Job ID = 4178498 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,862,130 reads read : 3,724,260 reads written : 3,724,260 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:36 1862130 reads; of these: 1862130 (100.00%) were paired; of these: 881955 (47.36%) aligned concordantly 0 times 654670 (35.16%) aligned concordantly exactly 1 time 325505 (17.48%) aligned concordantly >1 times ---- 881955 pairs aligned concordantly 0 times; of these: 12251 (1.39%) aligned discordantly 1 time ---- 869704 pairs aligned 0 times concordantly or discordantly; of these: 1739408 mates make up the pairs; of these: 1682717 (96.74%) aligned 0 times 26679 (1.53%) aligned exactly 1 time 30012 (1.73%) aligned >1 times 54.82% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:38 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] 643992 / 991595 = 0.6495 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:31:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.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, 05 Dec 2019 12:31:40: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:31:40: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:31:43: #1 tag size is determined as 42 bps INFO @ Thu, 05 Dec 2019 12:31:43: #1 tag size = 42 INFO @ Thu, 05 Dec 2019 12:31:43: #1 total tags in treatment: 341014 INFO @ Thu, 05 Dec 2019 12:31:43: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:31:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:31:43: #1 tags after filtering in treatment: 310066 INFO @ Thu, 05 Dec 2019 12:31:43: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 05 Dec 2019 12:31:43: #1 finished! INFO @ Thu, 05 Dec 2019 12:31:43: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:31:44: #2 number of paired peaks: 1652 INFO @ Thu, 05 Dec 2019 12:31:44: start model_add_line... INFO @ Thu, 05 Dec 2019 12:31:44: start X-correlation... INFO @ Thu, 05 Dec 2019 12:31:44: end of X-cor INFO @ Thu, 05 Dec 2019 12:31:44: #2 finished! INFO @ Thu, 05 Dec 2019 12:31:44: #2 predicted fragment length is 116 bps INFO @ Thu, 05 Dec 2019 12:31:44: #2 alternative fragment length(s) may be 116 bps INFO @ Thu, 05 Dec 2019 12:31:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.05_model.r INFO @ Thu, 05 Dec 2019 12:31:44: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:31:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:31:44: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:31:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:31:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:31:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.05_summits.bed INFO @ Thu, 05 Dec 2019 12:31:45: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (605 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:32:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.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, 05 Dec 2019 12:32:09: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:32:09: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:32:13: #1 tag size is determined as 42 bps INFO @ Thu, 05 Dec 2019 12:32:13: #1 tag size = 42 INFO @ Thu, 05 Dec 2019 12:32:13: #1 total tags in treatment: 341014 INFO @ Thu, 05 Dec 2019 12:32:13: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:32:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:32:13: #1 tags after filtering in treatment: 310066 INFO @ Thu, 05 Dec 2019 12:32:13: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 05 Dec 2019 12:32:13: #1 finished! INFO @ Thu, 05 Dec 2019 12:32:13: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:32:13: #2 number of paired peaks: 1652 INFO @ Thu, 05 Dec 2019 12:32:13: start model_add_line... INFO @ Thu, 05 Dec 2019 12:32:13: start X-correlation... INFO @ Thu, 05 Dec 2019 12:32:13: end of X-cor INFO @ Thu, 05 Dec 2019 12:32:13: #2 finished! INFO @ Thu, 05 Dec 2019 12:32:13: #2 predicted fragment length is 116 bps INFO @ Thu, 05 Dec 2019 12:32:13: #2 alternative fragment length(s) may be 116 bps INFO @ Thu, 05 Dec 2019 12:32:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.10_model.r INFO @ Thu, 05 Dec 2019 12:32:13: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:32:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:32:14: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.10_summits.bed INFO @ Thu, 05 Dec 2019 12:32:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (387 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:32:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.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, 05 Dec 2019 12:32:39: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:32:39: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:32:43: #1 tag size is determined as 42 bps INFO @ Thu, 05 Dec 2019 12:32:43: #1 tag size = 42 INFO @ Thu, 05 Dec 2019 12:32:43: #1 total tags in treatment: 341014 INFO @ Thu, 05 Dec 2019 12:32:43: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:32:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:32:43: #1 tags after filtering in treatment: 310066 INFO @ Thu, 05 Dec 2019 12:32:43: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 05 Dec 2019 12:32:43: #1 finished! INFO @ Thu, 05 Dec 2019 12:32:43: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:32:43: #2 number of paired peaks: 1652 INFO @ Thu, 05 Dec 2019 12:32:43: start model_add_line... INFO @ Thu, 05 Dec 2019 12:32:43: start X-correlation... INFO @ Thu, 05 Dec 2019 12:32:43: end of X-cor INFO @ Thu, 05 Dec 2019 12:32:43: #2 finished! INFO @ Thu, 05 Dec 2019 12:32:43: #2 predicted fragment length is 116 bps INFO @ Thu, 05 Dec 2019 12:32:43: #2 alternative fragment length(s) may be 116 bps INFO @ Thu, 05 Dec 2019 12:32:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.20_model.r INFO @ Thu, 05 Dec 2019 12:32:43: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:32:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:32:44: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5711998/SRX5711998.20_summits.bed INFO @ Thu, 05 Dec 2019 12:32:44: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (160 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。