Job ID = 2590554 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,145,899 reads read : 10,291,798 reads written : 10,291,798 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: 00:14:30 5145899 reads; of these: 5145899 (100.00%) were paired; of these: 902759 (17.54%) aligned concordantly 0 times 3041122 (59.10%) aligned concordantly exactly 1 time 1202018 (23.36%) aligned concordantly >1 times ---- 902759 pairs aligned concordantly 0 times; of these: 104463 (11.57%) aligned discordantly 1 time ---- 798296 pairs aligned 0 times concordantly or discordantly; of these: 1596592 mates make up the pairs; of these: 1224484 (76.69%) aligned 0 times 203695 (12.76%) aligned exactly 1 time 168413 (10.55%) aligned >1 times 88.10% overall alignment rate Time searching: 00:14:30 Overall time: 00:14:30 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] 902110 / 4336884 = 0.2080 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, 12 Aug 2019 22:38:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.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, 12 Aug 2019 22:38:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:38:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:38:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.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, 12 Aug 2019 22:38:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:38:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.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, 12 Aug 2019 22:38:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:38:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:38:13: 1000000 INFO @ Mon, 12 Aug 2019 22:38:14: 1000000 INFO @ Mon, 12 Aug 2019 22:38:14: 1000000 INFO @ Mon, 12 Aug 2019 22:38:22: 2000000 INFO @ Mon, 12 Aug 2019 22:38:22: 2000000 INFO @ Mon, 12 Aug 2019 22:38:23: 2000000 INFO @ Mon, 12 Aug 2019 22:38:29: 3000000 INFO @ Mon, 12 Aug 2019 22:38:31: 3000000 INFO @ Mon, 12 Aug 2019 22:38:32: 3000000 INFO @ Mon, 12 Aug 2019 22:38:37: 4000000 INFO @ Mon, 12 Aug 2019 22:38:39: 4000000 INFO @ Mon, 12 Aug 2019 22:38:40: 4000000 INFO @ Mon, 12 Aug 2019 22:38:44: 5000000 INFO @ Mon, 12 Aug 2019 22:38:49: 5000000 INFO @ Mon, 12 Aug 2019 22:38:50: 5000000 INFO @ Mon, 12 Aug 2019 22:38:52: 6000000 INFO @ Mon, 12 Aug 2019 22:38:58: 6000000 INFO @ Mon, 12 Aug 2019 22:38:59: 6000000 INFO @ Mon, 12 Aug 2019 22:39:00: 7000000 INFO @ Mon, 12 Aug 2019 22:39:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:39:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:39:02: #1 total tags in treatment: 3352316 INFO @ Mon, 12 Aug 2019 22:39:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:39:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:39:02: #1 tags after filtering in treatment: 2810426 INFO @ Mon, 12 Aug 2019 22:39:02: #1 Redundant rate of treatment: 0.16 INFO @ Mon, 12 Aug 2019 22:39:02: #1 finished! INFO @ Mon, 12 Aug 2019 22:39:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:39:02: #2 number of paired peaks: 4466 INFO @ Mon, 12 Aug 2019 22:39:02: start model_add_line... INFO @ Mon, 12 Aug 2019 22:39:02: start X-correlation... INFO @ Mon, 12 Aug 2019 22:39:02: end of X-cor INFO @ Mon, 12 Aug 2019 22:39:02: #2 finished! INFO @ Mon, 12 Aug 2019 22:39:02: #2 predicted fragment length is 189 bps INFO @ Mon, 12 Aug 2019 22:39:02: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 12 Aug 2019 22:39:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.20_model.r INFO @ Mon, 12 Aug 2019 22:39:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:39:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:39:07: 7000000 INFO @ Mon, 12 Aug 2019 22:39:08: 7000000 INFO @ Mon, 12 Aug 2019 22:39:09: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:39:09: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:39:09: #1 total tags in treatment: 3352316 INFO @ Mon, 12 Aug 2019 22:39:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:39:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:39:09: #1 tags after filtering in treatment: 2810426 INFO @ Mon, 12 Aug 2019 22:39:09: #1 Redundant rate of treatment: 0.16 INFO @ Mon, 12 Aug 2019 22:39:09: #1 finished! INFO @ Mon, 12 Aug 2019 22:39:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:39:10: #2 number of paired peaks: 4466 INFO @ Mon, 12 Aug 2019 22:39:10: start model_add_line... INFO @ Mon, 12 Aug 2019 22:39:10: start X-correlation... INFO @ Mon, 12 Aug 2019 22:39:10: end of X-cor INFO @ Mon, 12 Aug 2019 22:39:10: #2 finished! INFO @ Mon, 12 Aug 2019 22:39:10: #2 predicted fragment length is 189 bps INFO @ Mon, 12 Aug 2019 22:39:10: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 12 Aug 2019 22:39:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.05_model.r INFO @ Mon, 12 Aug 2019 22:39:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:39:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:39:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:39:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:39:10: #1 total tags in treatment: 3352316 INFO @ Mon, 12 Aug 2019 22:39:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:39:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:39:10: #1 tags after filtering in treatment: 2810426 INFO @ Mon, 12 Aug 2019 22:39:10: #1 Redundant rate of treatment: 0.16 INFO @ Mon, 12 Aug 2019 22:39:10: #1 finished! INFO @ Mon, 12 Aug 2019 22:39:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:39:11: #2 number of paired peaks: 4466 INFO @ Mon, 12 Aug 2019 22:39:11: start model_add_line... INFO @ Mon, 12 Aug 2019 22:39:11: start X-correlation... INFO @ Mon, 12 Aug 2019 22:39:11: end of X-cor INFO @ Mon, 12 Aug 2019 22:39:11: #2 finished! INFO @ Mon, 12 Aug 2019 22:39:11: #2 predicted fragment length is 189 bps INFO @ Mon, 12 Aug 2019 22:39:11: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 12 Aug 2019 22:39:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.10_model.r INFO @ Mon, 12 Aug 2019 22:39:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:39:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:39:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:39:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.20_summits.bed INFO @ Mon, 12 Aug 2019 22:39:18: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2161 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:39:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:39:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:39:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:39:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:39:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.05_summits.bed INFO @ Mon, 12 Aug 2019 22:39:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6280 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:39:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:39:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:39:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501946/SRX4501946.10_summits.bed INFO @ Mon, 12 Aug 2019 22:39:26: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3732 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。