Job ID = 1294039 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,152,864 reads read : 10,305,728 reads written : 10,305,728 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: 00:11:04 5152864 reads; of these: 5152864 (100.00%) were paired; of these: 1108205 (21.51%) aligned concordantly 0 times 3405735 (66.09%) aligned concordantly exactly 1 time 638924 (12.40%) aligned concordantly >1 times ---- 1108205 pairs aligned concordantly 0 times; of these: 327985 (29.60%) aligned discordantly 1 time ---- 780220 pairs aligned 0 times concordantly or discordantly; of these: 1560440 mates make up the pairs; of these: 1262898 (80.93%) aligned 0 times 134127 (8.60%) aligned exactly 1 time 163415 (10.47%) aligned >1 times 87.75% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 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_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] 169298 / 4364636 = 0.0388 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 04:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.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 04:37:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:37:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.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 04:37:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:37:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.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 04:37:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:37:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:38:06: 1000000 INFO @ Mon, 03 Jun 2019 04:38:06: 1000000 INFO @ Mon, 03 Jun 2019 04:38:06: 1000000 INFO @ Mon, 03 Jun 2019 04:38:15: 2000000 INFO @ Mon, 03 Jun 2019 04:38:15: 2000000 INFO @ Mon, 03 Jun 2019 04:38:15: 2000000 INFO @ Mon, 03 Jun 2019 04:38:24: 3000000 INFO @ Mon, 03 Jun 2019 04:38:25: 3000000 INFO @ Mon, 03 Jun 2019 04:38:25: 3000000 INFO @ Mon, 03 Jun 2019 04:38:33: 4000000 INFO @ Mon, 03 Jun 2019 04:38:34: 4000000 INFO @ Mon, 03 Jun 2019 04:38:34: 4000000 INFO @ Mon, 03 Jun 2019 04:38:42: 5000000 INFO @ Mon, 03 Jun 2019 04:38:44: 5000000 INFO @ Mon, 03 Jun 2019 04:38:44: 5000000 INFO @ Mon, 03 Jun 2019 04:38:50: 6000000 INFO @ Mon, 03 Jun 2019 04:38:53: 6000000 INFO @ Mon, 03 Jun 2019 04:38:53: 6000000 INFO @ Mon, 03 Jun 2019 04:38:59: 7000000 INFO @ Mon, 03 Jun 2019 04:39:03: 7000000 INFO @ Mon, 03 Jun 2019 04:39:03: 7000000 INFO @ Mon, 03 Jun 2019 04:39:09: 8000000 INFO @ Mon, 03 Jun 2019 04:39:12: 8000000 INFO @ Mon, 03 Jun 2019 04:39:12: 8000000 INFO @ Mon, 03 Jun 2019 04:39:16: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:39:16: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:39:16: #1 total tags in treatment: 3880844 INFO @ Mon, 03 Jun 2019 04:39:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:39:16: #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 04:39:16: #1 tags after filtering in treatment: 3680304 INFO @ Mon, 03 Jun 2019 04:39:16: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:39:16: #1 finished! INFO @ Mon, 03 Jun 2019 04:39:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:39:16: #2 number of paired peaks: 3364 INFO @ Mon, 03 Jun 2019 04:39:16: start model_add_line... INFO @ Mon, 03 Jun 2019 04:39:17: start X-correlation... INFO @ Mon, 03 Jun 2019 04:39:17: end of X-cor INFO @ Mon, 03 Jun 2019 04:39:17: #2 finished! INFO @ Mon, 03 Jun 2019 04:39:17: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 04:39:17: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 03 Jun 2019 04:39:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.05_model.r INFO @ Mon, 03 Jun 2019 04:39:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:39:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:39:19: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:39:19: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:39:19: #1 total tags in treatment: 3880844 INFO @ Mon, 03 Jun 2019 04:39:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:39:19: #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 04:39:19: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:39:19: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:39:19: #1 total tags in treatment: 3880844 INFO @ Mon, 03 Jun 2019 04:39:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:39:19: #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 04:39:19: #1 tags after filtering in treatment: 3680304 INFO @ Mon, 03 Jun 2019 04:39:19: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:39:19: #1 finished! INFO @ Mon, 03 Jun 2019 04:39:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:39:19: #1 tags after filtering in treatment: 3680304 INFO @ Mon, 03 Jun 2019 04:39:19: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:39:19: #1 finished! INFO @ Mon, 03 Jun 2019 04:39:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:39:20: #2 number of paired peaks: 3364 INFO @ Mon, 03 Jun 2019 04:39:20: start model_add_line... INFO @ Mon, 03 Jun 2019 04:39:20: #2 number of paired peaks: 3364 INFO @ Mon, 03 Jun 2019 04:39:20: start model_add_line... INFO @ Mon, 03 Jun 2019 04:39:20: start X-correlation... INFO @ Mon, 03 Jun 2019 04:39:20: end of X-cor INFO @ Mon, 03 Jun 2019 04:39:20: #2 finished! INFO @ Mon, 03 Jun 2019 04:39:20: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 04:39:20: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 03 Jun 2019 04:39:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.10_model.r INFO @ Mon, 03 Jun 2019 04:39:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:39:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:39:20: start X-correlation... INFO @ Mon, 03 Jun 2019 04:39:20: end of X-cor INFO @ Mon, 03 Jun 2019 04:39:20: #2 finished! INFO @ Mon, 03 Jun 2019 04:39:20: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 04:39:20: #2 alternative fragment length(s) may be 216 bps INFO @ Mon, 03 Jun 2019 04:39:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.20_model.r INFO @ Mon, 03 Jun 2019 04:39:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:39:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:39:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:39:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:39:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:39:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:39:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:39:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.05_summits.bed INFO @ Mon, 03 Jun 2019 04:39:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5381 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:39:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:39:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:39:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.20_summits.bed INFO @ Mon, 03 Jun 2019 04:39:38: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2406 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:39:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:39:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:39:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763405/SRX1763405.10_summits.bed INFO @ Mon, 03 Jun 2019 04:39:38: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3862 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。