Job ID = 1294821 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,981,175 reads read : 15,981,175 reads written : 15,981,175 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: 00:05:04 15981175 reads; of these: 15981175 (100.00%) were unpaired; of these: 914023 (5.72%) aligned 0 times 12431276 (77.79%) aligned exactly 1 time 2635876 (16.49%) aligned >1 times 94.28% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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_rmdupse_core] 4247737 / 15067152 = 0.2819 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 10:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.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 10:32:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:32:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.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 10:32:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:32:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.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 10:32:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:32:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:32:11: 1000000 INFO @ Mon, 03 Jun 2019 10:32:12: 1000000 INFO @ Mon, 03 Jun 2019 10:32:12: 1000000 INFO @ Mon, 03 Jun 2019 10:32:18: 2000000 INFO @ Mon, 03 Jun 2019 10:32:20: 2000000 INFO @ Mon, 03 Jun 2019 10:32:20: 2000000 INFO @ Mon, 03 Jun 2019 10:32:26: 3000000 INFO @ Mon, 03 Jun 2019 10:32:27: 3000000 INFO @ Mon, 03 Jun 2019 10:32:28: 3000000 INFO @ Mon, 03 Jun 2019 10:32:34: 4000000 INFO @ Mon, 03 Jun 2019 10:32:35: 4000000 INFO @ Mon, 03 Jun 2019 10:32:37: 4000000 INFO @ Mon, 03 Jun 2019 10:32:42: 5000000 INFO @ Mon, 03 Jun 2019 10:32:43: 5000000 INFO @ Mon, 03 Jun 2019 10:32:45: 5000000 INFO @ Mon, 03 Jun 2019 10:32:49: 6000000 INFO @ Mon, 03 Jun 2019 10:32:51: 6000000 INFO @ Mon, 03 Jun 2019 10:32:52: 6000000 INFO @ Mon, 03 Jun 2019 10:32:55: 7000000 INFO @ Mon, 03 Jun 2019 10:32:59: 7000000 INFO @ Mon, 03 Jun 2019 10:33:00: 7000000 INFO @ Mon, 03 Jun 2019 10:33:02: 8000000 INFO @ Mon, 03 Jun 2019 10:33:06: 8000000 INFO @ Mon, 03 Jun 2019 10:33:08: 8000000 INFO @ Mon, 03 Jun 2019 10:33:09: 9000000 INFO @ Mon, 03 Jun 2019 10:33:14: 9000000 INFO @ Mon, 03 Jun 2019 10:33:15: 9000000 INFO @ Mon, 03 Jun 2019 10:33:15: 10000000 INFO @ Mon, 03 Jun 2019 10:33:21: 10000000 INFO @ Mon, 03 Jun 2019 10:33:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:33:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:33:21: #1 total tags in treatment: 10819415 INFO @ Mon, 03 Jun 2019 10:33:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:33:21: #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 10:33:21: #1 tags after filtering in treatment: 10819415 INFO @ Mon, 03 Jun 2019 10:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:33:21: #1 finished! INFO @ Mon, 03 Jun 2019 10:33:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:33:22: #2 number of paired peaks: 622 WARNING @ Mon, 03 Jun 2019 10:33:22: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Mon, 03 Jun 2019 10:33:22: start model_add_line... INFO @ Mon, 03 Jun 2019 10:33:22: start X-correlation... INFO @ Mon, 03 Jun 2019 10:33:22: end of X-cor INFO @ Mon, 03 Jun 2019 10:33:22: #2 finished! INFO @ Mon, 03 Jun 2019 10:33:22: #2 predicted fragment length is 231 bps INFO @ Mon, 03 Jun 2019 10:33:22: #2 alternative fragment length(s) may be 231 bps INFO @ Mon, 03 Jun 2019 10:33:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.10_model.r INFO @ Mon, 03 Jun 2019 10:33:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:33:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:33:22: 10000000 INFO @ Mon, 03 Jun 2019 10:33:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:33:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:33:27: #1 total tags in treatment: 10819415 INFO @ Mon, 03 Jun 2019 10:33:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:33:27: #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 10:33:27: #1 tags after filtering in treatment: 10819415 INFO @ Mon, 03 Jun 2019 10:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:33:27: #1 finished! INFO @ Mon, 03 Jun 2019 10:33:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:33:28: #2 number of paired peaks: 622 WARNING @ Mon, 03 Jun 2019 10:33:28: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Mon, 03 Jun 2019 10:33:28: start model_add_line... INFO @ Mon, 03 Jun 2019 10:33:28: start X-correlation... INFO @ Mon, 03 Jun 2019 10:33:28: end of X-cor INFO @ Mon, 03 Jun 2019 10:33:28: #2 finished! INFO @ Mon, 03 Jun 2019 10:33:28: #2 predicted fragment length is 231 bps INFO @ Mon, 03 Jun 2019 10:33:28: #2 alternative fragment length(s) may be 231 bps INFO @ Mon, 03 Jun 2019 10:33:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.05_model.r INFO @ Mon, 03 Jun 2019 10:33:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:33:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:33:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:33:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:33:28: #1 total tags in treatment: 10819415 INFO @ Mon, 03 Jun 2019 10:33:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:33:28: #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 10:33:29: #1 tags after filtering in treatment: 10819415 INFO @ Mon, 03 Jun 2019 10:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:33:29: #1 finished! INFO @ Mon, 03 Jun 2019 10:33:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:33:30: #2 number of paired peaks: 622 WARNING @ Mon, 03 Jun 2019 10:33:30: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Mon, 03 Jun 2019 10:33:30: start model_add_line... INFO @ Mon, 03 Jun 2019 10:33:30: start X-correlation... INFO @ Mon, 03 Jun 2019 10:33:30: end of X-cor INFO @ Mon, 03 Jun 2019 10:33:30: #2 finished! INFO @ Mon, 03 Jun 2019 10:33:30: #2 predicted fragment length is 231 bps INFO @ Mon, 03 Jun 2019 10:33:30: #2 alternative fragment length(s) may be 231 bps INFO @ Mon, 03 Jun 2019 10:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.20_model.r INFO @ Mon, 03 Jun 2019 10:33:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:33:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:34:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:34:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:34:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:34:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:34:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.10_summits.bed INFO @ Mon, 03 Jun 2019 10:34:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3187 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:34:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:34:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:34:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.05_summits.bed INFO @ Mon, 03 Jun 2019 10:34:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4687 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:34:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:34:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:34:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287920/SRX287920.20_summits.bed INFO @ Mon, 03 Jun 2019 10:34:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1718 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。