Job ID = 1294045 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,803,066 reads read : 11,606,132 reads written : 11,606,132 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: 00:00:01 Multiseed full-index search: 00:13:52 5803066 reads; of these: 5803066 (100.00%) were paired; of these: 1108755 (19.11%) aligned concordantly 0 times 3904574 (67.28%) aligned concordantly exactly 1 time 789737 (13.61%) aligned concordantly >1 times ---- 1108755 pairs aligned concordantly 0 times; of these: 472234 (42.59%) aligned discordantly 1 time ---- 636521 pairs aligned 0 times concordantly or discordantly; of these: 1273042 mates make up the pairs; of these: 856873 (67.31%) aligned 0 times 176183 (13.84%) aligned exactly 1 time 239986 (18.85%) aligned >1 times 92.62% overall alignment rate Time searching: 00:13:53 Overall time: 00:13:53 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 223673 / 5160378 = 0.0433 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 04:48:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.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 04:48:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:48:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:48:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.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 04:48:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:48:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:48:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.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 04:48:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:48:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:48:13: 1000000 INFO @ Mon, 03 Jun 2019 04:48:13: 1000000 INFO @ Mon, 03 Jun 2019 04:48:16: 1000000 INFO @ Mon, 03 Jun 2019 04:48:24: 2000000 INFO @ Mon, 03 Jun 2019 04:48:24: 2000000 INFO @ Mon, 03 Jun 2019 04:48:29: 2000000 INFO @ Mon, 03 Jun 2019 04:48:35: 3000000 INFO @ Mon, 03 Jun 2019 04:48:35: 3000000 INFO @ Mon, 03 Jun 2019 04:48:42: 3000000 INFO @ Mon, 03 Jun 2019 04:48:46: 4000000 INFO @ Mon, 03 Jun 2019 04:48:46: 4000000 INFO @ Mon, 03 Jun 2019 04:48:55: 4000000 INFO @ Mon, 03 Jun 2019 04:48:56: 5000000 INFO @ Mon, 03 Jun 2019 04:48:56: 5000000 INFO @ Mon, 03 Jun 2019 04:49:07: 6000000 INFO @ Mon, 03 Jun 2019 04:49:07: 6000000 INFO @ Mon, 03 Jun 2019 04:49:08: 5000000 INFO @ Mon, 03 Jun 2019 04:49:18: 7000000 INFO @ Mon, 03 Jun 2019 04:49:18: 7000000 INFO @ Mon, 03 Jun 2019 04:49:21: 6000000 INFO @ Mon, 03 Jun 2019 04:49:28: 8000000 INFO @ Mon, 03 Jun 2019 04:49:28: 8000000 INFO @ Mon, 03 Jun 2019 04:49:34: 7000000 INFO @ Mon, 03 Jun 2019 04:49:39: 9000000 INFO @ Mon, 03 Jun 2019 04:49:39: 9000000 INFO @ Mon, 03 Jun 2019 04:49:46: 8000000 INFO @ Mon, 03 Jun 2019 04:49:49: 10000000 INFO @ Mon, 03 Jun 2019 04:49:49: 10000000 INFO @ Mon, 03 Jun 2019 04:49:52: #1 tag size is determined as 80 bps INFO @ Mon, 03 Jun 2019 04:49:52: #1 tag size = 80 INFO @ Mon, 03 Jun 2019 04:49:52: #1 total tags in treatment: 4479711 INFO @ Mon, 03 Jun 2019 04:49:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:49:52: #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 04:49:53: #1 tags after filtering in treatment: 4248319 INFO @ Mon, 03 Jun 2019 04:49:53: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:49:53: #1 finished! INFO @ Mon, 03 Jun 2019 04:49:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:49:53: #1 tag size is determined as 80 bps INFO @ Mon, 03 Jun 2019 04:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:49:53: #1 tag size = 80 INFO @ Mon, 03 Jun 2019 04:49:53: #1 total tags in treatment: 4479711 INFO @ Mon, 03 Jun 2019 04:49:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:49:53: #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 04:49:53: #1 tags after filtering in treatment: 4248319 INFO @ Mon, 03 Jun 2019 04:49:53: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:49:53: #1 finished! INFO @ Mon, 03 Jun 2019 04:49:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:49:53: #2 number of paired peaks: 2885 INFO @ Mon, 03 Jun 2019 04:49:53: start model_add_line... INFO @ Mon, 03 Jun 2019 04:49:53: start X-correlation... INFO @ Mon, 03 Jun 2019 04:49:53: end of X-cor INFO @ Mon, 03 Jun 2019 04:49:53: #2 finished! INFO @ Mon, 03 Jun 2019 04:49:53: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 04:49:53: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 03 Jun 2019 04:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.05_model.r INFO @ Mon, 03 Jun 2019 04:49:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:49:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:49:53: #2 number of paired peaks: 2885 INFO @ Mon, 03 Jun 2019 04:49:53: start model_add_line... INFO @ Mon, 03 Jun 2019 04:49:53: start X-correlation... INFO @ Mon, 03 Jun 2019 04:49:53: end of X-cor INFO @ Mon, 03 Jun 2019 04:49:53: #2 finished! INFO @ Mon, 03 Jun 2019 04:49:53: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 04:49:53: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 03 Jun 2019 04:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.10_model.r INFO @ Mon, 03 Jun 2019 04:49:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:49:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:49:59: 9000000 INFO @ Mon, 03 Jun 2019 04:50:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:50:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:50:11: 10000000 INFO @ Mon, 03 Jun 2019 04:50:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:50:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:50:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:50:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.10_summits.bed INFO @ Mon, 03 Jun 2019 04:50:14: Done! INFO @ Mon, 03 Jun 2019 04:50:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:50:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.05_summits.bed INFO @ Mon, 03 Jun 2019 04:50:14: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3759 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5317 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:50:14: #1 tag size is determined as 80 bps INFO @ Mon, 03 Jun 2019 04:50:14: #1 tag size = 80 INFO @ Mon, 03 Jun 2019 04:50:14: #1 total tags in treatment: 4479711 INFO @ Mon, 03 Jun 2019 04:50:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:50:14: #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 04:50:15: #1 tags after filtering in treatment: 4248319 INFO @ Mon, 03 Jun 2019 04:50:15: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:50:15: #1 finished! INFO @ Mon, 03 Jun 2019 04:50:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:50:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:50:15: #2 number of paired peaks: 2885 INFO @ Mon, 03 Jun 2019 04:50:15: start model_add_line... INFO @ Mon, 03 Jun 2019 04:50:15: start X-correlation... INFO @ Mon, 03 Jun 2019 04:50:15: end of X-cor INFO @ Mon, 03 Jun 2019 04:50:15: #2 finished! INFO @ Mon, 03 Jun 2019 04:50:15: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 04:50:15: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 03 Jun 2019 04:50:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.20_model.r INFO @ Mon, 03 Jun 2019 04:50:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:50:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:50:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:50:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:50:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:50:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763410/SRX1763410.20_summits.bed INFO @ Mon, 03 Jun 2019 04:50:37: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2374 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。