Job ID = 4303137 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 24,963,774 reads read : 49,927,548 reads written : 49,927,548 rm: cannot remove ‘[DSE]RR*’: 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: 00:29:17 24963774 reads; of these: 24963774 (100.00%) were paired; of these: 11006682 (44.09%) aligned concordantly 0 times 11432527 (45.80%) aligned concordantly exactly 1 time 2524565 (10.11%) aligned concordantly >1 times ---- 11006682 pairs aligned concordantly 0 times; of these: 203788 (1.85%) aligned discordantly 1 time ---- 10802894 pairs aligned 0 times concordantly or discordantly; of these: 21605788 mates make up the pairs; of these: 20633284 (95.50%) aligned 0 times 699949 (3.24%) aligned exactly 1 time 272555 (1.26%) aligned >1 times 58.67% overall alignment rate Time searching: 00:29:17 Overall time: 00:29:17 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 12 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] 11842163 / 14154471 = 0.8366 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 01:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.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 @ Thu, 12 Dec 2019 01:45:45: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:45:45: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:45:50: 1000000 INFO @ Thu, 12 Dec 2019 01:45:55: 2000000 INFO @ Thu, 12 Dec 2019 01:46:01: 3000000 INFO @ Thu, 12 Dec 2019 01:46:06: 4000000 INFO @ Thu, 12 Dec 2019 01:46:12: 5000000 INFO @ Thu, 12 Dec 2019 01:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.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 @ Thu, 12 Dec 2019 01:46:15: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:46:15: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:46:15: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:46:15: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:46:15: #1 total tags in treatment: 2262567 INFO @ Thu, 12 Dec 2019 01:46:15: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:46:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:46:15: #1 tags after filtering in treatment: 2167742 INFO @ Thu, 12 Dec 2019 01:46:15: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 12 Dec 2019 01:46:15: #1 finished! INFO @ Thu, 12 Dec 2019 01:46:15: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:46:15: #2 number of paired peaks: 4566 INFO @ Thu, 12 Dec 2019 01:46:15: start model_add_line... INFO @ Thu, 12 Dec 2019 01:46:15: start X-correlation... INFO @ Thu, 12 Dec 2019 01:46:15: end of X-cor INFO @ Thu, 12 Dec 2019 01:46:15: #2 finished! INFO @ Thu, 12 Dec 2019 01:46:15: #2 predicted fragment length is 190 bps INFO @ Thu, 12 Dec 2019 01:46:15: #2 alternative fragment length(s) may be 190 bps INFO @ Thu, 12 Dec 2019 01:46:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.05_model.r INFO @ Thu, 12 Dec 2019 01:46:15: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:46:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:46:20: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:46:21: 1000000 INFO @ Thu, 12 Dec 2019 01:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.05_summits.bed INFO @ Thu, 12 Dec 2019 01:46:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5644 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:46:28: 2000000 INFO @ Thu, 12 Dec 2019 01:46:35: 3000000 INFO @ Thu, 12 Dec 2019 01:46:41: 4000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 01:46:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.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 @ Thu, 12 Dec 2019 01:46:44: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:46:44: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:46:48: 5000000 INFO @ Thu, 12 Dec 2019 01:46:50: 1000000 INFO @ Thu, 12 Dec 2019 01:46:52: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:46:52: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:46:52: #1 total tags in treatment: 2262567 INFO @ Thu, 12 Dec 2019 01:46:52: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:46:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:46:52: #1 tags after filtering in treatment: 2167742 INFO @ Thu, 12 Dec 2019 01:46:52: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 12 Dec 2019 01:46:52: #1 finished! INFO @ Thu, 12 Dec 2019 01:46:52: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:46:52: #2 number of paired peaks: 4566 INFO @ Thu, 12 Dec 2019 01:46:52: start model_add_line... INFO @ Thu, 12 Dec 2019 01:46:52: start X-correlation... INFO @ Thu, 12 Dec 2019 01:46:52: end of X-cor INFO @ Thu, 12 Dec 2019 01:46:52: #2 finished! INFO @ Thu, 12 Dec 2019 01:46:52: #2 predicted fragment length is 190 bps INFO @ Thu, 12 Dec 2019 01:46:52: #2 alternative fragment length(s) may be 190 bps INFO @ Thu, 12 Dec 2019 01:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.10_model.r INFO @ Thu, 12 Dec 2019 01:46:53: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:46:55: 2000000 INFO @ Thu, 12 Dec 2019 01:46:57: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.10_summits.bed INFO @ Thu, 12 Dec 2019 01:47:01: Done! INFO @ Thu, 12 Dec 2019 01:47:01: 3000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3400 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:47:06: 4000000 INFO @ Thu, 12 Dec 2019 01:47:11: 5000000 INFO @ Thu, 12 Dec 2019 01:47:15: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:47:15: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:47:15: #1 total tags in treatment: 2262567 INFO @ Thu, 12 Dec 2019 01:47:15: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:47:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:47:15: #1 tags after filtering in treatment: 2167742 INFO @ Thu, 12 Dec 2019 01:47:15: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 12 Dec 2019 01:47:15: #1 finished! INFO @ Thu, 12 Dec 2019 01:47:15: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:47:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:47:15: #2 number of paired peaks: 4566 INFO @ Thu, 12 Dec 2019 01:47:15: start model_add_line... INFO @ Thu, 12 Dec 2019 01:47:15: start X-correlation... INFO @ Thu, 12 Dec 2019 01:47:15: end of X-cor INFO @ Thu, 12 Dec 2019 01:47:15: #2 finished! INFO @ Thu, 12 Dec 2019 01:47:15: #2 predicted fragment length is 190 bps INFO @ Thu, 12 Dec 2019 01:47:15: #2 alternative fragment length(s) may be 190 bps INFO @ Thu, 12 Dec 2019 01:47:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.20_model.r INFO @ Thu, 12 Dec 2019 01:47:15: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:47:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:47:20: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:47:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX683494/SRX683494.20_summits.bed INFO @ Thu, 12 Dec 2019 01:47:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1496 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。