Job ID = 1295640 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,268,678 reads read : 16,537,356 reads written : 16,537,356 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:40:08 8268678 reads; of these: 8268678 (100.00%) were paired; of these: 4286578 (51.84%) aligned concordantly 0 times 374962 (4.53%) aligned concordantly exactly 1 time 3607138 (43.62%) aligned concordantly >1 times ---- 4286578 pairs aligned concordantly 0 times; of these: 94745 (2.21%) aligned discordantly 1 time ---- 4191833 pairs aligned 0 times concordantly or discordantly; of these: 8383666 mates make up the pairs; of these: 7507124 (89.54%) aligned 0 times 294797 (3.52%) aligned exactly 1 time 581745 (6.94%) aligned >1 times 54.61% overall alignment rate Time searching: 00:40:09 Overall time: 00:40:09 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] 1803663 / 3970781 = 0.4542 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 15:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.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 15:37:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:37:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.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 15:37:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:37:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.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 15:37:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:37:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:37:15: 1000000 INFO @ Mon, 03 Jun 2019 15:37:16: 1000000 INFO @ Mon, 03 Jun 2019 15:37:16: 1000000 INFO @ Mon, 03 Jun 2019 15:37:27: 2000000 INFO @ Mon, 03 Jun 2019 15:37:29: 2000000 INFO @ Mon, 03 Jun 2019 15:37:30: 2000000 INFO @ Mon, 03 Jun 2019 15:37:40: 3000000 INFO @ Mon, 03 Jun 2019 15:37:43: 3000000 INFO @ Mon, 03 Jun 2019 15:37:44: 3000000 INFO @ Mon, 03 Jun 2019 15:37:51: 4000000 INFO @ Mon, 03 Jun 2019 15:37:56: 4000000 INFO @ Mon, 03 Jun 2019 15:37:58: 4000000 INFO @ Mon, 03 Jun 2019 15:38:03: 5000000 INFO @ Mon, 03 Jun 2019 15:38:08: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:38:08: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:38:08: #1 total tags in treatment: 2178985 INFO @ Mon, 03 Jun 2019 15:38:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:38:08: #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 15:38:08: #1 tags after filtering in treatment: 1770146 INFO @ Mon, 03 Jun 2019 15:38:08: #1 Redundant rate of treatment: 0.19 INFO @ Mon, 03 Jun 2019 15:38:08: #1 finished! INFO @ Mon, 03 Jun 2019 15:38:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:38:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:38:09: #2 number of paired peaks: 9186 INFO @ Mon, 03 Jun 2019 15:38:09: start model_add_line... INFO @ Mon, 03 Jun 2019 15:38:09: start X-correlation... INFO @ Mon, 03 Jun 2019 15:38:09: end of X-cor INFO @ Mon, 03 Jun 2019 15:38:09: #2 finished! INFO @ Mon, 03 Jun 2019 15:38:09: #2 predicted fragment length is 181 bps INFO @ Mon, 03 Jun 2019 15:38:09: #2 alternative fragment length(s) may be 181 bps INFO @ Mon, 03 Jun 2019 15:38:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.05_model.r INFO @ Mon, 03 Jun 2019 15:38:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:38:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:38:10: 5000000 INFO @ Mon, 03 Jun 2019 15:38:12: 5000000 INFO @ Mon, 03 Jun 2019 15:38:15: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:38:15: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:38:15: #1 total tags in treatment: 2178985 INFO @ Mon, 03 Jun 2019 15:38:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:38:15: #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 15:38:15: #1 tags after filtering in treatment: 1770146 INFO @ Mon, 03 Jun 2019 15:38:15: #1 Redundant rate of treatment: 0.19 INFO @ Mon, 03 Jun 2019 15:38:15: #1 finished! INFO @ Mon, 03 Jun 2019 15:38:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:38:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:38:16: #2 number of paired peaks: 9186 INFO @ Mon, 03 Jun 2019 15:38:16: start model_add_line... INFO @ Mon, 03 Jun 2019 15:38:16: start X-correlation... INFO @ Mon, 03 Jun 2019 15:38:16: end of X-cor INFO @ Mon, 03 Jun 2019 15:38:16: #2 finished! INFO @ Mon, 03 Jun 2019 15:38:16: #2 predicted fragment length is 181 bps INFO @ Mon, 03 Jun 2019 15:38:16: #2 alternative fragment length(s) may be 181 bps INFO @ Mon, 03 Jun 2019 15:38:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.20_model.r INFO @ Mon, 03 Jun 2019 15:38:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:38:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:38:17: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:38:17: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:38:17: #1 total tags in treatment: 2178985 INFO @ Mon, 03 Jun 2019 15:38:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:38:17: #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 15:38:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:38:17: #1 tags after filtering in treatment: 1770146 INFO @ Mon, 03 Jun 2019 15:38:17: #1 Redundant rate of treatment: 0.19 INFO @ Mon, 03 Jun 2019 15:38:17: #1 finished! INFO @ Mon, 03 Jun 2019 15:38:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:38:18: #2 number of paired peaks: 9186 INFO @ Mon, 03 Jun 2019 15:38:18: start model_add_line... INFO @ Mon, 03 Jun 2019 15:38:18: start X-correlation... INFO @ Mon, 03 Jun 2019 15:38:18: end of X-cor INFO @ Mon, 03 Jun 2019 15:38:18: #2 finished! INFO @ Mon, 03 Jun 2019 15:38:18: #2 predicted fragment length is 181 bps INFO @ Mon, 03 Jun 2019 15:38:18: #2 alternative fragment length(s) may be 181 bps INFO @ Mon, 03 Jun 2019 15:38:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.10_model.r INFO @ Mon, 03 Jun 2019 15:38:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:38:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:38:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:38:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:38:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.05_summits.bed INFO @ Mon, 03 Jun 2019 15:38:22: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6725 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:38:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:38:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:38:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:38:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:38:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.20_summits.bed INFO @ Mon, 03 Jun 2019 15:38:28: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1065 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:38:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:38:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:38:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3948311/SRX3948311.10_summits.bed INFO @ Mon, 03 Jun 2019 15:38:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3461 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。