Job ID = 1295853 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,044,663 reads read : 24,089,326 reads written : 24,089,326 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: 00:24:05 12044663 reads; of these: 12044663 (100.00%) were paired; of these: 2283361 (18.96%) aligned concordantly 0 times 7446515 (61.82%) aligned concordantly exactly 1 time 2314787 (19.22%) aligned concordantly >1 times ---- 2283361 pairs aligned concordantly 0 times; of these: 85571 (3.75%) aligned discordantly 1 time ---- 2197790 pairs aligned 0 times concordantly or discordantly; of these: 4395580 mates make up the pairs; of these: 3818636 (86.87%) aligned 0 times 365645 (8.32%) aligned exactly 1 time 211299 (4.81%) aligned >1 times 84.15% overall alignment rate Time searching: 00:24:05 Overall time: 00:24:05 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] 1521598 / 9813552 = 0.1551 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 16:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.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 16:23:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:23:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.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 16:23:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:23:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.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 16:23:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:23:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:23:47: 1000000 INFO @ Mon, 03 Jun 2019 16:23:48: 1000000 INFO @ Mon, 03 Jun 2019 16:23:51: 1000000 INFO @ Mon, 03 Jun 2019 16:23:55: 2000000 INFO @ Mon, 03 Jun 2019 16:23:57: 2000000 INFO @ Mon, 03 Jun 2019 16:24:02: 2000000 INFO @ Mon, 03 Jun 2019 16:24:02: 3000000 INFO @ Mon, 03 Jun 2019 16:24:05: 3000000 INFO @ Mon, 03 Jun 2019 16:24:10: 4000000 INFO @ Mon, 03 Jun 2019 16:24:13: 3000000 INFO @ Mon, 03 Jun 2019 16:24:13: 4000000 INFO @ Mon, 03 Jun 2019 16:24:17: 5000000 INFO @ Mon, 03 Jun 2019 16:24:22: 5000000 INFO @ Mon, 03 Jun 2019 16:24:24: 4000000 INFO @ Mon, 03 Jun 2019 16:24:25: 6000000 INFO @ Mon, 03 Jun 2019 16:24:30: 6000000 INFO @ Mon, 03 Jun 2019 16:24:33: 7000000 INFO @ Mon, 03 Jun 2019 16:24:35: 5000000 INFO @ Mon, 03 Jun 2019 16:24:39: 7000000 INFO @ Mon, 03 Jun 2019 16:24:41: 8000000 INFO @ Mon, 03 Jun 2019 16:24:46: 6000000 INFO @ Mon, 03 Jun 2019 16:24:49: 8000000 INFO @ Mon, 03 Jun 2019 16:24:50: 9000000 INFO @ Mon, 03 Jun 2019 16:24:58: 7000000 INFO @ Mon, 03 Jun 2019 16:24:58: 10000000 INFO @ Mon, 03 Jun 2019 16:24:59: 9000000 INFO @ Mon, 03 Jun 2019 16:25:06: 11000000 INFO @ Mon, 03 Jun 2019 16:25:07: 10000000 INFO @ Mon, 03 Jun 2019 16:25:09: 8000000 INFO @ Mon, 03 Jun 2019 16:25:14: 12000000 INFO @ Mon, 03 Jun 2019 16:25:16: 11000000 INFO @ Mon, 03 Jun 2019 16:25:21: 9000000 INFO @ Mon, 03 Jun 2019 16:25:22: 13000000 INFO @ Mon, 03 Jun 2019 16:25:24: 12000000 INFO @ Mon, 03 Jun 2019 16:25:30: 14000000 INFO @ Mon, 03 Jun 2019 16:25:32: 10000000 INFO @ Mon, 03 Jun 2019 16:25:33: 13000000 INFO @ Mon, 03 Jun 2019 16:25:38: 15000000 INFO @ Mon, 03 Jun 2019 16:25:41: 14000000 INFO @ Mon, 03 Jun 2019 16:25:43: 11000000 INFO @ Mon, 03 Jun 2019 16:25:46: 16000000 INFO @ Mon, 03 Jun 2019 16:25:50: 15000000 INFO @ Mon, 03 Jun 2019 16:25:55: 17000000 INFO @ Mon, 03 Jun 2019 16:25:55: 12000000 INFO @ Mon, 03 Jun 2019 16:25:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:25:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:25:57: #1 total tags in treatment: 8243572 INFO @ Mon, 03 Jun 2019 16:25:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:25:57: #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 16:25:57: #1 tags after filtering in treatment: 6424451 INFO @ Mon, 03 Jun 2019 16:25:57: #1 Redundant rate of treatment: 0.22 INFO @ Mon, 03 Jun 2019 16:25:57: #1 finished! INFO @ Mon, 03 Jun 2019 16:25:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:25:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:25:58: #2 number of paired peaks: 6146 INFO @ Mon, 03 Jun 2019 16:25:58: start model_add_line... INFO @ Mon, 03 Jun 2019 16:25:58: start X-correlation... INFO @ Mon, 03 Jun 2019 16:25:58: end of X-cor INFO @ Mon, 03 Jun 2019 16:25:58: #2 