Job ID = 2590566 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,223,856 reads read : 22,447,712 reads written : 22,447,712 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: 00:27:22 11223856 reads; of these: 11223856 (100.00%) were paired; of these: 1339137 (11.93%) aligned concordantly 0 times 6909859 (61.56%) aligned concordantly exactly 1 time 2974860 (26.50%) aligned concordantly >1 times ---- 1339137 pairs aligned concordantly 0 times; of these: 210279 (15.70%) aligned discordantly 1 time ---- 1128858 pairs aligned 0 times concordantly or discordantly; of these: 2257716 mates make up the pairs; of these: 1586086 (70.25%) aligned 0 times 372457 (16.50%) aligned exactly 1 time 299173 (13.25%) aligned >1 times 92.93% overall alignment rate Time searching: 00:27:22 Overall time: 00:27:22 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] 2699384 / 10079150 = 0.2678 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 23:09:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.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 23:09:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:09:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:09:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.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 23:09:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:09:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.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 23:09:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:09:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:09:33: 1000000 INFO @ Mon, 12 Aug 2019 23:09:33: 1000000 INFO @ Mon, 12 Aug 2019 23:09:34: 1000000 INFO @ Mon, 12 Aug 2019 23:09:41: 2000000 INFO @ Mon, 12 Aug 2019 23:09:41: 2000000 INFO @ Mon, 12 Aug 2019 23:09:41: 2000000 INFO @ Mon, 12 Aug 2019 23:09:49: 3000000 INFO @ Mon, 12 Aug 2019 23:09:49: 3000000 INFO @ Mon, 12 Aug 2019 23:09:50: 3000000 INFO @ Mon, 12 Aug 2019 23:09:56: 4000000 INFO @ Mon, 12 Aug 2019 23:09:58: 4000000 INFO @ Mon, 12 Aug 2019 23:09:58: 4000000 INFO @ Mon, 12 Aug 2019 23:10:03: 5000000 INFO @ Mon, 12 Aug 2019 23:10:06: 5000000 INFO @ Mon, 12 Aug 2019 23:10:06: 5000000 INFO @ Mon, 12 Aug 2019 23:10:10: 6000000 INFO @ Mon, 12 Aug 2019 23:10:14: 6000000 INFO @ Mon, 12 Aug 2019 23:10:15: 6000000 INFO @ Mon, 12 Aug 2019 23:10:17: 7000000 INFO @ Mon, 12 Aug 2019 23:10:21: 7000000 INFO @ Mon, 12 Aug 2019 23:10:23: 7000000 INFO @ Mon, 12 Aug 2019 23:10:24: 8000000 INFO @ Mon, 12 Aug 2019 23:10:29: 8000000 INFO @ Mon, 12 Aug 2019 23:10:31: 8000000 INFO @ Mon, 12 Aug 2019 23:10:31: 9000000 INFO @ Mon, 12 Aug 2019 23:10:37: 9000000 INFO @ Mon, 12 Aug 2019 23:10:38: 10000000 INFO @ Mon, 12 Aug 2019 23:10:39: 9000000 INFO @ Mon, 12 Aug 2019 23:10:45: 10000000 INFO @ Mon, 12 Aug 2019 23:10:45: 11000000 INFO @ Mon, 12 Aug 2019 23:10:47: 10000000 INFO @ Mon, 12 Aug 2019 23:10:52: 12000000 INFO @ Mon, 12 Aug 2019 23:10:52: 11000000 INFO @ Mon, 12 Aug 2019 23:10:55: 11000000 INFO @ Mon, 12 Aug 2019 23:10:59: 13000000 INFO @ Mon, 12 Aug 2019 23:11:00: 12000000 INFO @ Mon, 12 Aug 2019 23:11:03: 12000000 INFO @ Mon, 12 Aug 2019 23:11:06: 14000000 INFO @ Mon, 12 Aug 2019 23:11:08: 13000000 INFO @ Mon, 12 Aug 2019 23:11:11: 13000000 INFO @ Mon, 12 Aug 2019 23:11:13: 15000000 INFO @ Mon, 12 Aug 2019 23:11:15: 14000000 INFO @ Mon, 12 Aug 2019 23:11:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:11:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:11:16: #1 total tags in treatment: 7211950 INFO @ Mon, 12 Aug 2019 23:11:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:11:16: #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 23:11:16: #1 tags after filtering in treatment: 6822495 INFO @ Mon, 12 Aug 2019 23:11:16: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 12 Aug 2019 23:11:16: #1 finished! INFO @ Mon, 12 Aug 2019 23:11:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:11:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:11:17: #2 number of paired peaks: 1226 INFO @ Mon, 12 Aug 2019 23:11:17: start model_add_line... INFO @ Mon, 12 Aug 2019 23:11:17: start X-correlation... INFO @ Mon, 12 Aug 2019 23:11:17: end of X-cor INFO @ Mon, 12 Aug 2019 23:11:17: #2 finished! INFO @ Mon, 12 Aug 2019 23:11:17: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 23:11:17: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 12 Aug 2019 23:11:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.20_model.r INFO @ Mon, 12 Aug 2019 23:11:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:11:19: 14000000 INFO @ Mon, 12 Aug 2019 23:11:23: 15000000 INFO @ Mon, 12 Aug 2019 23:11:27: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:11:27: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:11:27: #1 total tags in treatment: 7211950 INFO @ Mon, 12 Aug 2019 23:11:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:11:27: #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 23:11:27: #1 tags after filtering in treatment: 6822495 INFO @ Mon, 12 Aug 2019 23:11:27: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 12 Aug 2019 23:11:27: #1 finished! INFO @ Mon, 12 Aug 2019 23:11:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:11:27: 15000000 INFO @ Mon, 12 Aug 2019 23:11:28: #2 number of paired peaks: 1226 INFO @ Mon, 12 Aug 2019 23:11:28: start model_add_line... INFO @ Mon, 12 Aug 2019 23:11:28: start X-correlation... INFO @ Mon, 12 Aug 2019 23:11:28: end of X-cor INFO @ Mon, 12 Aug 2019 23:11:28: #2 finished! INFO @ Mon, 12 Aug 2019 23:11:28: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 23:11:28: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 12 Aug 2019 23:11:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.10_model.r INFO @ Mon, 12 Aug 2019 23:11:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:11:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:11:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:11:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:11:31: #1 total tags in treatment: 7211950 INFO @ Mon, 12 Aug 2019 23:11:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:11:31: #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 23:11:31: #1 tags after filtering in treatment: 6822495 INFO @ Mon, 12 Aug 2019 23:11:31: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 12 Aug 2019 23:11:31: #1 finished! INFO @ Mon, 12 Aug 2019 23:11:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:11:32: #2 number of paired peaks: 1226 INFO @ Mon, 12 Aug 2019 23:11:32: start model_add_line... INFO @ Mon, 12 Aug 2019 23:11:32: start X-correlation... INFO @ Mon, 12 Aug 2019 23:11:32: end of X-cor INFO @ Mon, 12 Aug 2019 23:11:32: #2 finished! INFO @ Mon, 12 Aug 2019 23:11:32: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 23:11:32: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 12 Aug 2019 23:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.05_model.r INFO @ Mon, 12 Aug 2019 23:11:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:11:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:11:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:11:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:11:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:11:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.20_summits.bed INFO @ Mon, 12 Aug 2019 23:11:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:11:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:11:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:11:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:11:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.10_summits.bed INFO @ Mon, 12 Aug 2019 23:11:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1164 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501954/SRX4501954.05_summits.bed INFO @ Mon, 12 Aug 2019 23:12:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2046 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。