Job ID = 1293795 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,445,702 reads read : 12,445,702 reads written : 12,445,702 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: 00:03:05 12445702 reads; of these: 12445702 (100.00%) were unpaired; of these: 1110703 (8.92%) aligned 0 times 10213386 (82.06%) aligned exactly 1 time 1121613 (9.01%) aligned >1 times 91.08% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 6350448 / 11334999 = 0.5603 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 02:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.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 02:33:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:33:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.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 02:33:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:33:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.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 02:33:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:33:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:34:07: 1000000 INFO @ Mon, 03 Jun 2019 02:34:07: 1000000 INFO @ Mon, 03 Jun 2019 02:34:08: 1000000 INFO @ Mon, 03 Jun 2019 02:34:17: 2000000 INFO @ Mon, 03 Jun 2019 02:34:17: 2000000 INFO @ Mon, 03 Jun 2019 02:34:19: 2000000 INFO @ Mon, 03 Jun 2019 02:34:27: 3000000 INFO @ Mon, 03 Jun 2019 02:34:27: 3000000 INFO @ Mon, 03 Jun 2019 02:34:29: 3000000 INFO @ Mon, 03 Jun 2019 02:34:37: 4000000 INFO @ Mon, 03 Jun 2019 02:34:37: 4000000 INFO @ Mon, 03 Jun 2019 02:34:39: 4000000 INFO @ Mon, 03 Jun 2019 02:34:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:34:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:34:46: #1 total tags in treatment: 4984551 INFO @ Mon, 03 Jun 2019 02:34:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:34:46: #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 02:34:46: #1 tags after filtering in treatment: 4984551 INFO @ Mon, 03 Jun 2019 02:34:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:34:46: #1 finished! INFO @ Mon, 03 Jun 2019 02:34:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:34:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:34:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:34:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:34:47: #1 total tags in treatment: 4984551 INFO @ Mon, 03 Jun 2019 02:34:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:34:47: #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 02:34:47: #1 tags after filtering in treatment: 4984551 INFO @ Mon, 03 Jun 2019 02:34:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:34:47: #1 finished! INFO @ Mon, 03 Jun 2019 02:34:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:34:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:34:47: #2 number of paired peaks: 6334 INFO @ Mon, 03 Jun 2019 02:34:47: start model_add_line... INFO @ Mon, 03 Jun 2019 02:34:47: start X-correlation... INFO @ Mon, 03 Jun 2019 02:34:48: end of X-cor INFO @ Mon, 03 Jun 2019 02:34:48: #2 finished! INFO @ Mon, 03 Jun 2019 02:34:48: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 02:34:48: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 02:34:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.20_model.r INFO @ Mon, 03 Jun 2019 02:34:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:34:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:34:48: #2 number of paired peaks: 6334 INFO @ Mon, 03 Jun 2019 02:34:48: start model_add_line... INFO @ Mon, 03 Jun 2019 02:34:48: start X-correlation... INFO @ Mon, 03 Jun 2019 02:34:48: end of X-cor INFO @ Mon, 03 Jun 2019 02:34:48: #2 finished! INFO @ Mon, 03 Jun 2019 02:34:48: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 02:34:48: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 02:34:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.05_model.r INFO @ Mon, 03 Jun 2019 02:34:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:34:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:34:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:34:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:34:49: #1 total tags in treatment: 4984551 INFO @ Mon, 03 Jun 2019 02:34:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:34:49: #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 02:34:49: #1 tags after filtering in treatment: 4984551 INFO @ Mon, 03 Jun 2019 02:34:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:34:49: #1 finished! INFO @ Mon, 03 Jun 2019 02:34:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:34:50: #2 number of paired peaks: 6334 INFO @ Mon, 03 Jun 2019 02:34:50: start model_add_line... INFO @ Mon, 03 Jun 2019 02:34:50: start X-correlation... INFO @ Mon, 03 Jun 2019 02:34:50: end of X-cor INFO @ Mon, 03 Jun 2019 02:34:50: #2 finished! INFO @ Mon, 03 Jun 2019 02:34:50: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 02:34:50: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 02:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.10_model.r INFO @ Mon, 03 Jun 2019 02:34:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:35:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:35:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:35:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:35:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:35:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:35:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.20_summits.bed INFO @ Mon, 03 Jun 2019 02:35:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3409 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:35:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:35:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:35:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.05_summits.bed INFO @ Mon, 03 Jun 2019 02:35:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5785 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 02:35:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:35:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:35:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134696/SRX1134696.10_summits.bed INFO @ Mon, 03 Jun 2019 02:35:22: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4598 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。