 INFO @ Fri, 05 Jul 2019 12:02:22: 4000000 INFO @ Fri, 05 Jul 2019 12:02:26: 5000000 INFO @ Fri, 05 Jul 2019 12:02:30: 5000000 INFO @ Fri, 05 Jul 2019 12:02:31: 5000000 INFO @ Fri, 05 Jul 2019 12:02:35: 6000000 INFO @ Fri, 05 Jul 2019 12:02:40: 6000000 INFO @ Fri, 05 Jul 2019 12:02:40: 6000000 INFO @ Fri, 05 Jul 2019 12:02:44: 7000000 INFO @ Fri, 05 Jul 2019 12:02:49: 7000000 INFO @ Fri, 05 Jul 2019 12:02:50: 7000000 INFO @ Fri, 05 Jul 2019 12:02:53: 8000000 INFO @ Fri, 05 Jul 2019 12:02:59: 8000000 INFO @ Fri, 05 Jul 2019 12:03:00: 8000000 INFO @ Fri, 05 Jul 2019 12:03:03: 9000000 INFO @ Fri, 05 Jul 2019 12:03:09: 9000000 INFO @ Fri, 05 Jul 2019 12:03:10: 9000000 INFO @ Fri, 05 Jul 2019 12:03:12: 10000000 INFO @ Fri, 05 Jul 2019 12:03:19: 10000000 INFO @ Fri, 05 Jul 2019 12:03:19: 10000000 INFO @ Fri, 05 Jul 2019 12:03:21: 11000000 INFO @ Fri, 05 Jul 2019 12:03:28: 11000000 INFO @ Fri, 05 Jul 2019 12:03:29: 11000000 INFO @ Fri, 05 Jul 2019 12:03:30: 12000000 INFO @ Fri, 05 Jul 2019 12:03:38: 12000000 INFO @ Fri, 05 Jul 2019 12:03:38: 12000000 INFO @ Fri, 05 Jul 2019 12:03:40: 13000000 INFO @ Fri, 05 Jul 2019 12:03:47: 13000000 INFO @ Fri, 05 Jul 2019 12:03:47: 13000000 INFO @ Fri, 05 Jul 2019 12:03:50: 14000000 INFO @ Fri, 05 Jul 2019 12:03:57: 14000000 INFO @ Fri, 05 Jul 2019 12:03:58: 14000000 INFO @ Fri, 05 Jul 2019 12:03:59: 15000000 INFO @ Fri, 05 Jul 2019 12:04:07: 15000000 INFO @ Fri, 05 Jul 2019 12:04:07: 15000000 INFO @ Fri, 05 Jul 2019 12:04:08: 16000000 INFO @ Fri, 05 Jul 2019 12:04:16: 16000000 INFO @ Fri, 05 Jul 2019 12:04:17: 16000000 INFO @ Fri, 05 Jul 2019 12:04:18: 17000000 INFO @ Fri, 05 Jul 2019 12:04:26: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:04:26: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:04:26: #1 total tags in treatment: 17787890 INFO @ Fri, 05 Jul 2019 12:04:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:04:26: #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 12:04:26: #1 tags after filtering in treatment: 17787643 INFO @ Fri, 05 Jul 2019 12:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:04:26: #1 finished! INFO @ Fri, 05 Jul 2019 12:04:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:04:26: 17000000 INFO @ Fri, 05 Jul 2019 12:04:27: 17000000 INFO @ Fri, 05 Jul 2019 12:04:30: #2 number of paired peaks: 28648 INFO @ Fri, 05 Jul 2019 12:04:30: start model_add_line... INFO @ Fri, 05 Jul 2019 12:04:30: start X-correlation... INFO @ Fri, 05 Jul 2019 12:04:30: end of X-cor INFO @ Fri, 05 Jul 2019 12:04:30: #2 finished! INFO @ Fri, 05 Jul 2019 12:04:30: #2 predicted fragment length is 258 bps INFO @ Fri, 05 Jul 2019 12:04:30: #2 alternative fragment length(s) may be 258 bps INFO @ Fri, 05 Jul 2019 12:04:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.05_model.r INFO @ Fri, 05 Jul 2019 12:04:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:04:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:04:34: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:04:34: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:04:34: #1 total tags in treatment: 17787890 INFO @ Fri, 05 Jul 2019 12:04:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:04:34: #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 12:04:34: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:04:34: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:04:34: #1 total tags in treatment: 17787890 INFO @ Fri, 05 Jul 2019 12:04:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:04:34: #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 12:04:34: #1 tags after filtering in treatment: 17787643 INFO @ Fri, 05 Jul 2019 12:04:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:04:34: #1 finished! INFO @ Fri, 05 Jul 2019 12:04:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:04:35: #1 tags after filtering in treatment: 17787643 INFO @ Fri, 05 Jul 2019 12:04:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:04:35: #1 finished! INFO @ Fri, 05 Jul 2019 12:04:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:04:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:04:38: #2 number of paired peaks: 28648 INFO @ Fri, 05 Jul 2019 12:04:38: start model_add_line... INFO @ Fri, 05 Jul 2019 12:04:38: start X-correlation... INFO @ Fri, 05 Jul 2019 12:04:38: end of X-cor INFO @ Fri, 05 Jul 2019 12:04:38: #2 finished! INFO @ Fri, 05 Jul 2019 12:04:38: #2 predicted fragment length is 258 bps INFO @ Fri, 05 Jul 2019 12:04:38: #2 alternative fragment length(s) may be 258 bps INFO @ Fri, 05 Jul 2019 12:04:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.20_model.r INFO @ Fri, 05 Jul 2019 12:04:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:04:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:04:39: #2 number of paired peaks: 28648 INFO @ Fri, 05 Jul 2019 12:04:39: start model_add_line... INFO @ Fri, 05 Jul 2019 12:04:39: start X-correlation... INFO @ Fri, 05 Jul 2019 12:04:39: end of X-cor INFO @ Fri, 05 Jul 2019 12:04:39: #2 finished! INFO @ Fri, 05 Jul 2019 12:04:39: #2 predicted fragment length is 258 bps INFO @ Fri, 05 Jul 2019 12:04:39: #2 alternative fragment length(s) may be 258 bps INFO @ Fri, 05 Jul 2019 12:04:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.10_model.r INFO @ Fri, 05 Jul 2019 12:04:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:04:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:05:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:05:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:05:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:06:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:06:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:06:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.05_summits.bed INFO @ Fri, 05 Jul 2019 12:06:15: Done! pass1 - making usageList (144 chroms): 6 millis pass2 - checking and writing primary data (20038 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:06:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:06:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:06:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.20_summits.bed INFO @ Fri, 05 Jul 2019 12:06:20: Done! pass1 - making usageList (99 chroms): 5 millis pass2 - checking and writing primary data (15615 records, 4 fields): 29 millis INFO @ Fri, 05 Jul 2019 12:06:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:06:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:06:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530942/ERX530942.10_summits.bed INFO @ Fri, 05 Jul 2019 12:06:22: Done! pass1 - making usageList (126 chroms): 4 millis pass2 - checking and writing primary data (18089 records, 4 fields): 35 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。