Job ID = 1293841 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 23,177,963 reads read : 46,355,926 reads written : 46,355,926 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: 00:47:41 23177963 reads; of these: 23177963 (100.00%) were paired; of these: 5168732 (22.30%) aligned concordantly 0 times 13248361 (57.16%) aligned concordantly exactly 1 time 4760870 (20.54%) aligned concordantly >1 times ---- 5168732 pairs aligned concordantly 0 times; of these: 82051 (1.59%) aligned discordantly 1 time ---- 5086681 pairs aligned 0 times concordantly or discordantly; of these: 10173362 mates make up the pairs; of these: 9392399 (92.32%) aligned 0 times 513272 (5.05%) aligned exactly 1 time 267691 (2.63%) aligned >1 times 79.74% overall alignment rate Time searching: 00:47:41 Overall time: 00:47:41 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] 9195917 / 18060711 = 0.5092 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 03:43:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.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 03:43:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.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 03:43:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:43:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:43:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:43:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:43:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.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 03:43:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:43:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:43:27: 1000000 INFO @ Mon, 03 Jun 2019 03:43:28: 1000000 INFO @ Mon, 03 Jun 2019 03:43:29: 1000000 INFO @ Mon, 03 Jun 2019 03:43:34: 2000000 INFO @ Mon, 03 Jun 2019 03:43:35: 2000000 INFO @ Mon, 03 Jun 2019 03:43:38: 2000000 INFO @ Mon, 03 Jun 2019 03:43:42: 3000000 INFO @ Mon, 03 Jun 2019 03:43:42: 3000000 INFO @ Mon, 03 Jun 2019 03:43:47: 3000000 INFO @ Mon, 03 Jun 2019 03:43:49: 4000000 INFO @ Mon, 03 Jun 2019 03:43:49: 4000000 INFO @ Mon, 03 Jun 2019 03:43:56: 5000000 INFO @ Mon, 03 Jun 2019 03:43:56: 4000000 INFO @ Mon, 03 Jun 2019 03:43:56: 5000000 INFO @ Mon, 03 Jun 2019 03:44:03: 6000000 INFO @ Mon, 03 Jun 2019 03:44:03: 6000000 INFO @ Mon, 03 Jun 2019 03:44:05: 5000000 INFO @ Mon, 03 Jun 2019 03:44:10: 7000000 INFO @ Mon, 03 Jun 2019 03:44:10: 7000000 INFO @ Mon, 03 Jun 2019 03:44:13: 6000000 INFO @ Mon, 03 Jun 2019 03:44:16: 8000000 INFO @ Mon, 03 Jun 2019 03:44:17: 8000000 INFO @ Mon, 03 Jun 2019 03:44:22: 7000000 INFO @ Mon, 03 Jun 2019 03:44:23: 9000000 INFO @ Mon, 03 Jun 2019 03:44:23: 9000000 INFO @ Mon, 03 Jun 2019 03:44:30: 8000000 INFO @ Mon, 03 Jun 2019 03:44:30: 10000000 INFO @ Mon, 03 Jun 2019 03:44:30: 10000000 INFO @ Mon, 03 Jun 2019 03:44:37: 11000000 INFO @ Mon, 03 Jun 2019 03:44:37: 11000000 INFO @ Mon, 03 Jun 2019 03:44:39: 9000000 INFO @ Mon, 03 Jun 2019 03:44:44: 12000000 INFO @ Mon, 03 Jun 2019 03:44:44: 12000000 INFO @ Mon, 03 Jun 2019 03:44:47: 10000000 INFO @ Mon, 03 Jun 2019 03:44:51: 13000000 INFO @ Mon, 03 Jun 2019 03:44:52: 13000000 INFO @ Mon, 03 Jun 2019 03:44:56: 11000000 INFO @ Mon, 03 Jun 2019 03:44:58: 14000000 INFO @ Mon, 03 Jun 2019 03:44:59: 14000000 INFO @ Mon, 03 Jun 2019 03:45:05: 12000000 INFO @ Mon, 03 Jun 2019 03:45:05: 15000000 INFO @ Mon, 03 Jun 2019 03:45:05: 15000000 INFO @ Mon, 03 Jun 2019 03:45:12: 16000000 INFO @ Mon, 03 Jun 2019 03:45:12: 16000000 INFO @ Mon, 03 Jun 2019 03:45:14: 13000000 INFO @ Mon, 03 Jun 2019 03:45:19: 17000000 INFO @ Mon, 03 Jun 2019 03:45:19: 17000000 INFO @ Mon, 03 Jun 2019 03:45:22: 14000000 INFO @ Mon, 03 Jun 2019 03:45:26: 18000000 INFO @ Mon, 03 Jun 2019 03:45:26: 18000000 INFO @ Mon, 03 Jun 2019 03:45:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:45:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:45:30: #1 total tags in treatment: 8832202 INFO @ Mon, 03 Jun 2019 03:45:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:45:30: #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 03:45:30: #1 tags after filtering in treatment: 8121282 INFO @ Mon, 03 Jun 2019 03:45:30: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 03:45:30: #1 finished! INFO @ Mon, 03 Jun 2019 