Job ID = 1299771 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,601,136 reads read : 29,202,272 reads written : 29,202,272 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: 00:42:00 14601136 reads; of these: 14601136 (100.00%) were paired; of these: 1081102 (7.40%) aligned concordantly 0 times 9270987 (63.49%) aligned concordantly exactly 1 time 4249047 (29.10%) aligned concordantly >1 times ---- 1081102 pairs aligned concordantly 0 times; of these: 46189 (4.27%) aligned discordantly 1 time ---- 1034913 pairs aligned 0 times concordantly or discordantly; of these: 2069826 mates make up the pairs; of these: 1720588 (83.13%) aligned 0 times 243083 (11.74%) aligned exactly 1 time 106155 (5.13%) aligned >1 times 94.11% overall alignment rate Time searching: 00:42:00 Overall time: 00:42:00 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] 1122040 / 13542930 = 0.0829 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 19:35:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.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 19:35:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:35:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:35:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.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 19:35:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:35:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:35:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.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 19:35:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:35:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:35:15: 1000000 INFO @ Mon, 03 Jun 2019 19:35:16: 1000000 INFO @ Mon, 03 Jun 2019 19:35:17: 1000000 INFO @ Mon, 03 Jun 2019 19:35:22: 2000000 INFO @ Mon, 03 Jun 2019 19:35:24: 2000000 INFO @ Mon, 03 Jun 2019 19:35:24: 2000000 INFO @ Mon, 03 Jun 2019 19:35:29: 3000000 INFO @ Mon, 03 Jun 2019 19:35:32: 3000000 INFO @ Mon, 03 Jun 2019 19:35:32: 3000000 INFO @ Mon, 03 Jun 2019 19:35:35: 4000000 INFO @ Mon, 03 Jun 2019 19:35:40: 4000000 INFO @ Mon, 03 Jun 2019 19:35:40: 4000000 INFO @ Mon, 03 Jun 2019 19:35:42: 5000000 INFO @ Mon, 03 Jun 2019 19:35:48: 5000000 INFO @ Mon, 03 Jun 2019 19:35:48: 5000000 INFO @ Mon, 03 Jun 2019 19:35:49: 6000000 INFO @ Mon, 03 Jun 2019 19:35:55: 6000000 INFO @ Mon, 03 Jun 2019 19:35:55: 7000000 INFO @ Mon, 03 Jun 2019 19:35:55: 6000000 INFO @ Mon, 03 Jun 2019 19:36:02: 8000000 INFO @ Mon, 03 Jun 2019 19:36:03: 7000000 INFO @ Mon, 03 Jun 2019 19:36:03: 7000000 INFO @ Mon, 03 Jun 2019 19:36:09: 9000000 INFO @ Mon, 03 Jun 2019 19:36:11: 8000000 INFO @ Mon, 03 Jun 2019 19:36:11: 8000000 INFO @ Mon, 03 Jun 2019 19:36:15: 10000000 INFO @ Mon, 03 Jun 2019 19:36:19: 9000000 INFO @ Mon, 03 Jun 2019 19:36:19: 9000000 INFO @ Mon, 03 Jun 2019 19:36:22: 11000000 INFO @ Mon, 03 Jun 2019 19:36:26: 10000000 INFO @ Mon, 03 Jun 2019 19:36:26: 10000000 INFO @ Mon, 03 Jun 2019 19:36:29: 12000000 INFO @ Mon, 03 Jun 2019 19:36:34: 11000000 INFO @ Mon, 03 Jun 2019 19:36:34: 11000000 INFO @ Mon, 03 Jun 2019 19:36:35: 13000000 INFO @ Mon, 03 Jun 2019 19:36:42: 12000000 INFO @ Mon, 03 Jun 2019 19:36:42: 14000000 INFO @ Mon, 03 Jun 2019 19:36:42: 12000000 INFO @ Mon, 03 Jun 2019 19:36:48: 15000000 INFO @ Mon, 03 Jun 2019 19:36:49: 13000000 INFO @ Mon, 03 Jun 2019 19:36:49: 13000000 INFO @ Mon, 03 Jun 2019 19:36:55: 16000000 INFO @ Mon, 03 Jun 2019 19:36:57: 14000000 INFO @ Mon, 03 Jun 2019 19:36:57: 14000000 INFO @ Mon, 03 Jun 2019 19:37:02: 17000000 INFO @ Mon, 03 Jun 2019 19:37:05: 15000000 INFO @ Mon, 03 Jun 2019 19:37:05: 15000000 INFO @ Mon, 03 Jun 2019 19:37:08: 18000000 INFO @ Mon, 03 Jun 2019 19:37:12: 16000000 INFO @ Mon, 03 Jun 2019 19:37:13: 16000000 INFO @ Mon, 03 Jun 2019 19:37:16: 19000000 INFO @ Mon, 03 Jun 2019 19:37:20: 17000000 INFO @ Mon, 03 Jun 2019 19:37:20: 17000000 INFO @ Mon, 03 Jun 2019 19:37:22: 20000000 INFO @ Mon, 03 Jun 2019 19:37:27: 18000000 INFO @ Mon, 03 Jun 2019 19:37:28: 18000000 INFO @ Mon, 03 Jun 2019 19:37:30: 21000000 INFO @ Mon, 03 Jun 2019 19:37:35: 19000000 INFO @ Mon, 03 Jun 2019 19:37:35: 19000000 INFO @ Mon, 03 Jun 2019 19:37:36: 22000000 INFO @ Mon, 03 Jun 2019 19:37:42: 20000000 INFO @ Mon, 03 Jun 2019 19:37:43: 23000000 INFO @ Mon, 03 Jun 2019 19:37:43: 20000000 INFO @ Mon, 03 Jun 2019 19:37:49: 24000000 INFO @ Mon, 03 Jun 2019 19:37:50: 21000000 INFO @ Mon, 03 Jun 2019 19:37:50: 21000000 INFO @ Mon, 03 Jun 2019 19:37:56: 25000000 INFO @ Mon, 03 Jun 2019 19:37:57: 22000000 INFO @ Mon, 03 Jun 2019 19:37:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:37:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:37:58: #1 total tags in treatment: 12398920 INFO @ Mon, 03 Jun 2019 19:37:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:37:58: #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 