Job ID = 1295511 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,301,508 reads read : 19,301,508 reads written : 19,301,508 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: 00:05:16 19301508 reads; of these: 19301508 (100.00%) were unpaired; of these: 3236901 (16.77%) aligned 0 times 12202253 (63.22%) aligned exactly 1 time 3862354 (20.01%) aligned >1 times 83.23% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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] 4356149 / 16064607 = 0.2712 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 14:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.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 14:17:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:17:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.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 14:17:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:17:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.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 14:17:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:17:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:17:51: 1000000 INFO @ Mon, 03 Jun 2019 14:17:51: 1000000 INFO @ Mon, 03 Jun 2019 14:17:53: 1000000 INFO @ Mon, 03 Jun 2019 14:17:58: 2000000 INFO @ Mon, 03 Jun 2019 14:17:58: 2000000 INFO @ Mon, 03 Jun 2019 14:18:02: 2000000 INFO @ Mon, 03 Jun 2019 14:18:04: 3000000 INFO @ Mon, 03 Jun 2019 14:18:04: 3000000 INFO @ Mon, 03 Jun 2019 14:18:10: 3000000 INFO @ Mon, 03 Jun 2019 14:18:11: 4000000 INFO @ Mon, 03 Jun 2019 14:18:11: 4000000 INFO @ Mon, 03 Jun 2019 14:18:17: 5000000 INFO @ Mon, 03 Jun 2019 14:18:17: 5000000 INFO @ Mon, 03 Jun 2019 14:18:18: 4000000 INFO @ Mon, 03 Jun 2019 14:18:23: 6000000 INFO @ Mon, 03 Jun 2019 14:18:23: 6000000 INFO @ Mon, 03 Jun 2019 14:18:26: 5000000 INFO @ Mon, 03 Jun 2019 14:18:30: 7000000 INFO @ Mon, 03 Jun 2019 14:18:30: 7000000 INFO @ Mon, 03 Jun 2019 14:18:34: 6000000 INFO @ Mon, 03 Jun 2019 14:18:37: 8000000 INFO @ Mon, 03 Jun 2019 14:18:37: 8000000 INFO @ Mon, 03 Jun 2019 14:18:42: 7000000 INFO @ Mon, 03 Jun 2019 14:18:44: 9000000 INFO @ Mon, 03 Jun 2019 14:18:44: 9000000 INFO @ Mon, 03 Jun 2019 14:18:50: 8000000 INFO @ Mon, 03 Jun 2019 14:18:51: 10000000 INFO @ Mon, 03 Jun 2019 14:18:51: 10000000 INFO @ Mon, 03 Jun 2019 14:18:58: 9000000 INFO @ Mon, 03 Jun 2019 14:18:58: 11000000 INFO @ Mon, 03 Jun 2019 14:18:58: 11000000 INFO @ Mon, 03 Jun 2019 14:19:03: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 14:19:03: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 14:19:03: #1 total tags in treatment: 11708458 INFO @ Mon, 03 Jun 2019 14:19:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:19:03: #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 14:19:03: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 14:19:03: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 14:19:03: #1 total tags in treatment: 11708458 INFO @ Mon, 03 Jun 2019 14:19:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:19:03: #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 14:19:03: #1 tags after filtering in treatment: 11708458 INFO @ Mon, 03 Jun 2019 14:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:19:03: #1 finished! INFO @ Mon, 03 Jun 2019 14:19:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:19:04: #1 tags after filtering in treatment: 11708458 INFO @ Mon, 03 Jun 2019 14:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:19:04: #1 finished! INFO @ Mon, 03 Jun 2019 14:19:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:19:05: #2 number of paired peaks: 319 WARNING @ Mon, 03 Jun 2019 14:19:05: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Mon, 03 Jun 2019 14:19:05: start model_add_line... INFO @ Mon, 03 Jun 2019 14:19:05: start X-correlation... INFO @ Mon, 03 Jun 2019 14:19:05: #2 number of paired peaks: 319 WARNING @ Mon, 03 Jun 2019 14:19:05: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Mon, 03 Jun 2019 14:19:05: start model_add_line... INFO @ Mon, 03 Jun 2019 14:19:05: end of X-cor INFO @ Mon, 03 Jun 2019 14:19:05: #2 finished! INFO @ Mon, 03 Jun 2019 14:19:05: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 14:19:05: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 03 Jun 2019 14:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.05_model.r INFO @ Mon, 03 Jun 2019 14:19:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:19:05: start X-correlation... INFO @ Mon, 03 Jun 2019 14:19:05: end of X-cor INFO @ Mon, 03 Jun 2019 14:19:05: #2 finished! INFO @ Mon, 03 Jun 2019 14:19:05: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 14:19:05: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 03 Jun 2019 14:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.20_model.r INFO @ Mon, 03 Jun 2019 14:19:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:19:06: 10000000 INFO @ Mon, 03 Jun 2019 14:19:14: 11000000 INFO @ Mon, 03 Jun 2019 14:19:20: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 14:19:20: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 14:19:20: #1 total tags in treatment: 11708458 INFO @ Mon, 03 Jun 2019 14:19:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:19:20: #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 14:19:20: #1 tags after filtering in treatment: 11708458 INFO @ Mon, 03 Jun 2019 14:19:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:19:20: #1 finished! INFO @ Mon, 03 Jun 2019 14:19:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:19:22: #2 number of paired peaks: 319 WARNING @ Mon, 03 Jun 2019 14:19:22: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Mon, 03 Jun 2019 14:19:22: start model_add_line... INFO @ Mon, 03 Jun 2019 14:19:22: start X-correlation... INFO @ Mon, 03 Jun 2019 14:19:22: end of X-cor INFO @ Mon, 03 Jun 2019 14:19:22: #2 finished! INFO @ Mon, 03 Jun 2019 14:19:22: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 14:19:22: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 03 Jun 2019 14:19:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.10_model.r INFO @ Mon, 03 Jun 2019 14:19:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:19:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:19:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:19:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:19:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:19:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:19:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:19:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.20_summits.bed INFO @ Mon, 03 Jun 2019 14:19:54: Done! INFO @ Mon, 03 Jun 2019 14:19:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:19:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.05_summits.bed INFO @ Mon, 03 Jun 2019 14:19:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1481 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4574 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:19:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:20:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:20:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:20:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX348467/SRX348467.10_summits.bed INFO @ Mon, 03 Jun 2019 14:20:12: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2680 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。