Job ID = 1295780 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,659,712 reads read : 23,319,424 reads written : 23,319,424 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: 00:25:59 11659712 reads; of these: 11659712 (100.00%) were paired; of these: 2634448 (22.59%) aligned concordantly 0 times 6384953 (54.76%) aligned concordantly exactly 1 time 2640311 (22.64%) aligned concordantly >1 times ---- 2634448 pairs aligned concordantly 0 times; of these: 6313 (0.24%) aligned discordantly 1 time ---- 2628135 pairs aligned 0 times concordantly or discordantly; of these: 5256270 mates make up the pairs; of these: 5030016 (95.70%) aligned 0 times 164277 (3.13%) aligned exactly 1 time 61977 (1.18%) aligned >1 times 78.43% overall alignment rate Time searching: 00:25:59 Overall time: 00:25:59 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 8 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] 2927506 / 9020030 = 0.3246 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 16:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.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 16:03:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:03:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.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 16:03:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:03:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.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 16:03:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:03:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:03:59: 1000000 INFO @ Mon, 03 Jun 2019 16:04:00: 1000000 INFO @ Mon, 03 Jun 2019 16:04:01: 1000000 INFO @ Mon, 03 Jun 2019 16:04:07: 2000000 INFO @ Mon, 03 Jun 2019 16:04:08: 2000000 INFO @ Mon, 03 Jun 2019 16:04:10: 2000000 INFO @ Mon, 03 Jun 2019 16:04:15: 3000000 INFO @ Mon, 03 Jun 2019 16:04:16: 3000000 INFO @ Mon, 03 Jun 2019 16:04:20: 3000000 INFO @ Mon, 03 Jun 2019 16:04:23: 4000000 INFO @ Mon, 03 Jun 2019 16:04:24: 4000000 INFO @ Mon, 03 Jun 2019 16:04:30: 4000000 INFO @ Mon, 03 Jun 2019 16:04:31: 5000000 INFO @ Mon, 03 Jun 2019 16:04:33: 5000000 INFO @ Mon, 03 Jun 2019 16:04:39: 5000000 INFO @ Mon, 03 Jun 2019 16:04:39: 6000000 INFO @ Mon, 03 Jun 2019 16:04:41: 6000000 INFO @ Mon, 03 Jun 2019 16:04:47: 7000000 INFO @ Mon, 03 Jun 2019 16:04:49: 6000000 INFO @ Mon, 03 Jun 2019 16:04:51: 7000000 INFO @ Mon, 03 Jun 2019 16:04:55: 8000000 INFO @ Mon, 03 Jun 2019 16:04:59: 8000000 INFO @ Mon, 03 Jun 2019 16:04:59: 7000000 INFO @ Mon, 03 Jun 2019 16:05:04: 9000000 INFO @ Mon, 03 Jun 2019 16:05:06: 9000000 INFO @ Mon, 03 Jun 2019 16:05:09: 8000000 INFO @ Mon, 03 Jun 2019 16:05:13: 10000000 INFO @ Mon, 03 Jun 2019 16:05:17: 10000000 INFO @ Mon, 03 Jun 2019 16:05:19: 9000000 INFO @ Mon, 03 Jun 2019 16:05:21: 11000000 INFO @ Mon, 03 Jun 2019 16:05:24: 11000000 INFO @ Mon, 03 Jun 2019 16:05:28: 10000000 INFO @ Mon, 03 Jun 2019 16:05:29: 12000000 INFO @ Mon, 03 Jun 2019 16:05:31: 12000000 INFO @ Mon, 03 Jun 2019 16:05:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:05:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:05:32: #1 total tags in treatment: 6098681 INFO @ Mon, 03 Jun 2019 16:05:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:05:32: #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 16:05:32: #1 tags after filtering in treatment: 5660780 INFO @ Mon, 03 Jun 2019 16:05:32: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 16:05:32: #1 finished! INFO @ Mon, 03 Jun 2019 16:05:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:05:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:05:33: #2 number of paired peaks: 1104 INFO @ Mon, 03 Jun 2019 16:05:33: start model_add_line... INFO @ Mon, 03 Jun 2019 16:05:33: start X-correlation... INFO @ Mon, 03 Jun 2019 16:05:33: end of X-cor INFO @ Mon, 03 Jun 2019 16:05:33: #2 finished! INFO @ Mon, 03 Jun 2019 16:05:33: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 16:05:33: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 03 Jun 2019 16:05:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.10_model.r INFO @ Mon, 03 Jun 2019 16:05:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:05:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:05:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:05:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:05:34: #1 total tags in treatment: 6098681 INFO @ Mon, 03 Jun 2019 16:05:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:05:34: #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 16:05:35: #1 tags after filtering in treatment: 5660780 INFO @ Mon, 03 Jun 2019 16:05:35: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 16:05:35: #1 finished! INFO @ Mon, 03 Jun 2019 16:05:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:05:35: #2 number of paired peaks: 1104 INFO @ Mon, 03 Jun 2019 16:05:35: start model_add_line... INFO @ Mon, 03 Jun 2019 16:05:35: start X-correlation... INFO @ Mon, 03 Jun 2019 16:05:35: end of X-cor INFO @ Mon, 03 Jun 2019 16:05:35: #2 finished! INFO @ Mon, 03 Jun 2019 16:05:35: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 16:05:35: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 03 Jun 2019 16:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.05_model.r INFO @ Mon, 03 Jun 2019 16:05:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:05:37: 11000000 INFO @ Mon, 03 Jun 2019 16:05:45: 12000000 INFO @ Mon, 03 Jun 2019 16:05:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:05:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:05:49: #1 total tags in treatment: 6098681 INFO @ Mon, 03 Jun 2019 16:05:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:05:49: #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 16:05:49: #1 tags after filtering in treatment: 5660780 INFO @ Mon, 03 Jun 2019 16:05:49: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 16:05:49: #1 finished! INFO @ Mon, 03 Jun 2019 16:05:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:05:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:05:50: #2 number of paired peaks: 1104 INFO @ Mon, 03 Jun 2019 16:05:50: start model_add_line... INFO @ Mon, 03 Jun 2019 16:05:50: start X-correlation... INFO @ Mon, 03 Jun 2019 16:05:50: end of X-cor INFO @ Mon, 03 Jun 2019 16:05:50: #2 finished! INFO @ Mon, 03 Jun 2019 16:05:50: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 16:05:50: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 03 Jun 2019 16:05:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.20_model.r INFO @ Mon, 03 Jun 2019 16:05:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:05:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:05:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:05:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.10_summits.bed INFO @ Mon, 03 Jun 2019 16:05:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2058 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:06:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:06:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:06:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.05_summits.bed INFO @ Mon, 03 Jun 2019 16:06:02: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4387 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:06:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:06:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:06:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:06:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456149/SRX456149.20_summits.bed INFO @ Mon, 03 Jun 2019 16:06:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1005 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。