Job ID = 2590313 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,083,661 reads read : 21,083,661 reads written : 21,083,661 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:02 21083661 reads; of these: 21083661 (100.00%) were unpaired; of these: 3052921 (14.48%) aligned 0 times 14306378 (67.86%) aligned exactly 1 time 3724362 (17.66%) aligned >1 times 85.52% overall alignment rate Time searching: 00:07:03 Overall time: 00:07:03 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] 6700014 / 18030740 = 0.3716 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, 12 Aug 2019 21:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.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, 12 Aug 2019 21:00:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:00:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:00:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.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, 12 Aug 2019 21:00:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:00:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.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, 12 Aug 2019 21:00:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:00:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:01:05: 1000000 INFO @ Mon, 12 Aug 2019 21:01:06: 1000000 INFO @ Mon, 12 Aug 2019 21:01:07: 1000000 INFO @ Mon, 12 Aug 2019 21:01:15: 2000000 INFO @ Mon, 12 Aug 2019 21:01:16: 2000000 INFO @ Mon, 12 Aug 2019 21:01:18: 2000000 INFO @ Mon, 12 Aug 2019 21:01:24: 3000000 INFO @ Mon, 12 Aug 2019 21:01:28: 3000000 INFO @ Mon, 12 Aug 2019 21:01:30: 3000000 INFO @ Mon, 12 Aug 2019 21:01:32: 4000000 INFO @ Mon, 12 Aug 2019 21:01:39: 4000000 INFO @ Mon, 12 Aug 2019 21:01:40: 5000000 INFO @ Mon, 12 Aug 2019 21:01:41: 4000000 INFO @ Mon, 12 Aug 2019 21:01:48: 6000000 INFO @ Mon, 12 Aug 2019 21:01:50: 5000000 INFO @ Mon, 12 Aug 2019 21:01:52: 5000000 INFO @ Mon, 12 Aug 2019 21:01:56: 7000000 INFO @ Mon, 12 Aug 2019 21:02:01: 6000000 INFO @ Mon, 12 Aug 2019 21:02:03: 6000000 INFO @ Mon, 12 Aug 2019 21:02:04: 8000000 INFO @ Mon, 12 Aug 2019 21:02:12: 7000000 INFO @ Mon, 12 Aug 2019 21:02:13: 9000000 INFO @ Mon, 12 Aug 2019 21:02:14: 7000000 INFO @ Mon, 12 Aug 2019 21:02:22: 10000000 INFO @ Mon, 12 Aug 2019 21:02:23: 8000000 INFO @ Mon, 12 Aug 2019 21:02:25: 8000000 INFO @ Mon, 12 Aug 2019 21:02:30: 11000000 INFO @ Mon, 12 Aug 2019 21:02:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:02:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:02:33: #1 total tags in treatment: 11330726 INFO @ Mon, 12 Aug 2019 21:02:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:02:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:02:33: #1 tags after filtering in treatment: 11330726 INFO @ Mon, 12 Aug 2019 21:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:02:33: #1 finished! INFO @ Mon, 12 Aug 2019 21:02:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:02:34: 9000000 INFO @ Mon, 12 Aug 2019 21:02:35: #2 number of paired peaks: 9950 INFO @ Mon, 12 Aug 2019 21:02:35: start model_add_line... INFO @ Mon, 12 Aug 2019 21:02:35: start X-correlation... INFO @ Mon, 12 Aug 2019 21:02:35: end of X-cor INFO @ Mon, 12 Aug 2019 21:02:35: #2 finished! INFO @ Mon, 12 Aug 2019 21:02:35: #2 predicted fragment length is 234 bps INFO @ Mon, 12 Aug 2019 21:02:35: #2 alternative fragment length(s) may be 234 bps INFO @ Mon, 12 Aug 2019 21:02:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.20_model.r INFO @ Mon, 12 Aug 2019 21:02:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:02:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:02:35: 9000000 INFO @ Mon, 12 Aug 2019 21:02:44: 10000000 INFO @ Mon, 12 Aug 2019 21:02:45: 10000000 INFO @ Mon, 12 Aug 2019 21:02:55: 11000000 INFO @ Mon, 12 Aug 2019 21:02:56: 11000000 INFO @ Mon, 12 Aug 2019 21:02:58: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:02:58: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:02:58: #1 total tags in treatment: 11330726 INFO @ Mon, 12 Aug 2019 21:02:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:02:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:02:58: #1 tags after filtering in treatment: 11330726 INFO @ Mon, 12 Aug 2019 21:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:02:58: #1 finished! INFO @ Mon, 12 Aug 2019 21:02:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:03:00: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:03:00: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:03:00: #1 total tags in treatment: 11330726 INFO @ Mon, 12 Aug 2019 21:03:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:03:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:03:00: #1 tags after filtering in treatment: 11330726 INFO @ Mon, 12 Aug 2019 21:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:03:00: #1 finished! INFO @ Mon, 12 Aug 2019 21:03:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:03:00: #2 number of paired peaks: 9950 INFO @ Mon, 12 Aug 2019 21:03:00: start model_add_line... INFO @ Mon, 12 Aug 2019 21:03:01: start X-correlation... INFO @ Mon, 12 Aug 2019 21:03:01: end of X-cor INFO @ Mon, 12 Aug 2019 21:03:01: #2 finished! INFO @ Mon, 12 Aug 2019 21:03:01: #2 predicted fragment length is 234 bps INFO @ Mon, 12 Aug 2019 21:03:01: #2 alternative fragment length(s) may be 234 bps INFO @ Mon, 12 Aug 2019 21:03:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.05_model.r INFO @ Mon, 12 Aug 2019 21:03:01: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:03:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:03:02: #2 number of paired peaks: 9950 INFO @ Mon, 12 Aug 2019 21:03:02: start model_add_line... INFO @ Mon, 12 Aug 2019 21:03:02: start X-correlation... INFO @ Mon, 12 Aug 2019 21:03:02: end of X-cor INFO @ Mon, 12 Aug 2019 21:03:02: #2 finished! INFO @ Mon, 12 Aug 2019 21:03:02: #2 predicted fragment length is 234 bps INFO @ Mon, 12 Aug 2019 21:03:02: #2 alternative fragment length(s) may be 234 bps INFO @ Mon, 12 Aug 2019 21:03:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.10_model.r INFO @ Mon, 12 Aug 2019 21:03:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:03:23: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 21:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.20_summits.bed INFO @ Mon, 12 Aug 2019 21:03:40: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7024 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:03:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:03:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 12 Aug 2019 21:04:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:04:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:04:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.05_summits.bed INFO @ Mon, 12 Aug 2019 21:04:07: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9244 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:04:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:04:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:04:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331419/SRX331419.10_summits.bed INFO @ Mon, 12 Aug 2019 21:04:08: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8287 records, 4 fields): 16 millis CompletedMACS2peakCalling