Job ID = 1294065 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,615,065 reads read : 21,615,065 reads written : 21,615,065 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: 00:04:44 21615065 reads; of these: 21615065 (100.00%) were unpaired; of these: 2907718 (13.45%) aligned 0 times 16490090 (76.29%) aligned exactly 1 time 2217257 (10.26%) aligned >1 times 86.55% overall alignment rate Time searching: 00:04:44 Overall time: 00:04:44 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] 7789536 / 18707347 = 0.4164 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 04:41:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.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 04:41:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:41:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:41:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.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 04:41:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:41:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:41:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.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 04:41:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:41:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:41:36: 1000000 INFO @ Mon, 03 Jun 2019 04:41:37: 1000000 INFO @ Mon, 03 Jun 2019 04:41:38: 1000000 INFO @ Mon, 03 Jun 2019 04:41:44: 2000000 INFO @ Mon, 03 Jun 2019 04:41:44: 2000000 INFO @ Mon, 03 Jun 2019 04:41:47: 2000000 INFO @ Mon, 03 Jun 2019 04:41:51: 3000000 INFO @ Mon, 03 Jun 2019 04:41:51: 3000000 INFO @ Mon, 03 Jun 2019 04:41:56: 3000000 INFO @ Mon, 03 Jun 2019 04:41:57: 4000000 INFO @ Mon, 03 Jun 2019 04:41:58: 4000000 INFO @ Mon, 03 Jun 2019 04:42:04: 5000000 INFO @ Mon, 03 Jun 2019 04:42:04: 4000000 INFO @ Mon, 03 Jun 2019 04:42:05: 5000000 INFO @ Mon, 03 Jun 2019 04:42:10: 6000000 INFO @ Mon, 03 Jun 2019 04:42:12: 6000000 INFO @ Mon, 03 Jun 2019 04:42:12: 5000000 INFO @ Mon, 03 Jun 2019 04:42:16: 7000000 INFO @ Mon, 03 Jun 2019 04:42:19: 7000000 INFO @ Mon, 03 Jun 2019 04:42:21: 6000000 INFO @ Mon, 03 Jun 2019 04:42:23: 8000000 INFO @ Mon, 03 Jun 2019 04:42:25: 8000000 INFO @ Mon, 03 Jun 2019 04:42:29: 7000000 INFO @ Mon, 03 Jun 2019 04:42:29: 9000000 INFO @ Mon, 03 Jun 2019 04:42:32: 9000000 INFO @ Mon, 03 Jun 2019 04:42:35: 10000000 INFO @ Mon, 03 Jun 2019 04:42:37: 8000000 INFO @ Mon, 03 Jun 2019 04:42:39: 10000000 INFO @ Mon, 03 Jun 2019 04:42:41: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:42:41: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:42:41: #1 total tags in treatment: 10917811 INFO @ Mon, 03 Jun 2019 04:42:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:42:41: #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 04:42:41: #1 tags after filtering in treatment: 10917811 INFO @ Mon, 03 Jun 2019 04:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:42:41: #1 finished! INFO @ Mon, 03 Jun 2019 04:42:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:42:42: #2 number of paired peaks: 776 WARNING @ Mon, 03 Jun 2019 04:42:42: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 03 Jun 2019 04:42:42: start model_add_line... INFO @ Mon, 03 Jun 2019 04:42:42: start X-correlation... INFO @ Mon, 03 Jun 2019 04:42:42: end of X-cor INFO @ Mon, 03 Jun 2019 04:42:42: #2 finished! INFO @ Mon, 03 Jun 2019 04:42:42: #2 predicted fragment length is 132 bps INFO @ Mon, 03 Jun 2019 04:42:42: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 03 Jun 2019 04:42:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.05_model.r INFO @ Mon, 03 Jun 2019 04:42:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:42:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:42:45: 9000000 INFO @ Mon, 03 Jun 2019 04:42:46: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:42:46: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:42:46: #1 total tags in treatment: 10917811 INFO @ Mon, 03 Jun 2019 04:42:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:42:46: #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 04:42:46: #1 tags after filtering in treatment: 10917811 INFO @ Mon, 03 Jun 2019 04:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:42:46: #1 finished! INFO @ Mon, 03 Jun 2019 04:42:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:42:47: #2 number of paired peaks: 776 WARNING @ Mon, 03 Jun 2019 04:42:47: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 03 Jun 2019 04:42:47: start model_add_line... INFO @ Mon, 03 Jun 2019 04:42:47: start X-correlation... INFO @ Mon, 03 Jun 2019 04:42:47: end of X-cor INFO @ Mon, 03 Jun 2019 04:42:47: #2 finished! INFO @ Mon, 03 Jun 2019 04:42:47: #2 predicted fragment length is 132 bps INFO @ Mon, 03 Jun 2019 04:42:47: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 03 Jun 2019 04:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.20_model.r INFO @ Mon, 03 Jun 2019 04:42:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:42:53: 10000000 INFO @ Mon, 03 Jun 2019 04:43:00: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:43:00: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:43:00: #1 total tags in treatment: 10917811 INFO @ Mon, 03 Jun 2019 04:43:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:43:00: #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 04:43:01: #1 tags after filtering in treatment: 10917811 INFO @ Mon, 03 Jun 2019 04:43:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:43:01: #1 finished! INFO @ Mon, 03 Jun 2019 04:43:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:43:02: #2 number of paired peaks: 776 WARNING @ Mon, 03 Jun 2019 04:43:02: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 03 Jun 2019 04:43:02: start model_add_line... INFO @ Mon, 03 Jun 2019 04:43:02: start X-correlation... INFO @ Mon, 03 Jun 2019 04:43:02: end of X-cor INFO @ Mon, 03 Jun 2019 04:43:02: #2 finished! INFO @ Mon, 03 Jun 2019 04:43:02: #2 predicted fragment length is 132 bps INFO @ Mon, 03 Jun 2019 04:43:02: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 03 Jun 2019 04:43:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.10_model.r INFO @ Mon, 03 Jun 2019 04:43:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:43:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:43:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:43:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:43:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:43:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:43:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.05_summits.bed INFO @ Mon, 03 Jun 2019 04:43:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7173 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:43:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:43:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:43:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:43:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.20_summits.bed INFO @ Mon, 03 Jun 2019 04:43:36: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1130 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181423/SRX181423.10_summits.bed INFO @ Mon, 03 Jun 2019 04:43:51: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (3550 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。