Job ID = 2590564 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,300,646 reads read : 20,601,292 reads written : 20,601,292 rm: cannot remove ‘[DSE]RR*’: 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: 00:27:28 10300646 reads; of these: 10300646 (100.00%) were paired; of these: 1092297 (10.60%) aligned concordantly 0 times 6700239 (65.05%) aligned concordantly exactly 1 time 2508110 (24.35%) aligned concordantly >1 times ---- 1092297 pairs aligned concordantly 0 times; of these: 137391 (12.58%) aligned discordantly 1 time ---- 954906 pairs aligned 0 times concordantly or discordantly; of these: 1909812 mates make up the pairs; of these: 1326607 (69.46%) aligned 0 times 343875 (18.01%) aligned exactly 1 time 239330 (12.53%) aligned >1 times 93.56% overall alignment rate Time searching: 00:27:28 Overall time: 00:27:28 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] 286591 / 9334873 = 0.0307 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, 12 Aug 2019 23:02:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.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, 12 Aug 2019 23:02:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:02:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.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, 12 Aug 2019 23:02:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:02:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:02:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.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, 12 Aug 2019 23:02:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:02:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:02:30: 1000000 INFO @ Mon, 12 Aug 2019 23:02:31: 1000000 INFO @ Mon, 12 Aug 2019 23:02:31: 1000000 INFO @ Mon, 12 Aug 2019 23:02:37: 2000000 INFO @ Mon, 12 Aug 2019 23:02:37: 2000000 INFO @ Mon, 12 Aug 2019 23:02:37: 2000000 INFO @ Mon, 12 Aug 2019 23:02:43: 3000000 INFO @ Mon, 12 Aug 2019 23:02:44: 3000000 INFO @ Mon, 12 Aug 2019 23:02:44: 3000000 INFO @ Mon, 12 Aug 2019 23:02:49: 4000000 INFO @ Mon, 12 Aug 2019 23:02:50: 4000000 INFO @ Mon, 12 Aug 2019 23:02:50: 4000000 INFO @ Mon, 12 Aug 2019 23:02:55: 5000000 INFO @ Mon, 12 Aug 2019 23:02:55: 5000000 INFO @ Mon, 12 Aug 2019 23:02:57: 5000000 INFO @ Mon, 12 Aug 2019 23:03:01: 6000000 INFO @ Mon, 12 Aug 2019 23:03:01: 6000000 INFO @ Mon, 12 Aug 2019 23:03:03: 6000000 INFO @ Mon, 12 Aug 2019 23:03:07: 7000000 INFO @ Mon, 12 Aug 2019 23:03:07: 7000000 INFO @ Mon, 12 Aug 2019 23:03:09: 7000000 INFO @ Mon, 12 Aug 2019 23:03:13: 8000000 INFO @ Mon, 12 Aug 2019 23:03:13: 8000000 INFO @ Mon, 12 Aug 2019 23:03:15: 8000000 INFO @ Mon, 12 Aug 2019 23:03:19: 9000000 INFO @ Mon, 12 Aug 2019 23:03:19: 9000000 INFO @ Mon, 12 Aug 2019 23:03:22: 9000000 INFO @ Mon, 12 Aug 2019 23:03:25: 10000000 INFO @ Mon, 12 Aug 2019 23:03:25: 10000000 INFO @ Mon, 12 Aug 2019 23:03:28: 10000000 INFO @ Mon, 12 Aug 2019 23:03:31: 11000000 INFO @ Mon, 12 Aug 2019 23:03:31: 11000000 INFO @ Mon, 12 Aug 2019 23:03:34: 11000000 INFO @ Mon, 12 Aug 2019 23:03:37: 12000000 INFO @ Mon, 12 Aug 2019 23:03:37: 12000000 INFO @ Mon, 12 Aug 2019 23:03:40: 12000000 INFO @ Mon, 12 Aug 2019 23:03:43: 13000000 INFO @ Mon, 12 Aug 2019 23:03:43: 13000000 INFO @ Mon, 12 Aug 2019 23:03:46: 13000000 INFO @ Mon, 12 Aug 2019 23:03:49: 14000000 INFO @ Mon, 12 Aug 2019 23:03:49: 14000000 INFO @ Mon, 12 Aug 2019 23:03:53: 14000000 INFO @ Mon, 12 Aug 2019 23:03:55: 15000000 INFO @ Mon, 12 Aug 2019 23:03:55: 15000000 INFO @ Mon, 12 Aug 2019 23:03:59: 15000000 INFO @ Mon, 12 Aug 2019 23:04:00: 16000000 INFO @ Mon, 12 Aug 2019 23:04:01: 16000000 INFO @ Mon, 12 Aug 2019 23:04:05: 16000000 INFO @ Mon, 12 Aug 2019 23:04:06: 17000000 INFO @ Mon, 12 Aug 2019 23:04:06: 17000000 INFO @ Mon, 12 Aug 2019 23:04:11: 17000000 INFO @ Mon, 12 Aug 2019 23:04:12: 18000000 INFO @ Mon, 12 Aug 2019 23:04:12: 18000000 INFO @ Mon, 12 Aug 2019 23:04:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:04:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:04:16: #1 total tags in treatment: 8923033 INFO @ Mon, 12 Aug 2019 23:04:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:04:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:04:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:04:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:04:16: #1 total tags in treatment: 8923033 INFO @ Mon, 12 Aug 2019 23:04:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:04:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:04:17: #1 tags after filtering in treatment: 8321794 INFO @ Mon, 12 Aug 2019 23:04:17: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 12 Aug 2019 23:04:17: #1 finished! INFO @ Mon, 12 Aug 2019 23:04:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:04:17: #1 tags after filtering in treatment: 8321794 INFO @ Mon, 12 Aug 2019 23:04:17: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 12 Aug 2019 23:04:17: #1 finished! INFO @ Mon, 12 Aug 2019 23:04:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:04:17: #2 number of paired peaks: 1450 INFO @ Mon, 12 Aug 2019 23:04:17: start model_add_line... INFO @ Mon, 12 Aug 2019 23:04:17: 18000000 INFO @ Mon, 12 Aug 2019 23:04:17: start X-correlation... INFO @ Mon, 12 Aug 2019 23:04:18: end of X-cor INFO @ Mon, 12 Aug 2019 23:04:18: #2 finished! INFO @ Mon, 12 Aug 2019 23:04:18: #2 predicted fragment length is 188 bps INFO @ Mon, 12 Aug 2019 23:04:18: #2 alternative fragment length(s) may be 188 bps INFO @ Mon, 12 Aug 2019 23:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.05_model.r INFO @ Mon, 12 Aug 2019 23:04:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:04:18: #2 number of paired peaks: 1450 INFO @ Mon, 12 Aug 2019 23:04:18: start model_add_line... INFO @ Mon, 12 Aug 2019 23:04:18: start X-correlation... INFO @ Mon, 12 Aug 2019 23:04:18: end of X-cor INFO @ Mon, 12 Aug 2019 23:04:18: #2 finished! INFO @ Mon, 12 Aug 2019 23:04:18: #2 predicted fragment length is 188 bps INFO @ Mon, 12 Aug 2019 23:04:18: #2 alternative fragment length(s) may be 188 bps INFO @ Mon, 12 Aug 2019 23:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.20_model.r INFO @ Mon, 12 Aug 2019 23:04:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:04:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:04:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:04:22: #1 total tags in treatment: 8923033 INFO @ Mon, 12 Aug 2019 23:04:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:04:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:04:22: #1 tags after filtering in treatment: 8321794 INFO @ Mon, 12 Aug 2019 23:04:22: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 12 Aug 2019 23:04:22: #1 finished! INFO @ Mon, 12 Aug 2019 23:04:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:04:23: #2 number of paired peaks: 1450 INFO @ Mon, 12 Aug 2019 23:04:23: start model_add_line... INFO @ Mon, 12 Aug 2019 23:04:23: start X-correlation... INFO @ Mon, 12 Aug 2019 23:04:23: end of X-cor INFO @ Mon, 12 Aug 2019 23:04:23: #2 finished! INFO @ Mon, 12 Aug 2019 23:04:23: #2 predicted fragment length is 188 bps INFO @ Mon, 12 Aug 2019 23:04:23: #2 alternative fragment length(s) may be 188 bps INFO @ Mon, 12 Aug 2019 23:04:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.10_model.r INFO @ Mon, 12 Aug 2019 23:04:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:04:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:04:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:04:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:04:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:04:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:04:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.20_summits.bed INFO @ Mon, 12 Aug 2019 23:04:57: Done! INFO @ Mon, 12 Aug 2019 23:04:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.05_peaks.xls pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1542 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:04:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:04:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.05_summits.bed INFO @ Mon, 12 Aug 2019 23:04:58: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (5582 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:05:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:05:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:05:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501953/SRX4501953.10_summits.bed INFO @ Mon, 12 Aug 2019 23:05:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2971 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。