finished! INFO @ Mon, 03 Jun 2019 16:25:58: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 16:25:58: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 16:25:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.20_model.r INFO @ Mon, 03 Jun 2019 16:25:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:25:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:25:59: 16000000 INFO @ Mon, 03 Jun 2019 16:26:06: 13000000 INFO @ Mon, 03 Jun 2019 16:26:08: 17000000 INFO @ Mon, 03 Jun 2019 16:26:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:26:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:26:09: #1 total tags in treatment: 8243572 INFO @ Mon, 03 Jun 2019 16:26:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:26:09: #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 16:26:10: #1 tags after filtering in treatment: 6424451 INFO @ Mon, 03 Jun 2019 16:26:10: #1 Redundant rate of treatment: 0.22 INFO @ Mon, 03 Jun 2019 16:26:10: #1 finished! INFO @ Mon, 03 Jun 2019 16:26:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:26:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:26:11: #2 number of paired peaks: 6146 INFO @ Mon, 03 Jun 2019 16:26:11: start model_add_line... INFO @ Mon, 03 Jun 2019 16:26:11: start X-correlation... INFO @ Mon, 03 Jun 2019 16:26:11: end of X-cor INFO @ Mon, 03 Jun 2019 16:26:11: #2 finished! INFO @ Mon, 03 Jun 2019 16:26:11: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 16:26:11: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 16:26:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.10_model.r INFO @ Mon, 03 Jun 2019 16:26:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:26:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:26:17: 14000000 INFO @ Mon, 03 Jun 2019 16:26:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:26:29: 15000000 INFO @ Mon, 03 Jun 2019 16:26:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:26:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:26:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.20_summits.bed INFO @ Mon, 03 Jun 2019 16:26:32: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5999 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:26:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:26:40: 16000000 INFO @ Mon, 03 Jun 2019 16:26:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:26:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:26:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.10_summits.bed INFO @ Mon, 03 Jun 2019 16:26:44: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7788 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:26:51: 17000000 INFO @ Mon, 03 Jun 2019 16:26:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:26:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:26:53: #1 total tags in treatment: 8243572 INFO @ Mon, 03 Jun 2019 16:26:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:26:53: #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 16:26:53: #1 tags after filtering in treatment: 6424451 INFO @ Mon, 03 Jun 2019 16:26:53: #1 Redundant rate of treatment: 0.22 INFO @ Mon, 03 Jun 2019 16:26:53: #1 finished! INFO @ Mon, 03 Jun 2019 16:26:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:26:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:26:54: #2 number of paired peaks: 6146 INFO @ Mon, 03 Jun 2019 16:26:54: start model_add_line... INFO @ Mon, 03 Jun 2019 16:26:54: start X-correlation... INFO @ Mon, 03 Jun 2019 16:26:55: end of X-cor INFO @ Mon, 03 Jun 2019 16:26:55: #2 finished! INFO @ Mon, 03 Jun 2019 16:26:55: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 16:26:55: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 16:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.05_model.r INFO @ Mon, 03 Jun 2019 16:26:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:27:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:27:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:27:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:27:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577940/SRX4577940.05_summits.bed INFO @ Mon, 03 Jun 2019 16:27:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9284 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。