Job ID = 4303088 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 20,084,492 reads read : 40,168,984 reads written : 40,168,984 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1151100.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: 00:50:38 20084492 reads; of these: 20084492 (100.00%) were paired; of these: 1980993 (9.86%) aligned concordantly 0 times 13152028 (65.48%) aligned concordantly exactly 1 time 4951471 (24.65%) aligned concordantly >1 times ---- 1980993 pairs aligned concordantly 0 times; of these: 12173 (0.61%) aligned discordantly 1 time ---- 1968820 pairs aligned 0 times concordantly or discordantly; of these: 3937640 mates make up the pairs; of these: 3364598 (85.45%) aligned 0 times 403211 (10.24%) aligned exactly 1 time 169831 (4.31%) aligned >1 times 91.62% overall alignment rate Time searching: 00:50:39 Overall time: 00:50:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4607893 / 18100885 = 0.2546 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 01:45:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 12 Dec 2019 01:45:24: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:45:24: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:45:34: 1000000 INFO @ Thu, 12 Dec 2019 01:45:45: 2000000 INFO @ Thu, 12 Dec 2019 01:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 12 Dec 2019 01:45:54: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:45:54: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:45:55: 3000000 INFO @ Thu, 12 Dec 2019 01:46:03: 1000000 INFO @ Thu, 12 Dec 2019 01:46:06: 4000000 INFO @ Thu, 12 Dec 2019 01:46:12: 2000000 INFO @ Thu, 12 Dec 2019 01:46:17: 5000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 01:46:22: 3000000 INFO @ Thu, 12 Dec 2019 01:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 12 Dec 2019 01:46:24: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:46:24: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:46:27: 6000000 INFO @ Thu, 12 Dec 2019 01:46:31: 4000000 INFO @ Thu, 12 Dec 2019 01:46:33: 1000000 INFO @ Thu, 12 Dec 2019 01:46:38: 7000000 INFO @ Thu, 12 Dec 2019 01:46:40: 5000000 INFO @ Thu, 12 Dec 2019 01:46:43: 2000000 INFO @ Thu, 12 Dec 2019 01:46:49: 8000000 INFO @ Thu, 12 Dec 2019 01:46:49: 6000000 INFO @ Thu, 12 Dec 2019 01:46:52: 3000000 INFO @ Thu, 12 Dec 2019 01:46:58: 7000000 INFO @ Thu, 12 Dec 2019 01:47:00: 9000000 INFO @ Thu, 12 Dec 2019 01:47:02: 4000000 INFO @ Thu, 12 Dec 2019 01:47:07: 8000000 INFO @ Thu, 12 Dec 2019 01:47:11: 10000000 INFO @ Thu, 12 Dec 2019 01:47:12: 5000000 INFO @ Thu, 12 Dec 2019 01:47:16: 9000000 INFO @ Thu, 12 Dec 2019 01:47:21: 6000000 INFO @ Thu, 12 Dec 2019 01:47:22: 11000000 INFO @ Thu, 12 Dec 2019 01:47:25: 10000000 INFO @ Thu, 12 Dec 2019 01:47:31: 7000000 INFO @ Thu, 12 Dec 2019 01:47:34: 12000000 INFO @ Thu, 12 Dec 2019 01:47:37: 11000000 INFO @ Thu, 12 Dec 2019 01:47:41: 8000000 INFO @ Thu, 12 Dec 2019 01:47:45: 13000000 INFO @ Thu, 12 Dec 2019 01:47:47: 12000000 INFO @ Thu, 12 Dec 2019 01:47:50: 9000000 INFO @ Thu, 12 Dec 2019 01:47:56: 13000000 INFO @ Thu, 12 Dec 2019 01:47:56: 14000000 INFO @ Thu, 12 Dec 2019 01:47:59: 10000000 INFO @ Thu, 12 Dec 2019 01:48:05: 14000000 INFO @ Thu, 12 Dec 2019 01:48:07: 15000000 INFO @ Thu, 12 Dec 2019 01:48:09: 11000000 INFO @ Thu, 12 Dec 2019 01:48:14: 15000000 INFO @ Thu, 12 Dec 2019 01:48:18: 12000000 INFO @ Thu, 12 Dec 2019 01:48:18: 16000000 INFO @ Thu, 12 Dec 2019 01:48:23: 16000000 INFO @ Thu, 12 Dec 2019 01:48:26: 13000000 INFO @ Thu, 12 Dec 2019 01:48:29: 17000000 INFO @ Thu, 12 Dec 2019 01:48:32: 17000000 INFO @ Thu, 12 Dec 2019 01:48:35: 14000000 INFO @ Thu, 12 Dec 2019 01:48:41: 18000000 INFO @ Thu, 12 Dec 2019 01:48:41: 18000000 INFO @ Thu, 12 Dec 2019 01:48:44: 15000000 INFO @ Thu, 12 Dec 2019 01:48:50: 19000000 INFO @ Thu, 12 Dec 2019 01:48:53: 16000000 INFO @ Thu, 12 Dec 2019 01:48:53: 19000000 INFO @ Thu, 12 Dec 2019 01:48:59: 20000000 INFO @ Thu, 12 Dec 2019 01:49:01: 17000000 INFO @ Thu, 12 Dec 2019 01:49:05: 20000000 INFO @ Thu, 12 Dec 2019 01:49:08: 21000000 INFO @ Thu, 12 Dec 2019 01:49:10: 18000000 INFO @ Thu, 12 Dec 2019 01:49:17: 21000000 INFO @ Thu, 12 Dec 2019 01:49:17: 22000000 INFO @ Thu, 12 Dec 2019 01:49:19: 19000000 INFO @ Thu, 12 Dec 2019 01:49:26: 23000000 INFO @ Thu, 12 Dec 2019 01:49:28: 20000000 INFO @ Thu, 12 Dec 2019 01:49:29: 22000000 INFO @ Thu, 12 Dec 2019 01:49:36: 24000000 INFO @ Thu, 12 Dec 2019 01:49:38: 21000000 INFO @ Thu, 12 Dec 2019 01:49:40: 23000000 INFO @ Thu, 12 Dec 2019 01:49:45: 25000000 INFO @ Thu, 12 Dec 2019 01:49:47: 22000000 INFO @ Thu, 12 Dec 2019 01:49:52: 24000000 INFO @ Thu, 12 Dec 2019 01:49:54: 26000000 INFO @ Thu, 12 Dec 2019 01:49:57: 23000000 INFO @ Thu, 12 Dec 2019 01:50:03: 27000000 INFO @ Thu, 