Job ID = 1294604 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,220,535 reads read : 14,220,535 reads written : 14,220,535 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: 00:03:35 14220535 reads; of these: 14220535 (100.00%) were unpaired; of these: 3430332 (24.12%) aligned 0 times 9738850 (68.48%) aligned exactly 1 time 1051353 (7.39%) aligned >1 times 75.88% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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 8 files... [bam_rmdupse_core] 1460846 / 10790203 = 0.1354 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 09:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.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 09:23:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:23:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.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 09:23:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:23:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.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 09:23:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:23:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:23:56: 1000000 INFO @ Mon, 03 Jun 2019 09:23:56: 1000000 INFO @ Mon, 03 Jun 2019 09:23:57: 1000000 INFO @ Mon, 03 Jun 2019 09:24:02: 2000000 INFO @ Mon, 03 Jun 2019 09:24:03: 2000000 INFO @ Mon, 03 Jun 2019 09:24:05: 2000000 INFO @ Mon, 03 Jun 2019 09:24:09: 3000000 INFO @ Mon, 03 Jun 2019 09:24:10: 3000000 INFO @ Mon, 03 Jun 2019 09:24:12: 3000000 INFO @ Mon, 03 Jun 2019 09:24:17: 4000000 INFO @ Mon, 03 Jun 2019 09:24:18: 4000000 INFO @ Mon, 03 Jun 2019 09:24:20: 4000000 INFO @ Mon, 03 Jun 2019 09:24:24: 5000000 INFO @ Mon, 03 Jun 2019 09:24:25: 5000000 INFO @ Mon, 03 Jun 2019 09:24:27: 5000000 INFO @ Mon, 03 Jun 2019 09:24:31: 6000000 INFO @ Mon, 03 Jun 2019 09:24:32: 6000000 INFO @ Mon, 03 Jun 2019 09:24:34: 6000000 INFO @ Mon, 03 Jun 2019 09:24:38: 7000000 INFO @ Mon, 03 Jun 2019 09:24:40: 7000000 INFO @ Mon, 03 Jun 2019 09:24:42: 7000000 INFO @ Mon, 03 Jun 2019 09:24:46: 8000000 INFO @ Mon, 03 Jun 2019 09:24:47: 8000000 INFO @ Mon, 03 Jun 2019 09:24:49: 8000000 INFO @ Mon, 03 Jun 2019 09:24:54: 9000000 INFO @ Mon, 03 Jun 2019 09:24:55: 9000000 INFO @ Mon, 03 Jun 2019 09:24:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:24:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:24:56: #1 total tags in treatment: 9329357 INFO @ Mon, 03 Jun 2019 09:24:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:24:56: #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 09:24:57: #1 tags after filtering in treatment: 9329357 INFO @ Mon, 03 Jun 2019 09:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:24:57: #1 finished! INFO @ Mon, 03 Jun 2019 09:24:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:24:57: 9000000 INFO @ Mon, 03 Jun 2019 09:24:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:24:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:24:57: #1 total tags in treatment: 9329357 INFO @ Mon, 03 Jun 2019 09:24:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:24:57: #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 09:24:57: #1 tags after filtering in treatment: 9329357 INFO @ Mon, 03 Jun 2019 09:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:24:57: #1 finished! INFO @ Mon, 03 Jun 2019 09:24:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:24:57: #2 number of paired peaks: 721 WARNING @ Mon, 03 Jun 2019 09:24:57: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Mon, 03 Jun 2019 09:24:57: start model_add_line... INFO @ Mon, 03 Jun 2019 09:24:58: start X-correlation... INFO @ Mon, 03 Jun 2019 09:24:58: end of X-cor INFO @ Mon, 03 Jun 2019 09:24:58: #2 finished! INFO @ Mon, 03 Jun 2019 09:24:58: #2 predicted fragment length is 232 bps INFO @ Mon, 03 Jun 2019 09:24:58: #2 alternative fragment length(s) may be 3,169,213,232,249 bps INFO @ Mon, 03 Jun 2019 09:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.05_model.r INFO @ Mon, 03 Jun 2019 09:24:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:24:58: #2 number of paired peaks: 721 WARNING @ Mon, 03 Jun 2019 09:24:58: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Mon, 03 Jun 2019 09:24:58: start model_add_line... INFO @ Mon, 03 Jun 2019 09:24:58: start X-correlation... INFO @ Mon, 03 Jun 2019 09:24:58: end of X-cor INFO @ Mon, 03 Jun 2019 09:24:58: #2 finished! INFO @ Mon, 03 Jun 2019 09:24:58: #2 predicted fragment length is 232 bps INFO @ Mon, 03 Jun 2019 09:24:58: #2 alternative fragment length(s) may be 3,169,213,232,249 bps INFO @ Mon, 03 Jun 2019 09:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.10_model.r INFO @ Mon, 03 Jun 2019 09:24:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:24:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:24:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:24:59: #1 total tags in treatment: 9329357 INFO @ Mon, 03 Jun 2019 09:24:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:24:59: #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 09:25:00: #1 tags after filtering in treatment: 9329357 INFO @ Mon, 03 Jun 2019 09:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:25:00: #1 finished! INFO @ Mon, 03 Jun 2019 09:25:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:25:01: #2 number of paired peaks: 721 WARNING @ Mon, 03 Jun 2019 09:25:01: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Mon, 03 Jun 2019 09:25:01: start model_add_line... INFO @ Mon, 03 Jun 2019 09:25:01: start X-correlation... INFO @ Mon, 03 Jun 2019 09:25:01: end of X-cor INFO @ Mon, 03 Jun 2019 09:25:01: #2 finished! INFO @ Mon, 03 Jun 2019 09:25:01: #2 predicted fragment length is 232 bps INFO @ Mon, 03 Jun 2019 09:25:01: #2 alternative fragment length(s) may be 3,169,213,232,249 bps INFO @ Mon, 03 Jun 2019 09:25:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.20_model.r INFO @ Mon, 03 Jun 2019 09:25:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:25:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:25:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:25:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:25:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:25:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:25:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:25:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.10_summits.bed INFO @ Mon, 03 Jun 2019 09:25:42: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:25:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:25:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:25:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.05_summits.bed INFO @ Mon, 03 Jun 2019 09:25:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3112 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:25:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:25:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287772/SRX287772.20_summits.bed INFO @ Mon, 03 Jun 2019 09:25:46: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (353 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。