Job ID = 1295002 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 38,483,086 reads read : 76,966,172 reads written : 76,966,172 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: 00:56:48 38483086 reads; of these: 38483086 (100.00%) were paired; of these: 20846813 (54.17%) aligned concordantly 0 times 7855227 (20.41%) aligned concordantly exactly 1 time 9781046 (25.42%) aligned concordantly >1 times ---- 20846813 pairs aligned concordantly 0 times; of these: 1120385 (5.37%) aligned discordantly 1 time ---- 19726428 pairs aligned 0 times concordantly or discordantly; of these: 39452856 mates make up the pairs; of these: 29255888 (74.15%) aligned 0 times 7113264 (18.03%) aligned exactly 1 time 3083704 (7.82%) aligned >1 times 61.99% overall alignment rate Time searching: 00:56:49 Overall time: 00:56:49 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] 7265348 / 17805711 = 0.4080 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 12:36:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.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 12:36:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:36:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:36:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.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 12:36:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:36:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:36:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.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 12:36:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:36:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:36:06: 1000000 INFO @ Mon, 03 Jun 2019 12:36:07: 1000000 INFO @ Mon, 03 Jun 2019 12:36:08: 1000000 INFO @ Mon, 03 Jun 2019 12:36:12: 2000000 INFO @ Mon, 03 Jun 2019 12:36:14: 2000000 INFO @ Mon, 03 Jun 2019 12:36:14: 2000000 INFO @ Mon, 03 Jun 2019 12:36:17: 3000000 INFO @ Mon, 03 Jun 2019 12:36:20: 3000000 INFO @ Mon, 03 Jun 2019 12:36:21: 3000000 INFO @ Mon, 03 Jun 2019 12:36:23: 4000000 INFO @ Mon, 03 Jun 2019 12:36:26: 4000000 INFO @ Mon, 03 Jun 2019 12:36:28: 4000000 INFO @ Mon, 03 Jun 2019 12:36:28: 5000000 INFO @ Mon, 03 Jun 2019 12:36:33: 5000000 INFO @ Mon, 03 Jun 2019 12:36:33: 6000000 INFO @ Mon, 03 Jun 2019 12:36:35: 5000000 INFO @ Mon, 03 Jun 2019 12:36:39: 7000000 INFO @ Mon, 03 Jun 2019 12:36:39: 6000000 INFO @ Mon, 03 Jun 2019 12:36:41: 6000000 INFO @ Mon, 03 Jun 2019 12:36:44: 8000000 INFO @ Mon, 03 Jun 2019 12:36:45: 7000000 INFO @ Mon, 03 Jun 2019 12:36:48: 7000000 INFO @ Mon, 03 Jun 2019 12:36:49: 9000000 INFO @ Mon, 03 Jun 2019 12:36:52: 8000000 INFO @ Mon, 03 Jun 2019 12:36:55: 8000000 INFO @ Mon, 03 Jun 2019 12:36:55: 10000000 INFO @ Mon, 03 Jun 2019 12:36:58: 9000000 INFO @ Mon, 03 Jun 2019 12:37:00: 11000000 INFO @ Mon, 03 Jun 2019 12:37:01: 9000000 INFO @ Mon, 03 Jun 2019 12:37:04: 10000000 INFO @ Mon, 03 Jun 2019 12:37:06: 12000000 INFO @ Mon, 03 Jun 2019 12:37:08: 10000000 INFO @ Mon, 03 Jun 2019 12:37:11: 11000000 INFO @ Mon, 03 Jun 2019 12:37:11: 13000000 INFO @ Mon, 03 Jun 2019 12:37:15: 11000000 INFO @ Mon, 03 Jun 2019 12:37:17: 14000000 INFO @ Mon, 03 Jun 2019 12:37:17: 12000000 INFO @ Mon, 03 Jun 2019 12:37:22: 12000000 INFO @ Mon, 03 Jun 2019 12:37:22: 15000000 INFO @ Mon, 03 Jun 2019 12:37:23: 13000000 INFO @ Mon, 03 Jun 2019 12:37:27: 16000000 INFO @ Mon, 03 Jun 2019 12:37:28: 13000000 INFO @ Mon, 03 Jun 2019 12:37:30: 14000000 INFO @ Mon, 03 Jun 2019 12:37:33: 17000000 INFO @ Mon, 03 Jun 2019 12:37:35: 14000000 INFO @ Mon, 03 Jun 2019 12:37:36: 