Job ID = 1294071 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,778,981 reads read : 27,778,981 reads written : 27,778,981 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: 00:05:53 27778981 reads; of these: 27778981 (100.00%) were unpaired; of these: 5352792 (19.27%) aligned 0 times 19078504 (68.68%) aligned exactly 1 time 3347685 (12.05%) aligned >1 times 80.73% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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] 16500216 / 22426189 = 0.7358 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 04:50:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.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 04:50:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:50:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:50:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.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 04:50:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:50:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:50:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.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 04:50:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:50:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:50:44: 1000000 INFO @ Mon, 03 Jun 2019 04:50:45: 1000000 INFO @ Mon, 03 Jun 2019 04:50:45: 1000000 INFO @ Mon, 03 Jun 2019 04:50:53: 2000000 INFO @ Mon, 03 Jun 2019 04:50:53: 2000000 INFO @ Mon, 03 Jun 2019 04:50:53: 2000000 INFO @ Mon, 03 Jun 2019 04:51:01: 3000000 INFO @ Mon, 03 Jun 2019 04:51:01: 3000000 INFO @ Mon, 03 Jun 2019 04:51:01: 3000000 INFO @ Mon, 03 Jun 2019 04:51:08: 4000000 INFO @ Mon, 03 Jun 2019 04:51:09: 4000000 INFO @ Mon, 03 Jun 2019 04:51:09: 4000000 INFO @ Mon, 03 Jun 2019 04:51:14: 5000000 INFO @ Mon, 03 Jun 2019 04:51:17: 5000000 INFO @ Mon, 03 Jun 2019 04:51:17: 5000000 INFO @ Mon, 03 Jun 2019 04:51:20: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:51:20: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:51:20: #1 total tags in treatment: 5925973 INFO @ Mon, 03 Jun 2019 04:51:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:51:20: #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 04:51:20: #1 tags after filtering in treatment: 5925973 INFO @ Mon, 03 Jun 2019 04:51:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:51:20: #1 finished! INFO @ Mon, 03 Jun 2019 04:51:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:51:20: #2 number of paired peaks: 175 WARNING @ Mon, 03 Jun 2019 04:51:20: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Mon, 03 Jun 2019 04:51:20: start model_add_line... INFO @ Mon, 03 Jun 2019 04:51:20: start X-correlation... INFO @ Mon, 03 Jun 2019 04:51:20: end of X-cor INFO @ Mon, 03 Jun 2019 04:51:20: #2 finished! INFO @ Mon, 03 Jun 2019 04:51:20: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 04:51:20: #2 alternative fragment length(s) may be 105 bps INFO @ Mon, 03 Jun 2019 04:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.10_model.r INFO @ Mon, 03 Jun 2019 04:51:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:51:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:51:24: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:51:24: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:51:24: #1 total tags in treatment: 5925973 INFO @ Mon, 03 Jun 2019 04:51:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:51:24: #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 04:51:24: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:51:24: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:51:24: #1 total tags in treatment: 5925973 INFO @ Mon, 03 Jun 2019 04:51:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:51:24: #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 04:51:24: #1 tags after filtering in treatment: 5925973 INFO @ Mon, 03 Jun 2019 04:51:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:51:24: #1 finished! INFO @ Mon, 03 Jun 2019 04:51:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:51:24: #1 tags after filtering in treatment: 5925973 INFO @ Mon, 03 Jun 2019 04:51:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:51:24: #1 finished! INFO @ Mon, 03 Jun 2019 04:51:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:51:25: #2 number of paired peaks: 175 WARNING @ Mon, 03 Jun 2019 04:51:25: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Mon, 03 Jun 2019 04:51:25: start model_add_line... INFO @ Mon, 03 Jun 2019 04:51:25: #2 number of paired peaks: 175 WARNING @ Mon, 03 Jun 2019 04:51:25: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Mon, 03 Jun 2019 04:51:25: start model_add_line... INFO @ Mon, 03 Jun 2019 04:51:25: start X-correlation... INFO @ Mon, 03 Jun 2019 04:51:25: end of X-cor INFO @ Mon, 03 Jun 2019 04:51:25: #2 finished! INFO @ Mon, 03 Jun 2019 04:51:25: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 04:51:25: #2 alternative fragment length(s) may be 105 bps INFO @ Mon, 03 Jun 2019 04:51:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.20_model.r INFO @ Mon, 03 Jun 2019 04:51:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:51:25: start X-correlation... INFO @ Mon, 03 Jun 2019 04:51:25: end of X-cor INFO @ Mon, 03 Jun 2019 04:51:25: #2 finished! INFO @ Mon, 03 Jun 2019 04:51:25: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 04:51:25: #2 alternative fragment length(s) may be 105 bps INFO @ Mon, 03 Jun 2019 04:51:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.05_model.r INFO @ Mon, 03 Jun 2019 04:51:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:51:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:51:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:51:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:51:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:51:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:51:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.10_summits.bed INFO @ Mon, 03 Jun 2019 04:51:47: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (634 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:51:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:51:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:51:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.05_summits.bed INFO @ Mon, 03 Jun 2019 04:51:51: Done! pass1 - making usageList (14 chroms): 1 millis INFO @ Mon, 03 Jun 2019 04:51:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.20_peaks.xls pass2 - checking and writing primary data (1706 records, 4 fields): 5 millis INFO @ Mon, 03 Jun 2019 04:51:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:51:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181429/SRX181429.20_summits.bed INFO @ Mon, 03 Jun 2019 04:51:51: Done! CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。