Job ID = 1295643 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 15,146,852 reads read : 30,293,704 reads written : 30,293,704 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: 00:36:58 15146852 reads; of these: 15146852 (100.00%) were paired; of these: 3368134 (22.24%) aligned concordantly 0 times 6854180 (45.25%) aligned concordantly exactly 1 time 4924538 (32.51%) aligned concordantly >1 times ---- 3368134 pairs aligned concordantly 0 times; of these: 17865 (0.53%) aligned discordantly 1 time ---- 3350269 pairs aligned 0 times concordantly or discordantly; of these: 6700538 mates make up the pairs; of these: 6059399 (90.43%) aligned 0 times 318952 (4.76%) aligned exactly 1 time 322187 (4.81%) aligned >1 times 80.00% overall alignment rate Time searching: 00:36:58 Overall time: 00:36:58 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] 1150795 / 11764834 = 0.0978 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 15:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.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 15:43:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:43:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.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 15:43:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:43:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.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 15:43:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:43:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:43:53: 1000000 INFO @ Mon, 03 Jun 2019 15:43:53: 1000000 INFO @ Mon, 03 Jun 2019 15:43:54: 1000000 INFO @ Mon, 03 Jun 2019 15:44:00: 2000000 INFO @ Mon, 03 Jun 2019 15:44:01: 2000000 INFO @ Mon, 03 Jun 2019 15:44:04: 2000000 INFO @ Mon, 03 Jun 2019 15:44:08: 3000000 INFO @ Mon, 03 Jun 2019 15:44:08: 3000000 INFO @ Mon, 03 Jun 2019 15:44:13: 3000000 INFO @ Mon, 03 Jun 2019 15:44:16: 4000000 INFO @ Mon, 03 Jun 2019 15:44:16: 4000000 INFO @ Mon, 03 Jun 2019 15:44:22: 4000000 INFO @ Mon, 03 Jun 2019 15:44:23: 5000000 INFO @ Mon, 03 Jun 2019 15:44:23: 5000000 INFO @ Mon, 03 Jun 2019 15:44:31: 6000000 INFO @ Mon, 03 Jun 2019 15:44:31: 6000000 INFO @ Mon, 03 Jun 2019 15:44:32: 5000000 INFO @ Mon, 03 Jun 2019 15:44:38: 7000000 INFO @ Mon, 03 Jun 2019 15:44:39: 7000000 INFO @ Mon, 03 Jun 2019 15:44:41: 6000000 INFO @ Mon, 03 Jun 2019 15:44:46: 8000000 INFO @ Mon, 03 Jun 2019 15:44:46: 8000000 INFO @ Mon, 03 Jun 2019 15:44:51: 7000000 INFO @ Mon, 03 Jun 2019 15:44:54: 9000000 INFO @ Mon, 03 Jun 2019 15:44:54: 9000000 INFO @ Mon, 03 Jun 2019 15:45:00: 8000000 INFO @ Mon, 03 Jun 2019 15:45:01: 10000000 INFO @ Mon, 03 Jun 2019 15:45:01: 10000000 INFO @ Mon, 03 Jun 2019 15:45:09: 11000000 INFO @ Mon, 03 Jun 2019 15:45:09: 11000000 INFO @ Mon, 03 Jun 2019 15:45:10: 9000000 INFO @ Mon, 03 Jun 2019 15:45:16: 12000000 INFO @ Mon, 03 Jun 2019 15:45:16: 12000000 INFO @ Mon, 03 Jun 2019 15:45:20: 10000000 INFO @ Mon, 03 Jun 2019 15:45:24: 13000000 INFO @ Mon, 03 Jun 2019 15:45:24: 13000000 INFO @ Mon, 03 Jun 2019 15:45:29: 11000000 INFO @ Mon, 03 Jun 2019 15:45:31: 14000000 INFO @ Mon, 03 Jun 2019 15:45:32: 14000000 INFO @ Mon, 03 Jun 2019 15:45:39: 12000000 INFO @ Mon, 03 Jun 2019 15:45:39: 15000000 INFO @ Mon, 03 Jun 2019 15:45:39: 15000000 INFO @ Mon, 03 Jun 2019 15:45:47: 16000000 INFO @ Mon, 03 Jun 2019 15:45:47: 16000000 INFO @ Mon, 03 Jun 2019 15:45:48: 13000000 INFO @ Mon, 03 Jun 2019 15:45:54: 17000000 INFO @ Mon, 03 Jun 2019 15:45:55: 17000000 INFO @ Mon, 03 Jun 2019 15:45:58: 14000000 INFO @ Mon, 03 Jun 2019 15:46:02: 18000000 INFO @ Mon, 03 Jun 2019 15:46:02: 18000000 INFO @ Mon, 03 Jun 2019 15:46:07: 15000000 INFO @ Mon, 03 Jun 2019 15:46:10: 19000000 INFO @ Mon, 03 Jun 2019 15:46:10: 19000000 INFO @ Mon, 03 Jun 2019 15:46:16: 16000000 INFO @ Mon, 03 Jun 2019 15:46:17: 20000000 INFO @ Mon, 03 Jun 2019 15:46:18: 20000000 INFO @ Mon, 03 Jun 2019 15:46:25: 21000000 INFO @ Mon, 03 Jun 2019 15:46:25: 21000000 INFO @ Mon, 03 Jun 2019 15:46:26: 17000000 INFO @ Mon, 03 Jun 2019 15:46:32: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:46:32: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:46:32: #1 total tags in treatment: 10628182 INFO @ Mon, 03 Jun 2019 15:46:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:46:32: #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 