15000000 INFO @ Mon, 03 Jun 2019 12:37:38: 18000000 INFO @ Mon, 03 Jun 2019 12:37:42: 15000000 INFO @ Mon, 03 Jun 2019 12:37:42: 16000000 INFO @ Mon, 03 Jun 2019 12:37:44: 19000000 INFO @ Mon, 03 Jun 2019 12:37:49: 16000000 INFO @ Mon, 03 Jun 2019 12:37:49: 17000000 INFO @ Mon, 03 Jun 2019 12:37:50: 20000000 INFO @ Mon, 03 Jun 2019 12:37:55: 21000000 INFO @ Mon, 03 Jun 2019 12:37:55: 18000000 INFO @ Mon, 03 Jun 2019 12:37:55: 17000000 INFO @ Mon, 03 Jun 2019 12:38:00: 22000000 INFO @ Mon, 03 Jun 2019 12:38:01: 19000000 INFO @ Mon, 03 Jun 2019 12:38:02: 18000000 INFO @ Mon, 03 Jun 2019 12:38:06: 23000000 INFO @ Mon, 03 Jun 2019 12:38:07: 20000000 INFO @ Mon, 03 Jun 2019 12:38:09: 19000000 INFO @ Mon, 03 Jun 2019 12:38:11: 24000000 INFO @ Mon, 03 Jun 2019 12:38:14: 21000000 INFO @ Mon, 03 Jun 2019 12:38:15: 20000000 INFO @ Mon, 03 Jun 2019 12:38:17: 25000000 INFO @ Mon, 03 Jun 2019 12:38:20: 22000000 INFO @ Mon, 03 Jun 2019 12:38:22: 21000000 INFO @ Mon, 03 Jun 2019 12:38:22: 26000000 INFO @ Mon, 03 Jun 2019 12:38:26: 23000000 INFO @ Mon, 03 Jun 2019 12:38:28: 27000000 INFO @ Mon, 03 Jun 2019 12:38:29: 22000000 INFO @ Mon, 03 Jun 2019 12:38:33: 24000000 INFO @ Mon, 03 Jun 2019 12:38:33: 28000000 INFO @ Mon, 03 Jun 2019 12:38:35: 23000000 INFO @ Mon, 03 Jun 2019 12:38:38: 29000000 INFO @ Mon, 03 Jun 2019 12:38:39: 25000000 INFO @ Mon, 03 Jun 2019 12:38:42: 24000000 INFO @ Mon, 03 Jun 2019 12:38:44: 30000000 INFO @ Mon, 03 Jun 2019 12:38:45: 26000000 INFO @ Mon, 03 Jun 2019 12:38:49: 25000000 INFO @ Mon, 03 Jun 2019 12:38:49: 31000000 INFO @ Mon, 03 Jun 2019 12:38:51: 27000000 INFO @ Mon, 03 Jun 2019 12:38:54: 32000000 INFO @ Mon, 03 Jun 2019 12:38:55: 26000000 INFO @ Mon, 03 Jun 2019 12:38:57: 28000000 INFO @ Mon, 03 Jun 2019 12:39:00: 33000000 INFO @ Mon, 03 Jun 2019 12:39:01: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:39:01: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:39:01: #1 total tags in treatment: 10442949 INFO @ Mon, 03 Jun 2019 12:39:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:39:01: #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 12:39:01: #1 tags after filtering in treatment: 7886466 INFO @ Mon, 03 Jun 2019 12:39:01: #1 Redundant rate of treatment: 0.24 INFO @ Mon, 03 Jun 2019 12:39:01: #1 finished! INFO @ Mon, 03 Jun 2019 12:39:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:39:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:39:02: #2 number of paired peaks: 1487 INFO @ Mon, 03 Jun 2019 12:39:02: start model_add_line... INFO @ Mon, 03 Jun 2019 12:39:02: 27000000 INFO @ Mon, 03 Jun 2019 12:39:02: start X-correlation... INFO @ Mon, 03 Jun 2019 12:39:02: end of X-cor INFO @ Mon, 03 Jun 2019 12:39:02: #2 finished! INFO @ Mon, 03 Jun 2019 12:39:02: #2 predicted fragment length is 94 bps INFO @ Mon, 03 Jun 2019 12:39:02: #2 alternative fragment length(s) may be 94 bps INFO @ Mon, 03 Jun 2019 12:39:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.05_model.r INFO @ Mon, 03 Jun 2019 12:39:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:39:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:39:04: 29000000 INFO @ Mon, 03 Jun 2019 12:39:08: 28000000 INFO @ Mon, 03 Jun 2019 12:39:10: 30000000 INFO @ Mon, 03 Jun 2019 12:39:15: 29000000 INFO @ Mon, 03 Jun 2019 12:39:16: 31000000 INFO @ Mon, 03 Jun 2019 12:39:22: 30000000 INFO @ Mon, 03 Jun 2019 12:39:22: 32000000 INFO @ Mon, 03 Jun 2019 12:39:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:39:28: 33000000 INFO @ Mon, 03 Jun 2019 12:39:28: 31000000 INFO @ Mon, 03 Jun 2019 