Job ID = 1299206 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 17,588,405 reads read : 35,176,810 reads written : 35,176,810 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:25:34 17588405 reads; of these: 17588405 (100.00%) were paired; of these: 3829909 (21.78%) aligned concordantly 0 times 11706554 (66.56%) aligned concordantly exactly 1 time 2051942 (11.67%) aligned concordantly >1 times ---- 3829909 pairs aligned concordantly 0 times; of these: 910219 (23.77%) aligned discordantly 1 time ---- 2919690 pairs aligned 0 times concordantly or discordantly; of these: 5839380 mates make up the pairs; of these: 5087956 (87.13%) aligned 0 times 458171 (7.85%) aligned exactly 1 time 293253 (5.02%) aligned >1 times 85.54% overall alignment rate Time searching: 00:25:35 Overall time: 00:25:35 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] 6717437 / 14659672 = 0.4582 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 18:49:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.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 18:49:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:49:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:49:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.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 18:49:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:49:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:49:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.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 18:49:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:49:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:49:36: 1000000 INFO @ Mon, 03 Jun 2019 18:49:38: 1000000 INFO @ Mon, 03 Jun 2019 18:49:39: 1000000 INFO @ Mon, 03 Jun 2019 18:49:44: 2000000 INFO @ Mon, 03 Jun 2019 18:49:47: 2000000 INFO @ Mon, 03 Jun 2019 18:49:48: 2000000 INFO @ Mon, 03 Jun 2019 18:49:51: 3000000 INFO @ Mon, 03 Jun 2019 18:49:56: 3000000 INFO @ Mon, 03 Jun 2019 18:49:58: 3000000 INFO @ Mon, 03 Jun 2019 18:49:59: 4000000 INFO @ Mon, 03 Jun 2019 18:50:05: 4000000 INFO @ Mon, 03 Jun 2019 18:50:06: 5000000 INFO @ Mon, 03 Jun 2019 18:50:07: 4000000 INFO @ Mon, 03 Jun 2019 18:50:13: 5000000 INFO @ Mon, 03 Jun 2019 18:50:14: 6000000 INFO @ Mon, 03 Jun 2019 18:50:17: 5000000 INFO @ Mon, 03 Jun 2019 18:50:21: 7000000 INFO @ Mon, 03 Jun 2019 18:50:22: 6000000 INFO @ Mon, 03 Jun 2019 18:50:25: 6000000 INFO @ Mon, 03 Jun 2019 18:50:28: 8000000 INFO @ Mon, 03 Jun 2019 18:50:30: 7000000 INFO @ Mon, 03 Jun 2019 18:50:33: 7000000 INFO @ Mon, 03 Jun 2019 18:50:35: 9000000 INFO @ Mon, 03 Jun 2019 18:50:38: 8000000 INFO @ Mon, 03 Jun 2019 18:50:42: 10000000 INFO @ Mon, 03 Jun 2019 18:50:42: 8000000 INFO @ Mon, 03 Jun 2019 18:50:46: 9000000 INFO @ Mon, 03 Jun 2019 18:50:49: 11000000 INFO @ Mon, 03 Jun 2019 18:50:50: 9000000 INFO @ Mon, 03 Jun 2019 18:50:54: 10000000 INFO @ Mon, 03 Jun 2019 18:50:57: 12000000 INFO @ Mon, 03 Jun 2019 18:50:58: 10000000 INFO @ Mon, 03 Jun 2019 18:51:02: 11000000 INFO @ Mon, 03 Jun 2019 18:51:04: 13000000 INFO @ Mon, 03 Jun 2019 18:51:07: 11000000 INFO @ Mon, 03 Jun 2019 18:51:11: 12000000 INFO @ Mon, 03 Jun 2019 18:51:11: 14000000 INFO @ Mon, 03 Jun 2019 18:51:15: 12000000 INFO @ Mon, 03 Jun 2019 18:51:18: 15000000 INFO @ Mon, 03 Jun 2019 18:51:19: 13000000 INFO @ Mon, 03 Jun 2019 18:51:24: 13000000 INFO @ Mon, 03 Jun 2019 18:51:25: 16000000 INFO @ Mon, 03 Jun 2019 18:51:27: 14000000 INFO @ Mon, 03 Jun 2019 18:51:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:51:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:51:30: #1 total tags in treatment: 7327351 INFO @ Mon, 03 Jun 2019 18:51:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:51:30: #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 18:51:30: #1 tags after filtering in treatment: 5832655 INFO @ Mon, 03 Jun 2019 18:51:30: #1 Redundant rate of treatment: 0.20 INFO @ Mon, 03 Jun 2019 18:51:30: #1 finished! INFO @ Mon, 03 Jun 2019 18:51:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:51:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:51:31: #2 number of paired peaks: 2031 INFO @ Mon, 03 Jun 2019 18:51:31: start model_add_line... INFO @ Mon, 03 Jun 2019 18:51:31: start X-correlation... INFO @ Mon, 03 Jun 2019 18:51:31: end of X-cor INFO @ Mon, 03 Jun 2019 18:51:31: #2 