15:46:32: #1 tags after filtering in treatment: 9786974 INFO @ Mon, 03 Jun 2019 15:46:32: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 15:46:32: #1 finished! INFO @ Mon, 03 Jun 2019 15:46:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:46:33: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:46:33: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:46:33: #1 total tags in treatment: 10628182 INFO @ Mon, 03 Jun 2019 15:46:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:46:33: #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 15:46:33: #1 tags after filtering in treatment: 9786974 INFO @ Mon, 03 Jun 2019 15:46:33: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 15:46:33: #1 finished! INFO @ Mon, 03 Jun 2019 15:46:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:46:33: #2 number of paired peaks: 1708 INFO @ Mon, 03 Jun 2019 15:46:33: start model_add_line... INFO @ Mon, 03 Jun 2019 15:46:33: start X-correlation... INFO @ Mon, 03 Jun 2019 15:46:33: end of X-cor INFO @ Mon, 03 Jun 2019 15:46:33: #2 finished! INFO @ Mon, 03 Jun 2019 15:46:33: #2 predicted fragment length is 126 bps INFO @ Mon, 03 Jun 2019 15:46:33: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 03 Jun 2019 15:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.10_model.r INFO @ Mon, 03 Jun 2019 15:46:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:46:34: #2 number of paired peaks: 1708 INFO @ Mon, 03 Jun 2019 15:46:34: start model_add_line... INFO @ Mon, 03 Jun 2019 15:46:34: start X-correlation... INFO @ Mon, 03 Jun 2019 15:46:34: end of X-cor INFO @ Mon, 03 Jun 2019 15:46:34: #2 finished! INFO @ Mon, 03 Jun 2019 15:46:34: #2 predicted fragment length is 126 bps INFO @ Mon, 03 Jun 2019 15:46:34: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 03 Jun 2019 15:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.05_model.r INFO @ Mon, 03 Jun 2019 15:46:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:46:35: 18000000 INFO @ Mon, 03 Jun 2019 15:46:44: 19000000 INFO @ Mon, 03 Jun 2019 15:46:53: 20000000 INFO @ Mon, 03 Jun 2019 15:47:02: 21000000 INFO @ Mon, 03 Jun 2019 15:47:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:47:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:47:11: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:47:11: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:47:11: #1 total tags in treatment: 10628182 INFO @ Mon, 03 Jun 2019 15:47:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:47:11: #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 15:47:11: #1 tags after filtering in treatment: 9786974 INFO @ Mon, 03 Jun 2019 15:47:11: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 15:47:11: #1 finished! INFO @ Mon, 03 Jun 2019 15:47:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:47:12: #2 number of paired peaks: 1708 INFO @ Mon, 03 Jun 2019 15:47:12: start model_add_line... INFO @ Mon, 03 Jun 2019 15:47:12: start X-correlation... INFO @ Mon, 03 Jun 2019 15:47:12: end of X-cor INFO @ Mon, 03 Jun 2019 15:47:12: #2 finished! INFO @ Mon, 03 Jun 2019 15:47:12: #2 predicted fragment length is 126 bps INFO @ Mon, 03 Jun 2019 15:47:12: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 03 Jun 2019 15:47:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.20_model.r INFO @ Mon, 03 Jun 2019 15:47:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:47:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:47:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:47:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.10_summits.bed INFO @ Mon, 03 Jun 2019 15:47:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1709 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:47:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:47:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:47:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.05_summits.bed INFO @ Mon, 03 Jun 2019 15:47:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2987 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:47:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:47:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3948313/SRX3948313.20_summits.bed INFO @ Mon, 03 Jun 2019 15:47:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (986 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。