12:39:29: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:39:29: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:39:29: #1 total tags in treatment: 10442949 INFO @ Mon, 03 Jun 2019 12:39:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:39:29: #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 12:39:29: #1 tags after filtering in treatment: 7886466 INFO @ Mon, 03 Jun 2019 12:39:29: #1 Redundant rate of treatment: 0.24 INFO @ Mon, 03 Jun 2019 12:39:29: #1 finished! INFO @ Mon, 03 Jun 2019 12:39:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:39:30: #2 number of paired peaks: 1487 INFO @ Mon, 03 Jun 2019 12:39:30: start model_add_line... INFO @ Mon, 03 Jun 2019 12:39:30: start X-correlation... INFO @ Mon, 03 Jun 2019 12:39:30: end of X-cor INFO @ Mon, 03 Jun 2019 12:39:30: #2 finished! INFO @ Mon, 03 Jun 2019 12:39:30: #2 predicted fragment length is 94 bps INFO @ Mon, 03 Jun 2019 12:39:30: #2 alternative fragment length(s) may be 94 bps INFO @ Mon, 03 Jun 2019 12:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.20_model.r INFO @ Mon, 03 Jun 2019 12:39:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:39:34: 32000000 INFO @ Mon, 03 Jun 2019 12:39:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:39:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:39:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.05_summits.bed INFO @ Mon, 03 Jun 2019 12:39:37: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6109 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:39:41: 33000000 INFO @ Mon, 03 Jun 2019 12:39:42: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:39:42: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:39:42: #1 total tags in treatment: 10442949 INFO @ Mon, 03 Jun 2019 12:39:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:39:42: #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 12:39:42: #1 tags after filtering in treatment: 7886466 INFO @ Mon, 03 Jun 2019 12:39:42: #1 Redundant rate of treatment: 0.24 INFO @ Mon, 03 Jun 2019 12:39:42: #1 finished! INFO @ Mon, 03 Jun 2019 12:39:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:39:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:39:43: #2 number of paired peaks: 1487 INFO @ Mon, 03 Jun 2019 12:39:43: start model_add_line... INFO @ Mon, 03 Jun 2019 12:39:43: start X-correlation... INFO @ Mon, 03 Jun 2019 12:39:43: end of X-cor INFO @ Mon, 03 Jun 2019 12:39:43: #2 finished! INFO @ Mon, 03 Jun 2019 12:39:43: #2 predicted fragment length is 94 bps INFO @ Mon, 03 Jun 2019 12:39:43: #2 alternative fragment length(s) may be 94 bps INFO @ Mon, 03 Jun 2019 12:39:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.10_model.r INFO @ Mon, 03 Jun 2019 12:39:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:39:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:39:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:40:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:40:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:40:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.20_summits.bed INFO @ Mon, 03 Jun 2019 12:40:06: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1045 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:40:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:40:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:40:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300936/SRX300936.10_summits.bed INFO @ Mon, 03 Jun 2019 12:40:18: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2510 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。