Job ID = 1295421 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,597,605 reads read : 21,195,210 reads written : 21,195,210 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: 00:49:34 10597605 reads; of these: 10597605 (100.00%) were paired; of these: 1814529 (17.12%) aligned concordantly 0 times 4218423 (39.81%) aligned concordantly exactly 1 time 4564653 (43.07%) aligned concordantly >1 times ---- 1814529 pairs aligned concordantly 0 times; of these: 102880 (5.67%) aligned discordantly 1 time ---- 1711649 pairs aligned 0 times concordantly or discordantly; of these: 3423298 mates make up the pairs; of these: 2421157 (70.73%) aligned 0 times 343587 (10.04%) aligned exactly 1 time 658554 (19.24%) aligned >1 times 88.58% overall alignment rate Time searching: 00:49:34 Overall time: 00:49:34 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 8 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] 1221407 / 8836514 = 0.1382 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 14:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.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 14:36:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:36:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.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 14:36:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:36:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.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 14:36:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:36:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:37:05: 1000000 INFO @ Mon, 03 Jun 2019 14:37:06: 1000000 INFO @ Mon, 03 Jun 2019 14:37:08: 1000000 INFO @ Mon, 03 Jun 2019 14:37:16: 2000000 INFO @ Mon, 03 Jun 2019 14:37:16: 2000000 INFO @ Mon, 03 Jun 2019 14:37:21: 2000000 INFO @ Mon, 03 Jun 2019 14:37:26: 3000000 INFO @ Mon, 03 Jun 2019 14:37:26: 3000000 INFO @ Mon, 03 Jun 2019 14:37:33: 3000000 INFO @ Mon, 03 Jun 2019 14:37:36: 4000000 INFO @ Mon, 03 Jun 2019 14:37:36: 4000000 INFO @ Mon, 03 Jun 2019 14:37:45: 4000000 INFO @ Mon, 03 Jun 2019 14:37:47: 5000000 INFO @ Mon, 03 Jun 2019 14:37:47: 5000000 INFO @ Mon, 03 Jun 2019 14:37:57: 6000000 INFO @ Mon, 03 Jun 2019 14:37:57: 6000000 INFO @ Mon, 03 Jun 2019 14:37:58: 5000000 INFO @ Mon, 03 Jun 2019 14:38:07: 7000000 INFO @ Mon, 03 Jun 2019 14:38:07: 7000000 INFO @ Mon, 03 Jun 2019 14:38:11: 6000000 INFO @ Mon, 03 Jun 2019 14:38:17: 8000000 INFO @ Mon, 03 Jun 2019 14:38:18: 8000000 INFO @ Mon, 03 Jun 2019 14:38:23: 7000000 INFO @ Mon, 03 Jun 2019 14:38:27: 9000000 INFO @ Mon, 03 Jun 2019 14:38:28: 9000000 INFO @ Mon, 03 Jun 2019 14:38:36: 8000000 INFO @ Mon, 03 Jun 2019 14:38:37: 10000000 INFO @ Mon, 03 Jun 2019 14:38:38: 10000000 INFO @ Mon, 03 Jun 2019 14:38:48: 11000000 INFO @ Mon, 03 Jun 2019 14:38:48: 11000000 INFO @ Mon, 03 Jun 2019 14:38:49: 9000000 INFO @ Mon, 03 Jun 2019 14:38:57: 12000000 INFO @ Mon, 03 Jun 2019 14:39:00: 12000000 INFO @ Mon, 03 Jun 2019 14:39:02: 10000000 INFO @ Mon, 03 Jun 2019 14:39:05: 13000000 INFO @ Mon, 03 Jun 2019 14:39:12: 13000000 INFO @ Mon, 03 Jun 2019 14:39:14: 11000000 INFO @ Mon, 03 Jun 2019 14:39:14: 14000000 INFO @ Mon, 03 Jun 2019 14:39:23: 15000000 INFO @ Mon, 03 Jun 2019 14:39:24: 14000000 INFO @ Mon, 03 Jun 2019 14:39:27: 12000000 INFO @ Mon, 03 Jun 2019 14:39:31: 16000000 INFO @ Mon, 03 Jun 2019 14:39:34: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 14:39:34: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 14:39:34: #1 total tags in treatment: 7568549 INFO @ Mon, 03 Jun 2019 14:39:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:39:34: #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 14:39:34: #1 tags after filtering in treatment: 6816268 INFO @ Mon, 03 Jun 2019 14:39:34: #1 Redundant rate of treatment: 0.10 INFO @ Mon, 03 Jun 2019 14:39:34: #1 finished! INFO @ Mon, 03 Jun 2019 14:39:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:39:35: #2 number of paired peaks: 2799 INFO @ Mon, 03 Jun 2019 14:39:35: start model_add_line... INFO @ Mon, 03 Jun 2019 14:39:36: start X-correlation... INFO @ Mon, 03 Jun 2019 14:39:36: end of X-cor INFO @ Mon, 03 Jun 2019 14:39:36: #2 finished! INFO @ Mon, 03 Jun 2019 14:39:36: #2 predicted fragment length is 155 bps INFO @ Mon, 03 Jun 2019 14:39:36: #2 alternative fragment length(s) may be 155 bps INFO @ Mon, 03 Jun 2019 14:39:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.05_model.r INFO @ Mon, 03 Jun 2019 14:39:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:39:36: 15000000 INFO @ Mon, 03 Jun 2019 14:39:39: 13000000 INFO @ Mon, 03 Jun 2019 14:39:47: 16000000 INFO @ Mon, 03 Jun 2019 14:39:50: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 14:39:50: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 14:39:50: #1 total tags in treatment: 7568549 INFO @ Mon, 03 Jun 2019 14:39:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:39:50: #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 14:39:50: #1 tags after filtering in treatment: 6816268 INFO @ Mon, 03 Jun 2019 14:39:50: #1 Redundant rate of treatment: 0.10 INFO @ Mon, 03 Jun 2019 14:39:50: #1 finished! INFO @ Mon, 03 Jun 2019 14:39:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:39:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:39:51: #2 number of paired peaks: 2799 INFO @ Mon, 03 Jun 2019 14:39:51: start model_add_line... INFO @ Mon, 03 Jun 2019 14:39:51: 14000000 INFO @ Mon, 03 Jun 2019 14:39:52: start X-correlation... INFO @ Mon, 03 Jun 2019 14:39:52: end of X-cor INFO @ Mon, 03 Jun 2019 14:39:52: #2 finished! INFO @ Mon, 03 Jun 2019 14:39:52: #2 predicted fragment length is 155 bps INFO @ Mon, 03 Jun 2019 14:39:52: #2 alternative fragment length(s) may be 155 bps INFO @ Mon, 03 Jun 2019 14:39:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.10_model.r INFO @ Mon, 03 Jun 2019 14:39:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:39:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:40:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:40:04: 15000000 INFO @ Mon, 03 Jun 2019 14:40:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:40:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:40:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.05_summits.bed INFO @ Mon, 03 Jun 2019 14:40:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6886 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:40:15: 16000000 INFO @ Mon, 03 Jun 2019 14:40:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:40:18: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 14:40:18: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 14:40:18: #1 total tags in treatment: 7568549 INFO @ Mon, 03 Jun 2019 14:40:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:40:18: #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 14:40:19: #1 tags after filtering in treatment: 6816268 INFO @ Mon, 03 Jun 2019 14:40:19: #1 Redundant rate of treatment: 0.10 INFO @ Mon, 03 Jun 2019 14:40:19: #1 finished! INFO @ Mon, 03 Jun 2019 14:40:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:40:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:40:20: #2 number of paired peaks: 2799 INFO @ Mon, 03 Jun 2019 14:40:20: start model_add_line... INFO @ Mon, 03 Jun 2019 14:40:20: start X-correlation... INFO @ Mon, 03 Jun 2019 14:40:20: end of X-cor INFO @ Mon, 03 Jun 2019 14:40:20: #2 finished! INFO @ Mon, 03 Jun 2019 14:40:20: #2 predicted fragment length is 155 bps INFO @ Mon, 03 Jun 2019 14:40:20: #2 alternative fragment length(s) may be 155 bps INFO @ Mon, 03 Jun 2019 14:40:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.20_model.r INFO @ Mon, 03 Jun 2019 14:40:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:40:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:40:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:40:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:40:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.10_summits.bed INFO @ Mon, 03 Jun 2019 14:40:28: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3546 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:40:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393641/SRX3393641.20_summits.bed INFO @ Mon, 03 Jun 2019 14:40:56: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1472 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。