finished! INFO @ Mon, 03 Jun 2019 18:51:31: #2 predicted fragment length is 197 bps INFO @ Mon, 03 Jun 2019 18:51:31: #2 alternative fragment length(s) may be 197 bps INFO @ Mon, 03 Jun 2019 18:51:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.05_model.r INFO @ Mon, 03 Jun 2019 18:51:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:51:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:51:32: 14000000 INFO @ Mon, 03 Jun 2019 18:51:35: 15000000 INFO @ Mon, 03 Jun 2019 18:51:40: 15000000 INFO @ Mon, 03 Jun 2019 18:51:43: 16000000 INFO @ Mon, 03 Jun 2019 18:51:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:51:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:51:49: #1 total tags in treatment: 7327351 INFO @ Mon, 03 Jun 2019 18:51:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:51:49: #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 18:51:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:51:49: 16000000 INFO @ Mon, 03 Jun 2019 18:51:49: #1 tags after filtering in treatment: 5832655 INFO @ Mon, 03 Jun 2019 18:51:49: #1 Redundant rate of treatment: 0.20 INFO @ Mon, 03 Jun 2019 18:51:49: #1 finished! INFO @ Mon, 03 Jun 2019 18:51:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:51:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:51:49: #2 number of paired peaks: 2031 INFO @ Mon, 03 Jun 2019 18:51:49: start model_add_line... INFO @ Mon, 03 Jun 2019 18:51:50: start X-correlation... INFO @ Mon, 03 Jun 2019 18:51:50: end of X-cor INFO @ Mon, 03 Jun 2019 18:51:50: #2 finished! INFO @ Mon, 03 Jun 2019 18:51:50: #2 predicted fragment length is 197 bps INFO @ Mon, 03 Jun 2019 18:51:50: #2 alternative fragment length(s) may be 197 bps INFO @ Mon, 03 Jun 2019 18:51:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.20_model.r INFO @ Mon, 03 Jun 2019 18:51:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:51:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:51:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:51:54: #1 total tags in treatment: 7327351 INFO @ Mon, 03 Jun 2019 18:51:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:51:54: #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 18:51:54: #1 tags after filtering in treatment: 5832655 INFO @ Mon, 03 Jun 2019 18:51:54: #1 Redundant rate of treatment: 0.20 INFO @ Mon, 03 Jun 2019 18:51:54: #1 finished! INFO @ Mon, 03 Jun 2019 18:51:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:51:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:51:55: #2 number of paired peaks: 2031 INFO @ Mon, 03 Jun 2019 18:51:55: start model_add_line... INFO @ Mon, 03 Jun 2019 18:51:55: start X-correlation... INFO @ Mon, 03 Jun 2019 18:51:55: end of X-cor INFO @ Mon, 03 Jun 2019 18:51:55: #2 finished! INFO @ Mon, 03 Jun 2019 18:51:55: #2 predicted fragment length is 197 bps INFO @ Mon, 03 Jun 2019 18:51:55: #2 alternative fragment length(s) may be 197 bps INFO @ Mon, 03 Jun 2019 18:51:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.10_model.r INFO @ Mon, 03 Jun 2019 18:51:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:51:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.05_peaks.xls INFO @ Mon, 03 Jun 2019 18:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:51:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.05_summits.bed INFO @ Mon, 03 Jun 2019 18:51:58: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9026 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:52:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:52:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:52:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.20_peaks.xls INFO @ Mon, 03 Jun 2019 18:52:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:52:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.20_summits.bed INFO @ Mon, 03 Jun 2019 18:52:16: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (551 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:52:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.10_peaks.xls INFO @ Mon, 03 Jun 2019 18:52:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:52:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474566/SRX474566.10_summits.bed INFO @ Mon, 03 Jun 2019 18:52:22: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (2867 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。