Job ID = 2003689 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,511,054 reads read : 26,511,054 reads written : 26,511,054 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1103815.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:10 26511054 reads; of these: 26511054 (100.00%) were unpaired; of these: 1620199 (6.11%) aligned 0 times 17318774 (65.33%) aligned exactly 1 time 7572081 (28.56%) aligned >1 times 93.89% overall alignment rate Time searching: 00:25:12 Overall time: 00:25:12 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] 1109400 / 24890855 = 0.0446 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 13:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.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 13:47:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:47:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.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 13:47:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:47:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.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 13:47:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:47:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:47:10: 1000000 INFO @ Fri, 05 Jul 2019 13:47:10: 1000000 INFO @ Fri, 05 Jul 2019 13:47:10: 1000000 INFO @ Fri, 05 Jul 2019 13:47:18: 2000000 INFO @ Fri, 05 Jul 2019 13:47:20: 2000000 INFO @ Fri, 05 Jul 2019 13:47:20: 2000000 INFO @ Fri, 05 Jul 2019 13:47:26: 3000000 INFO @ Fri, 05 Jul 2019 13:47:29: 3000000 INFO @ Fri, 05 Jul 2019 13:47:29: 3000000 INFO @ Fri, 05 Jul 2019 13:47:34: 4000000 INFO @ Fri, 05 Jul 2019 13:47:38: 4000000 INFO @ Fri, 05 Jul 2019 13:47:38: 4000000 INFO @ Fri, 05 Jul 2019 13:47:42: 5000000 INFO @ Fri, 05 Jul 2019 13:47:47: 5000000 INFO @ Fri, 05 Jul 2019 13:47:47: 5000000 INFO @ Fri, 05 Jul 2019 13:47:50: 6000000 INFO @ Fri, 05 Jul 2019 13:47:56: 6000000 INFO @ Fri, 05 Jul 2019 13:47:56: 6000000 INFO @ Fri, 05 Jul 2019 13:47:58: 7000000 INFO @ Fri, 05 Jul 2019 13:48:05: 7000000 INFO @ Fri, 05 Jul 2019 13:48:05: 7000000 INFO @ Fri, 05 Jul 2019 13:48:06: 8000000 INFO @ Fri, 05 Jul 2019 13:48:14: 8000000 INFO @ Fri, 05 Jul 2019 13:48:14: 8000000 INFO @ Fri, 05 Jul 2019 13:48:15: 9000000 INFO @ Fri, 05 Jul 2019 13:48:22: 9000000 INFO @ Fri, 05 Jul 2019 13:48:23: 10000000 INFO @ Fri, 05 Jul 2019 13:48:23: 9000000 INFO @ Fri, 05 Jul 2019 13:48:31: 11000000 INFO @ Fri, 05 Jul 2019 13:48:31: 10000000 INFO @ Fri, 05 Jul 2019 13:48:32: 10000000 INFO @ Fri, 05 Jul 2019 13:48:39: 12000000 INFO @ Fri, 05 Jul 2019 13:48:40: 11000000 INFO @ Fri, 05 Jul 2019 13:48:42: 11000000 INFO @ Fri, 05 Jul 2019 13:48:47: 13000000 INFO @ Fri, 05 Jul 2019 13:48:48: 12000000 INFO @ Fri, 05 Jul 2019 13:48:51: 12000000 INFO @ Fri, 05 Jul 2019 13:48:55: 14000000 INFO @ Fri, 05 Jul 2019 13:48:57: 13000000 INFO @ Fri, 05 Jul 2019 13:49:00: 13000000 INFO @ Fri, 05 Jul 2019 13:49:03: 15000000 INFO @ Fri, 05 Jul 2019 13:49:06: 14000000 INFO @ Fri, 05 Jul 2019 13:49:08: 14000000 INFO @ Fri, 05 Jul 2019 13:49:11: 16000000 INFO @ Fri, 05 Jul 2019 13:49:15: 15000000 INFO @ Fri, 05 Jul 2019 13:49:17: 15000000 INFO @ Fri, 05 Jul 2019 13:49:18: 17000000 INFO @ Fri, 05 Jul 2019 13:49:24: 16000000 INFO @ Fri, 05 Jul 2019 13:49:26: 16000000 INFO @ Fri, 05 Jul 2019 13:49:26: 18000000 INFO @ Fri, 05 Jul 2019 13:49:32: 17000000 INFO @ Fri, 05 Jul 2019 13:49:33: 17000000 INFO @ Fri, 05 Jul 2019 13:49:34: 19000000 INFO @ Fri, 05 Jul 2019 13:49:41: 18000000 INFO @ Fri, 05 Jul 2019 13:49:42: 18000000 INFO @ Fri, 05 Jul 2019 13:49:42: 20000000 INFO @ Fri, 05 Jul 2019 13:49:50: 19000000 INFO @ Fri, 05 Jul 2019 13:49:50: 19000000 INFO @ Fri, 05 Jul 2019 13:49:51: 21000000 INFO @ Fri, 05 Jul 2019 13:49:59: 22000000 INFO @ Fri, 05 Jul 2019 13:49:59: 20000000 INFO @ Fri, 05 Jul 2019 13:50:00: 20000000 INFO @ Fri, 05 Jul 2019 13:50:07: 23000000 INFO @ Fri, 05 Jul 2019 13:50:08: 21000000 INFO @ Fri, 05 Jul 2019 13:50:09: 21000000 INFO @ Fri, 05 Jul 2019 13:50:13: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:50:13: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:50:13: #1 total tags in treatment: 23781455 INFO @ Fri, 05 Jul 2019 13:50:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:50:13: #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 13:50:14: #1 tags after filtering in treatment: 23781348 INFO @ Fri, 05 Jul 2019 13:50:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:50:14: #1 finished! INFO @ Fri, 05 Jul 2019 13:50:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:50:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:50:17: #2 number of paired peaks: 7233 INFO @ Fri, 05 Jul 2019 13:50:17: start model_add_line... INFO @ Fri, 05 Jul 2019 13:50:17: 22000000 INFO @ Fri, 05 Jul 2019 13:50:17: start X-correlation... INFO @ Fri, 05 Jul 2019 13:50:17: end of X-cor INFO @ Fri, 05 Jul 2019 13:50:17: #2 finished! INFO @ Fri, 05 Jul 2019 13:50:17: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 13:50:17: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 05 Jul 2019 13:50:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.20_model.r INFO @ Fri, 05 Jul 2019 13:50:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:50:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:50:18: 22000000 INFO @ Fri, 05 Jul 2019 13:50:26: 23000000 INFO @ Fri, 05 Jul 2019 13:50:27: 23000000 INFO @ Fri, 05 Jul 2019 13:50:33: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:50:33: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:50:33: #1 total tags in treatment: 23781455 INFO @ Fri, 05 Jul 2019 13:50:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:50:33: #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 13:50:33: #1 tags after filtering in treatment: 23781348 INFO @ Fri, 05 Jul 2019 13:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:50:33: #1 finished! INFO @ Fri, 05 Jul 2019 13:50:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:50:34: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:50:34: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:50:34: #1 total tags in treatment: 23781455 INFO @ Fri, 05 Jul 2019 13:50:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:50:34: #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 13:50:35: #1 tags after filtering in treatment: 23781348 INFO @ Fri, 05 Jul 2019 13:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:50:35: #1 finished! INFO @ Fri, 05 Jul 2019 13:50:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:50:36: #2 number of paired peaks: 7233 INFO @ Fri, 05 Jul 2019 13:50:36: start model_add_line... INFO @ Fri, 05 Jul 2019 13:50:37: start X-correlation... INFO @ Fri, 05 Jul 2019 13:50:37: end of X-cor INFO @ Fri, 05 Jul 2019 13:50:37: #2 finished! INFO @ Fri, 05 Jul 2019 13:50:37: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 13:50:37: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 05 Jul 2019 13:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.10_model.r INFO @ Fri, 05 Jul 2019 13:50:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:50:38: #2 number of paired peaks: 7233 INFO @ Fri, 05 Jul 2019 13:50:38: start model_add_line... INFO @ Fri, 05 Jul 2019 13:50:38: start X-correlation... INFO @ Fri, 05 Jul 2019 13:50:38: end of X-cor INFO @ Fri, 05 Jul 2019 13:50:38: #2 finished! INFO @ Fri, 05 Jul 2019 13:50:38: #2 predicted fragment length is 111 bps INFO @ Fri, 05 Jul 2019 13:50:38: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 05 Jul 2019 13:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.05_model.r INFO @ Fri, 05 Jul 2019 13:50:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:51:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:51:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:51:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:52:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:52:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:52:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.20_summits.bed INFO @ Fri, 05 Jul 2019 13:52:10: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (562 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:52:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:52:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:52:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.10_summits.bed INFO @ Fri, 05 Jul 2019 13:52:29: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (1613 records, 4 fields): 8 millis INFO @ Fri, 05 Jul 2019 13:52:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:52:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:52:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423106/SRX423106.05_summits.bed INFO @ Fri, 05 Jul 2019 13:52:29: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (3300 records, 4 fields): 11 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。