Job ID = 4178531 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,397,291 reads read : 20,397,291 reads written : 20,397,291 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:32 20397291 reads; of these: 20397291 (100.00%) were unpaired; of these: 2400848 (11.77%) aligned 0 times 13951433 (68.40%) aligned exactly 1 time 4045010 (19.83%) aligned >1 times 88.23% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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] 5551634 / 17996443 = 0.3085 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.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 @ Thu, 05 Dec 2019 12:59:53: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:59:53: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:00:00: 1000000 INFO @ Thu, 05 Dec 2019 13:00:07: 2000000 INFO @ Thu, 05 Dec 2019 13:00:14: 3000000 INFO @ Thu, 05 Dec 2019 13:00:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.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 @ Thu, 05 Dec 2019 13:00:23: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:00:23: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:00:23: 4000000 INFO @ Thu, 05 Dec 2019 13:00:30: 1000000 INFO @ Thu, 05 Dec 2019 13:00:31: 5000000 INFO @ Thu, 05 Dec 2019 13:00:37: 2000000 INFO @ Thu, 05 Dec 2019 13:00:40: 6000000 INFO @ Thu, 05 Dec 2019 13:00:44: 3000000 INFO @ Thu, 05 Dec 2019 13:00:49: 7000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:00:51: 4000000 INFO @ Thu, 05 Dec 2019 13:00:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.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 @ Thu, 05 Dec 2019 13:00:53: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:00:53: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:00:56: 8000000 INFO @ Thu, 05 Dec 2019 13:00:59: 5000000 INFO @ Thu, 05 Dec 2019 13:01:00: 1000000 INFO @ Thu, 05 Dec 2019 13:01:04: 9000000 INFO @ Thu, 05 Dec 2019 13:01:06: 6000000 INFO @ Thu, 05 Dec 2019 13:01:08: 2000000 INFO @ Thu, 05 Dec 2019 13:01:11: 10000000 INFO @ Thu, 05 Dec 2019 13:01:13: 7000000 INFO @ Thu, 05 Dec 2019 13:01:15: 3000000 INFO @ Thu, 05 Dec 2019 13:01:18: 11000000 INFO @ Thu, 05 Dec 2019 13:01:21: 8000000 INFO @ Thu, 05 Dec 2019 13:01:22: 4000000 INFO @ Thu, 05 Dec 2019 13:01:26: 12000000 INFO @ Thu, 05 Dec 2019 13:01:28: 9000000 INFO @ Thu, 05 Dec 2019 13:01:29: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:01:29: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:01:29: #1 total tags in treatment: 12444809 INFO @ Thu, 05 Dec 2019 13:01:29: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:01:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:01:29: #1 tags after filtering in treatment: 12444809 INFO @ Thu, 05 Dec 2019 13:01:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:01:29: #1 finished! INFO @ Thu, 05 Dec 2019 13:01:29: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:01:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:01:30: 5000000 INFO @ Thu, 05 Dec 2019 13:01:30: #2 number of paired peaks: 1951 INFO @ Thu, 05 Dec 2019 13:01:30: start model_add_line... INFO @ Thu, 05 Dec 2019 13:01:31: start X-correlation... INFO @ Thu, 05 Dec 2019 13:01:31: end of X-cor INFO @ Thu, 05 Dec 2019 13:01:31: #2 finished! INFO @ Thu, 05 Dec 2019 13:01:31: #2 predicted fragment length is 160 bps INFO @ Thu, 05 Dec 2019 13:01:31: #2 alternative fragment length(s) may be 19,46,160,246,270,295,308,492 bps INFO @ Thu, 05 Dec 2019 13:01:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.05_model.r INFO @ Thu, 05 Dec 2019 13:01:31: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:01:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:01:35: 10000000 INFO @ Thu, 05 Dec 2019 13:01:37: 6000000 INFO @ Thu, 05 Dec 2019 13:01:43: 11000000 INFO @ Thu, 05 Dec 2019 13:01:44: 7000000 INFO @ Thu, 05 Dec 2019 13:01:50: 12000000 INFO @ Thu, 05 Dec 2019 13:01:51: 8000000 INFO @ Thu, 05 Dec 2019 13:01:53: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:01:53: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:01:53: #1 total tags in treatment: 12444809 INFO @ Thu, 05 Dec 2019 13:01:53: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:01:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:01:53: #1 tags after filtering in treatment: 12444809 INFO @ Thu, 05 Dec 2019 13:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:01:53: #1 finished! INFO @ Thu, 05 Dec 2019 13:01:53: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:01:55: #2 number of paired peaks: 1951 INFO @ Thu, 05 Dec 2019 13:01:55: start model_add_line... INFO @ Thu, 05 Dec 2019 13:01:55: start X-correlation... INFO @ Thu, 05 Dec 2019 13:01:55: end of X-cor INFO @ Thu, 05 Dec 2019 13:01:55: #2 finished! INFO @ Thu, 05 Dec 2019 13:01:55: #2 predicted fragment length is 160 bps INFO @ Thu, 05 Dec 2019 13:01:55: #2 alternative fragment length(s) may be 19,46,160,246,270,295,308,492 bps INFO @ Thu, 05 Dec 2019 13:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.10_model.r INFO @ Thu, 05 Dec 2019 13:01:55: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:01:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:01:59: 9000000 INFO @ Thu, 05 Dec 2019 13:02:06: 10000000 INFO @ Thu, 05 Dec 2019 13:02:09: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:02:13: 11000000 INFO @ Thu, 05 Dec 2019 13:02:20: 12000000 INFO @ Thu, 05 Dec 2019 13:02:23: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:02:23: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:02:23: #1 total tags in treatment: 12444809 INFO @ Thu, 05 Dec 2019 13:02:23: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:02:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:02:23: #1 tags after filtering in treatment: 12444809 INFO @ Thu, 05 Dec 2019 13:02:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:02:23: #1 finished! INFO @ Thu, 05 Dec 2019 13:02:23: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:02:24: #2 number of paired peaks: 1951 INFO @ Thu, 05 Dec 2019 13:02:24: start model_add_line... INFO @ Thu, 05 Dec 2019 13:02:25: start X-correlation... INFO @ Thu, 05 Dec 2019 13:02:25: end of X-cor INFO @ Thu, 05 Dec 2019 13:02:25: #2 finished! INFO @ Thu, 05 Dec 2019 13:02:25: #2 predicted fragment length is 160 bps INFO @ Thu, 05 Dec 2019 13:02:25: #2 alternative fragment length(s) may be 19,46,160,246,270,295,308,492 bps INFO @ Thu, 05 Dec 2019 13:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.20_model.r INFO @ Thu, 05 Dec 2019 13:02:25: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:02:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.05_summits.bed INFO @ Thu, 05 Dec 2019 13:02:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2247 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:02:32: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:02:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:02:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:02:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.10_summits.bed INFO @ Thu, 05 Dec 2019 13:02:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (985 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:03:02: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:03:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:03:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:03:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717048/SRX5717048.20_summits.bed INFO @ Thu, 05 Dec 2019 13:03:19: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (350 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。