12 Dec 2019 01:50:04: 25000000 INFO @ Thu, 12 Dec 2019 01:50:06: 24000000 INFO @ Thu, 12 Dec 2019 01:50:09: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:50:09: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:50:09: #1 total tags in treatment: 13497723 INFO @ Thu, 12 Dec 2019 01:50:09: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:50:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:50:09: #1 tags after filtering in treatment: 11936852 INFO @ Thu, 12 Dec 2019 01:50:09: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 12 Dec 2019 01:50:09: #1 finished! INFO @ Thu, 12 Dec 2019 01:50:09: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:50:10: #2 number of paired peaks: 3067 INFO @ Thu, 12 Dec 2019 01:50:10: start model_add_line... INFO @ Thu, 12 Dec 2019 01:50:11: start X-correlation... INFO @ Thu, 12 Dec 2019 01:50:11: end of X-cor INFO @ Thu, 12 Dec 2019 01:50:11: #2 finished! INFO @ Thu, 12 Dec 2019 01:50:11: #2 predicted fragment length is 148 bps INFO @ Thu, 12 Dec 2019 01:50:11: #2 alternative fragment length(s) may be 148 bps INFO @ Thu, 12 Dec 2019 01:50:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.10_model.r INFO @ Thu, 12 Dec 2019 01:50:11: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:50:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:50:14: 25000000 INFO @ Thu, 12 Dec 2019 01:50:16: 26000000 INFO @ Thu, 12 Dec 2019 01:50:23: 26000000 INFO @ Thu, 12 Dec 2019 01:50:27: 27000000 INFO @ Thu, 12 Dec 2019 01:50:32: 27000000 INFO @ Thu, 12 Dec 2019 01:50:34: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:50:34: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:50:34: #1 total tags in treatment: 13497723 INFO @ Thu, 12 Dec 2019 01:50:34: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:50:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:50:34: #1 tags after filtering in treatment: 11936852 INFO @ Thu, 12 Dec 2019 01:50:34: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 12 Dec 2019 01:50:34: #1 finished! INFO @ Thu, 12 Dec 2019 01:50:34: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:50:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:50:36: #2 number of paired peaks: 3067 INFO @ Thu, 12 Dec 2019 01:50:36: start model_add_line... INFO @ Thu, 12 Dec 2019 01:50:36: start X-correlation... INFO @ Thu, 12 Dec 2019 01:50:36: end of X-cor INFO @ Thu, 12 Dec 2019 01:50:36: #2 finished! INFO @ Thu, 12 Dec 2019 01:50:36: #2 predicted fragment length is 148 bps INFO @ Thu, 12 Dec 2019 01:50:36: #2 alternative fragment length(s) may be 148 bps INFO @ Thu, 12 Dec 2019 01:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.05_model.r INFO @ Thu, 12 Dec 2019 01:50:36: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:50:37: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:50:37: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:50:37: #1 total tags in treatment: 13497723 INFO @ Thu, 12 Dec 2019 01:50:37: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:50:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:50:37: #1 tags after filtering in treatment: 11936852 INFO @ Thu, 12 Dec 2019 01:50:37: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 12 Dec 2019 01:50:37: #1 finished! INFO @ Thu, 12 Dec 2019 01:50:37: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:50:38: #2 number of paired peaks: 3067 INFO @ Thu, 12 Dec 2019 01:50:38: start model_add_line... INFO @ Thu, 12 Dec 2019 01:50:38: start X-correlation... INFO @ Thu, 12 Dec 2019 01:50:38: end of X-cor INFO @ Thu, 12 Dec 2019 01:50:38: #2 finished! INFO @ Thu, 12 Dec 2019 01:50:38: #2 predicted fragment length is 148 bps INFO @ Thu, 12 Dec 2019 01:50:38: #2 alternative fragment length(s) may be 148 bps INFO @ Thu, 12 Dec 2019 01:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.20_model.r INFO @ Thu, 12 Dec 2019 01:50:39: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:50:49: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.10_summits.bed INFO @ Thu, 12 Dec 2019 01:51:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7514 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:51:14: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:51:16: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.05_summits.bed INFO @ Thu, 12 Dec 2019 01:51:32: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (11617 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:51:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:51:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:51:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456152/SRX456152.20_summits.bed INFO @ Thu, 12 Dec 2019 01:51:34: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4314 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。