19:37:58: 22000000 INFO @ Mon, 03 Jun 2019 19:37:58: #1 tags after filtering in treatment: 10861493 INFO @ Mon, 03 Jun 2019 19:37:58: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 19:37:58: #1 finished! INFO @ Mon, 03 Jun 2019 19:37:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:37:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:37:59: #2 number of paired peaks: 136 WARNING @ Mon, 03 Jun 2019 19:37:59: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Mon, 03 Jun 2019 19:37:59: start model_add_line... INFO @ Mon, 03 Jun 2019 19:37:59: start X-correlation... INFO @ Mon, 03 Jun 2019 19:37:59: end of X-cor INFO @ Mon, 03 Jun 2019 19:37:59: #2 finished! INFO @ Mon, 03 Jun 2019 19:37:59: #2 predicted fragment length is 101 bps INFO @ Mon, 03 Jun 2019 19:37:59: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 03 Jun 2019 19:37:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.10_model.r INFO @ Mon, 03 Jun 2019 19:37:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:37:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:38:05: 23000000 INFO @ Mon, 03 Jun 2019 19:38:05: 23000000 INFO @ Mon, 03 Jun 2019 19:38:12: 24000000 INFO @ Mon, 03 Jun 2019 19:38:13: 24000000 INFO @ Mon, 03 Jun 2019 19:38:20: 25000000 INFO @ Mon, 03 Jun 2019 19:38:20: 25000000 INFO @ Mon, 03 Jun 2019 19:38:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:38:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:38:22: #1 total tags in treatment: 12398920 INFO @ Mon, 03 Jun 2019 19:38:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:38:22: #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 19:38:22: #1 tags after filtering in treatment: 10861493 INFO @ Mon, 03 Jun 2019 19:38:22: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 19:38:22: #1 finished! INFO @ Mon, 03 Jun 2019 19:38:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:38:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:38:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:38:22: #1 total tags in treatment: 12398920 INFO @ Mon, 03 Jun 2019 19:38:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:38:22: #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 19:38:22: #1 tags after filtering in treatment: 10861493 INFO @ Mon, 03 Jun 2019 19:38:22: #1 Redundant rate of treatment: 0.12 INFO @ Mon, 03 Jun 2019 19:38:22: #1 finished! INFO @ Mon, 03 Jun 2019 19:38:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:38:23: #2 number of paired peaks: 136 WARNING @ Mon, 03 Jun 2019 19:38:23: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Mon, 03 Jun 2019 19:38:23: start model_add_line... INFO @ Mon, 03 Jun 2019 19:38:23: start X-correlation... INFO @ Mon, 03 Jun 2019 19:38:23: end of X-cor INFO @ Mon, 03 Jun 2019 19:38:23: #2 finished! INFO @ Mon, 03 Jun 2019 19:38:23: #2 predicted fragment length is 101 bps INFO @ Mon, 03 Jun 2019 19:38:23: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 03 Jun 2019 19:38:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.05_model.r INFO @ Mon, 03 Jun 2019 19:38:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:38:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:38:23: #2 number of paired peaks: 136 WARNING @ Mon, 03 Jun 2019 19:38:23: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Mon, 03 Jun 2019 19:38:23: start model_add_line... INFO @ Mon, 03 Jun 2019 19:38:24: start X-correlation... INFO @ Mon, 03 Jun 2019 19:38:24: end of X-cor INFO @ Mon, 03 Jun 2019 19:38:24: #2 finished! INFO @ Mon, 03 Jun 2019 19:38:24: #2 predicted fragment length is 101 bps INFO @ Mon, 03 Jun 2019 19:38:24: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 03 Jun 2019 19:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.20_model.r INFO @ Mon, 03 Jun 2019 19:38:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:38:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.10_summits.bed INFO @ Mon, 03 Jun 2019 19:38:45: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (850 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:38:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:38:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:39:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:39:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:39:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.05_summits.bed INFO @ Mon, 03 Jun 2019 19:39:09: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1111 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:39:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:39:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:39:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474605/SRX474605.20_summits.bed INFO @ Mon, 03 Jun 2019 19:39:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (591 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。