03:45:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:45:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:45:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:45:30: #1 total tags in treatment: 8832202 INFO @ Mon, 03 Jun 2019 03:45:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:45:30: #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 03:45:30: #1 tags after filtering in treatment: 8121282 INFO @ Mon, 03 Jun 2019 03:45:30: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 03:45:30: #1 finished! INFO @ Mon, 03 Jun 2019 03:45:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:45:31: #2 number of paired peaks: 1382 INFO @ Mon, 03 Jun 2019 03:45:31: start model_add_line... INFO @ Mon, 03 Jun 2019 03:45:31: 15000000 INFO @ Mon, 03 Jun 2019 03:45:31: start X-correlation... INFO @ Mon, 03 Jun 2019 03:45:31: end of X-cor INFO @ Mon, 03 Jun 2019 03:45:31: #2 finished! INFO @ Mon, 03 Jun 2019 03:45:31: #2 predicted fragment length is 110 bps INFO @ Mon, 03 Jun 2019 03:45:31: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 03 Jun 2019 03:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.20_model.r INFO @ Mon, 03 Jun 2019 03:45:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:45:31: #2 number of paired peaks: 1382 INFO @ Mon, 03 Jun 2019 03:45:31: start model_add_line... INFO @ Mon, 03 Jun 2019 03:45:31: start X-correlation... INFO @ Mon, 03 Jun 2019 03:45:31: end of X-cor INFO @ Mon, 03 Jun 2019 03:45:31: #2 finished! INFO @ Mon, 03 Jun 2019 03:45:31: #2 predicted fragment length is 110 bps INFO @ Mon, 03 Jun 2019 03:45:31: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 03 Jun 2019 03:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.05_model.r INFO @ Mon, 03 Jun 2019 03:45:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:45:39: 16000000 INFO @ Mon, 03 Jun 2019 03:45:47: 17000000 INFO @ Mon, 03 Jun 2019 03:45:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:45:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:45:56: 18000000 INFO @ Mon, 03 Jun 2019 03:46:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:46:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:46:00: #1 total tags in treatment: 8832202 INFO @ Mon, 03 Jun 2019 03:46:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:46:00: #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 03:46:01: #1 tags after filtering in treatment: 8121282 INFO @ Mon, 03 Jun 2019 03:46:01: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 03:46:01: #1 finished! INFO @ Mon, 03 Jun 2019 03:46:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:46:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:46:01: #2 number of paired peaks: 1382 INFO @ Mon, 03 Jun 2019 03:46:01: start model_add_line... INFO @ Mon, 03 Jun 2019 03:46:02: start X-correlation... INFO @ Mon, 03 Jun 2019 03:46:02: end of X-cor INFO @ Mon, 03 Jun 2019 03:46:02: #2 finished! INFO @ Mon, 03 Jun 2019 03:46:02: #2 predicted fragment length is 110 bps INFO @ Mon, 03 Jun 2019 03:46:02: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 03 Jun 2019 03:46:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.10_model.r INFO @ Mon, 03 Jun 2019 03:46:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:46:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:46:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:46:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:46:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.20_summits.bed INFO @ Mon, 03 Jun 2019 03:46:07: Done! INFO @ Mon, 03 Jun 2019 03:46:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.05_peaks.xls pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1369 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:46:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:46:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.05_summits.bed INFO @ Mon, 03 Jun 2019 03:46:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7119 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:46:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:46:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:46:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:46:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128327/SRX128327.10_summits.bed INFO @ Mon, 03 Jun 2019 03:46:38: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3440 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。