Job ID = 1294946 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,157,899 reads read : 14,157,899 reads written : 14,157,899 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: 00:05:27 14157899 reads; of these: 14157899 (100.00%) were unpaired; of these: 1292415 (9.13%) aligned 0 times 10646982 (75.20%) aligned exactly 1 time 2218502 (15.67%) aligned >1 times 90.87% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 2664705 / 12865484 = 0.2071 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 11:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.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 11:08:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:08:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.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 11:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.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 11:08:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:08:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:08:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:08:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:08:14: 1000000 INFO @ Mon, 03 Jun 2019 11:08:15: 1000000 INFO @ Mon, 03 Jun 2019 11:08:15: 1000000 INFO @ Mon, 03 Jun 2019 11:08:23: 2000000 INFO @ Mon, 03 Jun 2019 11:08:24: 2000000 INFO @ Mon, 03 Jun 2019 11:08:24: 2000000 INFO @ Mon, 03 Jun 2019 11:08:31: 3000000 INFO @ Mon, 03 Jun 2019 11:08:33: 3000000 INFO @ Mon, 03 Jun 2019 11:08:33: 3000000 INFO @ Mon, 03 Jun 2019 11:08:39: 4000000 INFO @ Mon, 03 Jun 2019 11:08:42: 4000000 INFO @ Mon, 03 Jun 2019 11:08:42: 4000000 INFO @ Mon, 03 Jun 2019 11:08:47: 5000000 INFO @ Mon, 03 Jun 2019 11:08:51: 5000000 INFO @ Mon, 03 Jun 2019 11:08:51: 5000000 INFO @ Mon, 03 Jun 2019 11:08:55: 6000000 INFO @ Mon, 03 Jun 2019 11:09:00: 6000000 INFO @ Mon, 03 Jun 2019 11:09:00: 6000000 INFO @ Mon, 03 Jun 2019 11:09:03: 7000000 INFO @ Mon, 03 Jun 2019 11:09:08: 7000000 INFO @ Mon, 03 Jun 2019 11:09:08: 7000000 INFO @ Mon, 03 Jun 2019 11:09:11: 8000000 INFO @ Mon, 03 Jun 2019 11:09:17: 8000000 INFO @ Mon, 03 Jun 2019 11:09:17: 8000000 INFO @ Mon, 03 Jun 2019 11:09:19: 9000000 INFO @ Mon, 03 Jun 2019 11:09:26: 9000000 INFO @ Mon, 03 Jun 2019 11:09:26: 9000000 INFO @ Mon, 03 Jun 2019 11:09:27: 10000000 INFO @ Mon, 03 Jun 2019 11:09:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:09:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:09:29: #1 total tags in treatment: 10200779 INFO @ Mon, 03 Jun 2019 11:09:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:09:29: #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 11:09:29: #1 tags after filtering in treatment: 10200779 INFO @ Mon, 03 Jun 2019 11:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:09:29: #1 finished! INFO @ Mon, 03 Jun 2019 11:09:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:09:31: #2 number of paired peaks: 4392 INFO @ Mon, 03 Jun 2019 11:09:31: start model_add_line... INFO @ Mon, 03 Jun 2019 11:09:31: start X-correlation... INFO @ Mon, 03 Jun 2019 11:09:31: end of X-cor INFO @ Mon, 03 Jun 2019 11:09:31: #2 finished! INFO @ Mon, 03 Jun 2019 11:09:31: #2 predicted fragment length is 245 bps INFO @ Mon, 03 Jun 2019 11:09:31: #2 alternative fragment length(s) may be 245 bps INFO @ Mon, 03 Jun 2019 11:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.05_model.r INFO @ Mon, 03 Jun 2019 11:09:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:09:35: 10000000 INFO @ Mon, 03 Jun 2019 11:09:35: 10000000 INFO @ Mon, 03 Jun 2019 11:09:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:09:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:09:37: #1 total tags in treatment: 10200779 INFO @ Mon, 03 Jun 2019 11:09:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:09:37: #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 11:09:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:09:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:09:37: #1 total tags in treatment: 10200779 INFO @ Mon, 03 Jun 2019 11:09:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:09:37: #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 11:09:37: #1 tags after filtering in treatment: 10200779 INFO @ Mon, 03 Jun 2019 11:09:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:09:37: #1 finished! INFO @ Mon, 03 Jun 2019 11:09:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:09:37: #1 tags after filtering in treatment: 10200779 INFO @ Mon, 03 Jun 2019 11:09:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:09:37: #1 finished! INFO @ Mon, 03 Jun 2019 11:09:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:09:38: #2 number of paired peaks: 4392 INFO @ Mon, 03 Jun 2019 11:09:38: start model_add_line... INFO @ Mon, 03 Jun 2019 11:09:38: #2 number of paired peaks: 4392 INFO @ Mon, 03 Jun 2019 11:09:38: start model_add_line... INFO @ Mon, 03 Jun 2019 11:09:38: start X-correlation... INFO @ Mon, 03 Jun 2019 11:09:38: end of X-cor INFO @ Mon, 03 Jun 2019 11:09:38: #2 finished! INFO @ Mon, 03 Jun 2019 11:09:38: #2 predicted fragment length is 245 bps INFO @ Mon, 03 Jun 2019 11:09:38: #2 alternative fragment length(s) may be 245 bps INFO @ Mon, 03 Jun 2019 11:09:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.10_model.r INFO @ Mon, 03 Jun 2019 11:09:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:09:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:09:38: start X-correlation... INFO @ Mon, 03 Jun 2019 11:09:39: end of X-cor INFO @ Mon, 03 Jun 2019 11:09:39: #2 finished! INFO @ Mon, 03 Jun 2019 11:09:39: #2 predicted fragment length is 245 bps INFO @ Mon, 03 Jun 2019 11:09:39: #2 alternative fragment length(s) may be 245 bps INFO @ Mon, 03 Jun 2019 11:09:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.20_model.r INFO @ Mon, 03 Jun 2019 11:09:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:09:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:10:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:10:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:10:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:10:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:10:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:10:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.05_summits.bed INFO @ Mon, 03 Jun 2019 11:10:26: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7816 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:10:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:10:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:10:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.20_summits.bed INFO @ Mon, 03 Jun 2019 11:10:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4696 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:10:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:10:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:10:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288010/SRX288010.10_summits.bed INFO @ Mon, 03 Jun 2019 11:10:34: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6229 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。