Job ID = 1294333 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,676,495 reads read : 25,352,990 reads written : 25,352,990 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:18:14 12676495 reads; of these: 12676495 (100.00%) were paired; of these: 579934 (4.57%) aligned concordantly 0 times 10447841 (82.42%) aligned concordantly exactly 1 time 1648720 (13.01%) aligned concordantly >1 times ---- 579934 pairs aligned concordantly 0 times; of these: 6924 (1.19%) aligned discordantly 1 time ---- 573010 pairs aligned 0 times concordantly or discordantly; of these: 1146020 mates make up the pairs; of these: 947220 (82.65%) aligned 0 times 162045 (14.14%) aligned exactly 1 time 36755 (3.21%) aligned >1 times 96.26% overall alignment rate Time searching: 00:18:14 Overall time: 00:18:14 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 12 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] 6869628 / 12097061 = 0.5679 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 @ Mon, 03 Jun 2019 07:02:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.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 @ Mon, 03 Jun 2019 07:02:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:02:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:02:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.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 @ Mon, 03 Jun 2019 07:02:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:02:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:02:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.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 @ Mon, 03 Jun 2019 07:02:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:02:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:02:45: 1000000 INFO @ Mon, 03 Jun 2019 07:02:46: 1000000 INFO @ Mon, 03 Jun 2019 07:02:47: 1000000 INFO @ Mon, 03 Jun 2019 07:02:52: 2000000 INFO @ Mon, 03 Jun 2019 07:02:54: 2000000 INFO @ Mon, 03 Jun 2019 07:02:56: 2000000 INFO @ Mon, 03 Jun 2019 07:02:59: 3000000 INFO @ Mon, 03 Jun 2019 07:03:02: 3000000 INFO @ Mon, 03 Jun 2019 07:03:05: 3000000 INFO @ Mon, 03 Jun 2019 07:03:06: 4000000 INFO @ Mon, 03 Jun 2019 07:03:09: 4000000 INFO @ Mon, 03 Jun 2019 07:03:12: 5000000 INFO @ Mon, 03 Jun 2019 07:03:14: 4000000 INFO @ Mon, 03 Jun 2019 07:03:17: 5000000 INFO @ Mon, 03 Jun 2019 07:03:19: 6000000 INFO @ Mon, 03 Jun 2019 07:03:23: 5000000 INFO @ Mon, 03 Jun 2019 07:03:24: 6000000 INFO @ Mon, 03 Jun 2019 07:03:25: 7000000 INFO @ Mon, 03 Jun 2019 07:03:31: 6000000 INFO @ Mon, 03 Jun 2019 07:03:31: 7000000 INFO @ Mon, 03 Jun 2019 07:03:32: 8000000 INFO @ Mon, 03 Jun 2019 07:03:39: 8000000 INFO @ Mon, 03 Jun 2019 07:03:39: 9000000 INFO @ Mon, 03 Jun 2019 07:03:40: 7000000 INFO @ Mon, 03 Jun 2019 07:03:46: 10000000 INFO @ Mon, 03 Jun 2019 07:03:47: 9000000 INFO @ Mon, 03 Jun 2019 07:03:49: 8000000 INFO @ Mon, 03 Jun 2019 07:03:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:03:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:03:50: #1 total tags in treatment: 5228151 INFO @ Mon, 03 Jun 2019 07:03:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:03:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 07:03:50: #1 tags after filtering in treatment: 3782449 INFO @ Mon, 03 Jun 2019 07:03:50: #1 Redundant rate of treatment: 0.28 INFO @ Mon, 03 Jun 2019 07:03:50: #1 finished! INFO @ Mon, 03 Jun 2019 07:03:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:03:51: #2 number of paired peaks: 4338 INFO @ Mon, 03 Jun 2019 07:03:51: start model_add_line... INFO @ Mon, 03 Jun 2019 07:03:51: start X-correlation... INFO @ Mon, 03 Jun 2019 07:03:51: end of X-cor INFO @ Mon, 03 Jun 2019 07:03:51: #2 finished! INFO @ Mon, 03 Jun 2019 07:03:51: #2 predicted fragment length is 135 bps INFO @ Mon, 03 Jun 2019 07:03:51: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 03 Jun 2019 07:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.10_model.r INFO @ Mon, 03 Jun 2019 07:03:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:03:55: 10000000 INFO @ Mon, 03 Jun 2019 07:03:57: 9000000 INFO @ Mon, 03 Jun 2019 07:03:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:03:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:03:59: #1 total tags in treatment: 5228151 INFO @ Mon, 03 Jun 2019 07:03:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:03:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 07:04:00: #1 tags after filtering in treatment: 3782449 INFO @ Mon, 03 Jun 2019 07:04:00: #1 Redundant rate of treatment: 0.28 INFO @ Mon, 03 Jun 2019 07:04:00: #1 finished! INFO @ Mon, 03 Jun 2019 07:04:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:04:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:04:00: #2 number of paired peaks: 4338 INFO @ Mon, 03 Jun 2019 07:04:00: start model_add_line... INFO @ Mon, 03 Jun 2019 07:04:00: start X-correlation... INFO @ Mon, 03 Jun 2019 07:04:00: end of X-cor INFO @ Mon, 03 Jun 2019 07:04:00: #2 finished! INFO @ Mon, 03 Jun 2019 07:04:00: #2 predicted fragment length is 135 bps INFO @ Mon, 03 Jun 2019 07:04:00: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 03 Jun 2019 07:04:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.05_model.r INFO @ Mon, 03 Jun 2019 07:04:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:04:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:04:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:04:05: 10000000 INFO @ Mon, 03 Jun 2019 07:04:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.10_summits.bed INFO @ Mon, 03 Jun 2019 07:04:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5076 records, 4 fields): 12 millis INFO @ Mon, 03 Jun 2019 07:04:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:04:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:04:10: #1 total tags in treatment: 5228151 INFO @ Mon, 03 Jun 2019 07:04:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:04:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:04:11: #1 tags after filtering in treatment: 3782449 INFO @ Mon, 03 Jun 2019 07:04:11: #1 Redundant rate of treatment: 0.28 INFO @ Mon, 03 Jun 2019 07:04:11: #1 finished! INFO @ Mon, 03 Jun 2019 07:04:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:04:11: #2 number of paired peaks: 4338 INFO @ Mon, 03 Jun 2019 07:04:11: start model_add_line... INFO @ Mon, 03 Jun 2019 07:04:11: start X-correlation... INFO @ Mon, 03 Jun 2019 07:04:11: end of X-cor INFO @ Mon, 03 Jun 2019 07:04:11: #2 finished! INFO @ Mon, 03 Jun 2019 07:04:11: #2 predicted fragment length is 135 bps INFO @ Mon, 03 Jun 2019 07:04:11: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 03 Jun 2019 07:04:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.20_model.r INFO @ Mon, 03 Jun 2019 07:04:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:04:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:04:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:04:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:04:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:04:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.05_summits.bed INFO @ Mon, 03 Jun 2019 07:04:20: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7555 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:04:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252224/SRX252224.20_summits.bed INFO @ Mon, 03 Jun 2019 07:04:30: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3505 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。