Job ID = 1293823 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,426,333 reads read : 4,426,333 reads written : 4,426,333 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: 00:01:12 4426333 reads; of these: 4426333 (100.00%) were unpaired; of these: 279872 (6.32%) aligned 0 times 3241428 (73.23%) aligned exactly 1 time 905033 (20.45%) aligned >1 times 93.68% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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_rmdupse_core] 257710 / 4146461 = 0.0622 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 02:41:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.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 02:41:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:41:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:41:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.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 02:41:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:41:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:41:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.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 02:41:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:41:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:41:21: 1000000 INFO @ Mon, 03 Jun 2019 02:41:22: 1000000 INFO @ Mon, 03 Jun 2019 02:41:23: 1000000 INFO @ Mon, 03 Jun 2019 02:41:28: 2000000 INFO @ Mon, 03 Jun 2019 02:41:31: 2000000 INFO @ Mon, 03 Jun 2019 02:41:33: 2000000 INFO @ Mon, 03 Jun 2019 02:41:36: 3000000 INFO @ Mon, 03 Jun 2019 02:41:39: 3000000 INFO @ Mon, 03 Jun 2019 02:41:42: 3000000 INFO @ Mon, 03 Jun 2019 02:41:43: #1 tag size is determined as 30 bps INFO @ Mon, 03 Jun 2019 02:41:43: #1 tag size = 30 INFO @ Mon, 03 Jun 2019 02:41:43: #1 total tags in treatment: 3888751 INFO @ Mon, 03 Jun 2019 02:41:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:41:43: #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 02:41:43: #1 tags after filtering in treatment: 3888751 INFO @ Mon, 03 Jun 2019 02:41:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:41:43: #1 finished! INFO @ Mon, 03 Jun 2019 02:41:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:41:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:41:44: #2 number of paired peaks: 711 WARNING @ Mon, 03 Jun 2019 02:41:44: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Mon, 03 Jun 2019 02:41:44: start model_add_line... INFO @ Mon, 03 Jun 2019 02:41:44: start X-correlation... INFO @ Mon, 03 Jun 2019 02:41:44: end of X-cor INFO @ Mon, 03 Jun 2019 02:41:44: #2 finished! INFO @ Mon, 03 Jun 2019 02:41:44: #2 predicted fragment length is 74 bps INFO @ Mon, 03 Jun 2019 02:41:44: #2 alternative fragment length(s) may be 74 bps INFO @ Mon, 03 Jun 2019 02:41:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.20_model.r INFO @ Mon, 03 Jun 2019 02:41:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:41:47: #1 tag size is determined as 30 bps INFO @ Mon, 03 Jun 2019 02:41:47: #1 tag size = 30 INFO @ Mon, 03 Jun 2019 02:41:47: #1 total tags in treatment: 3888751 INFO @ Mon, 03 Jun 2019 02:41:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:41:47: #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 02:41:47: #1 tags after filtering in treatment: 3888751 INFO @ Mon, 03 Jun 2019 02:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:41:47: #1 finished! INFO @ Mon, 03 Jun 2019 02:41:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:41:47: #2 number of paired peaks: 711 WARNING @ Mon, 03 Jun 2019 02:41:47: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Mon, 03 Jun 2019 02:41:47: start model_add_line... INFO @ Mon, 03 Jun 2019 02:41:47: start X-correlation... INFO @ Mon, 03 Jun 2019 02:41:47: end of X-cor INFO @ Mon, 03 Jun 2019 02:41:47: #2 finished! INFO @ Mon, 03 Jun 2019 02:41:47: #2 predicted fragment length is 74 bps INFO @ Mon, 03 Jun 2019 02:41:47: #2 alternative fragment length(s) may be 74 bps INFO @ Mon, 03 Jun 2019 02:41:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.05_model.r INFO @ Mon, 03 Jun 2019 02:41:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:41:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:41:52: #1 tag size is determined as 30 bps INFO @ Mon, 03 Jun 2019 02:41:52: #1 tag size = 30 INFO @ Mon, 03 Jun 2019 02:41:52: #1 total tags in treatment: 3888751 INFO @ Mon, 03 Jun 2019 02:41:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:41:52: #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 02:41:52: #1 tags after filtering in treatment: 3888751 INFO @ Mon, 03 Jun 2019 02:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:41:52: #1 finished! INFO @ Mon, 03 Jun 2019 02:41:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:41:52: #2 number of paired peaks: 711 WARNING @ Mon, 03 Jun 2019 02:41:52: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Mon, 03 Jun 2019 02:41:52: start model_add_line... INFO @ Mon, 03 Jun 2019 02:41:52: start X-correlation... INFO @ Mon, 03 Jun 2019 02:41:52: end of X-cor INFO @ Mon, 03 Jun 2019 02:41:52: #2 finished! INFO @ Mon, 03 Jun 2019 02:41:52: #2 predicted fragment length is 74 bps INFO @ Mon, 03 Jun 2019 02:41:52: #2 alternative fragment length(s) may be 74 bps INFO @ Mon, 03 Jun 2019 02:41:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.10_model.r INFO @ Mon, 03 Jun 2019 02:41:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:41:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:41:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:41:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:42:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:42:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:42:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.20_summits.bed INFO @ Mon, 03 Jun 2019 02:42:02: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (515 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:42:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.05_summits.bed INFO @ Mon, 03 Jun 2019 02:42:05: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1465 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:42:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:42:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:42:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX124480/SRX124480.10_summits.bed INFO @ Mon, 03 Jun 2019 02:42:11: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (974 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。