Job ID = 4303092 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 23,656,456 reads read : 47,312,912 reads written : 47,312,912 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1151103.sra.cache’: 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: 00:48:46 23656456 reads; of these: 23656456 (100.00%) were paired; of these: 2628904 (11.11%) aligned concordantly 0 times 14841393 (62.74%) aligned concordantly exactly 1 time 6186159 (26.15%) aligned concordantly >1 times ---- 2628904 pairs aligned concordantly 0 times; of these: 19776 (0.75%) aligned discordantly 1 time ---- 2609128 pairs aligned 0 times concordantly or discordantly; of these: 5218256 mates make up the pairs; of these: 4400753 (84.33%) aligned 0 times 540039 (10.35%) aligned exactly 1 time 277464 (5.32%) aligned >1 times 90.70% overall alignment rate Time searching: 00:48:46 Overall time: 00:48:46 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 20 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] 15684920 / 21016453 = 0.7463 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 01:41:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.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 @ Thu, 12 Dec 2019 01:41:24: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:41:24: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:41:32: 1000000 INFO @ Thu, 12 Dec 2019 01:41:41: 2000000 INFO @ Thu, 12 Dec 2019 01:41:49: 3000000 INFO @ Thu, 12 Dec 2019 01:41:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.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 @ Thu, 12 Dec 2019 01:41:53: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:41:53: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:41:57: 4000000 INFO @ Thu, 12 Dec 2019 01:42:00: 1000000 INFO @ Thu, 12 Dec 2019 01:42:05: 5000000 INFO @ Thu, 12 Dec 2019 01:42:07: 2000000 INFO @ Thu, 12 Dec 2019 01:42:13: 6000000 INFO @ Thu, 12 Dec 2019 01:42:14: 3000000 INFO @ Thu, 12 Dec 2019 01:42:20: 4000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 01:42:22: 7000000 INFO @ Thu, 12 Dec 2019 01:42:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.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 @ Thu, 12 Dec 2019 01:42:23: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:42:23: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:42:26: 5000000 INFO @ Thu, 12 Dec 2019 01:42:31: 8000000 INFO @ Thu, 12 Dec 2019 01:42:32: 1000000 INFO @ Thu, 12 Dec 2019 01:42:33: 6000000 INFO @ Thu, 12 Dec 2019 01:42:40: 9000000 INFO @ Thu, 12 Dec 2019 01:42:40: 7000000 INFO @ Thu, 12 Dec 2019 01:42:41: 2000000 INFO @ Thu, 12 Dec 2019 01:42:47: 8000000 INFO @ Thu, 12 Dec 2019 01:42:49: 10000000 INFO @ Thu, 12 Dec 2019 01:42:50: 3000000 INFO @ Thu, 12 Dec 2019 01:42:53: 9000000 INFO @ Thu, 12 Dec 2019 01:42:58: 11000000 INFO @ Thu, 12 Dec 2019 01:42:59: 4000000 INFO @ Thu, 12 Dec 2019 01:43:00: 10000000 INFO @ Thu, 12 Dec 2019 01:43:03: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:43:03: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:43:03: #1 total tags in treatment: 5355534 INFO @ Thu, 12 Dec 2019 01:43:03: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:43:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:43:03: #1 tags after filtering in treatment: 4836855 INFO @ Thu, 12 Dec 2019 01:43:03: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 12 Dec 2019 01:43:03: #1 finished! INFO @ Thu, 12 Dec 2019 01:43:03: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:43:03: #2 number of paired peaks: 4867 INFO @ Thu, 12 Dec 2019 01:43:03: start model_add_line... INFO @ Thu, 12 Dec 2019 01:43:03: start X-correlation... INFO @ Thu, 12 Dec 2019 01:43:03: end of X-cor INFO @ Thu, 12 Dec 2019 01:43:03: #2 finished! INFO @ Thu, 12 Dec 2019 01:43:03: #2 predicted fragment length is 180 bps INFO @ Thu, 12 Dec 2019 01:43:03: #2 alternative fragment length(s) may be 180 bps INFO @ Thu, 12 Dec 2019 01:43:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.05_model.r INFO @ Thu, 12 Dec 2019 01:43:03: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:43:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:43:07: 11000000 INFO @ Thu, 12 Dec 2019 01:43:07: 5000000 INFO @ Thu, 12 Dec 2019 01:43:10: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:43:10: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:43:10: #1 total tags in treatment: 5355534 INFO @ Thu, 12 Dec 2019 01:43:10: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:43:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:43:10: #1 tags after filtering in treatment: 4836855 INFO @ Thu, 12 Dec 2019 01:43:10: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 12 Dec 2019 01:43:10: #1 finished! INFO @ Thu, 12 Dec 2019 01:43:10: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:43:11: #2 number of paired peaks: 4867 INFO @ Thu, 12 Dec 2019 01:43:11: start model_add_line... INFO @ Thu, 12 Dec 2019 01:43:11: start X-correlation... INFO @ Thu, 12 Dec 2019 01:43:11: end of X-cor INFO @ Thu, 12 Dec 2019 01:43:11: #2 finished! INFO @ Thu, 12 Dec 2019 01:43:11: #2 predicted fragment length is 180 bps INFO @ Thu, 12 Dec 2019 01:43:11: #2 alternative fragment length(s) may be 180 bps INFO @ Thu, 12 Dec 2019 01:43:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.10_model.r INFO @ Thu, 12 Dec 2019 01:43:11: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:43:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:43:16: 6000000 INFO @ Thu, 12 Dec 2019 01:43:16: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:43:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:43:23: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:43:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:43:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.05_summits.bed INFO @ Thu, 12 Dec 2019 01:43:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (10128 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:43:24: 7000000 INFO @ Thu, 12 Dec 2019 01:43:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:43:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:43:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.10_summits.bed INFO @ Thu, 12 Dec 2019 01:43:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6639 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:43:33: 8000000 INFO @ Thu, 12 Dec 2019 01:43:41: 9000000 INFO @ Thu, 12 Dec 2019 01:43:50: 10000000 INFO @ Thu, 12 Dec 2019 01:43:58: 11000000 INFO @ Thu, 12 Dec 2019 01:44:02: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:44:02: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:44:02: #1 total tags in treatment: 5355534 INFO @ Thu, 12 Dec 2019 01:44:02: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:44:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:44:02: #1 tags after filtering in treatment: 4836855 INFO @ Thu, 12 Dec 2019 01:44:02: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 12 Dec 2019 01:44:02: #1 finished! INFO @ Thu, 12 Dec 2019 01:44:02: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:44:03: #2 number of paired peaks: 4867 INFO @ Thu, 12 Dec 2019 01:44:03: start model_add_line... INFO @ Thu, 12 Dec 2019 01:44:03: start X-correlation... INFO @ Thu, 12 Dec 2019 01:44:03: end of X-cor INFO @ Thu, 12 Dec 2019 01:44:03: #2 finished! INFO @ Thu, 12 Dec 2019 01:44:03: #2 predicted fragment length is 180 bps INFO @ Thu, 12 Dec 2019 01:44:03: #2 alternative fragment length(s) may be 180 bps INFO @ Thu, 12 Dec 2019 01:44:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.20_model.r INFO @ Thu, 12 Dec 2019 01:44:03: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:44:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:44:15: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:44:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:44:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:44:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456155/SRX456155.20_summits.bed INFO @ Thu, 12 Dec 2019 01:44:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2997 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。