Job ID = 10480722 sra ファイルのダウンロード中... Completed: 877189K bytes transferred in 56 seconds (126551K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 13729188 spots for /home/okishinya/chipatlas/results/dm3/SRX3087198/SRR5926830.sra Written 13729188 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:39:53 13729188 reads; of these: 13729188 (100.00%) were paired; of these: 1368685 (9.97%) aligned concordantly 0 times 9085403 (66.18%) aligned concordantly exactly 1 time 3275100 (23.86%) aligned concordantly >1 times ---- 1368685 pairs aligned concordantly 0 times; of these: 10152 (0.74%) aligned discordantly 1 time ---- 1358533 pairs aligned 0 times concordantly or discordantly; of these: 2717066 mates make up the pairs; of these: 2228504 (82.02%) aligned 0 times 312960 (11.52%) aligned exactly 1 time 175602 (6.46%) aligned >1 times 91.88% overall alignment rate Time searching: 00:39:53 Overall time: 00:39:53 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] 2598509 / 12360866 = 0.2102 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 @ Fri, 16 Mar 2018 08:33:24: # Command line: callpeak -t SRX3087198.bam -f BAM -g dm -n SRX3087198.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087198.20 # format = BAM # ChIP-seq file = ['SRX3087198.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 @ Fri, 16 Mar 2018 08:33:24: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:33:24: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:33:24: # Command line: callpeak -t SRX3087198.bam -f BAM -g dm -n SRX3087198.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087198.10 # format = BAM # ChIP-seq file = ['SRX3087198.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 @ Fri, 16 Mar 2018 08:33:24: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:33:24: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:33:24: # Command line: callpeak -t SRX3087198.bam -f BAM -g dm -n SRX3087198.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087198.05 # format = BAM # ChIP-seq file = ['SRX3087198.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 @ Fri, 16 Mar 2018 08:33:24: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:33:24: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:33:31: 1000000 INFO @ Fri, 16 Mar 2018 08:33:32: 1000000 INFO @ Fri, 16 Mar 2018 08:33:32: 1000000 INFO @ Fri, 16 Mar 2018 08:33:38: 2000000 INFO @ Fri, 16 Mar 2018 08:33:39: 2000000 INFO @ Fri, 16 Mar 2018 08:33:39: 2000000 INFO @ Fri, 16 Mar 2018 08:33:44: 3000000 INFO @ Fri, 16 Mar 2018 08:33:47: 3000000 INFO @ Fri, 16 Mar 2018 08:33:47: 3000000 INFO @ Fri, 16 Mar 2018 08:33:51: 4000000 INFO @ Fri, 16 Mar 2018 08:33:54: 4000000 INFO @ Fri, 16 Mar 2018 08:33:54: 4000000 INFO @ Fri, 16 Mar 2018 08:33:57: 5000000 INFO @ Fri, 16 Mar 2018 08:34:02: 5000000 INFO @ Fri, 16 Mar 2018 08:34:02: 5000000 INFO @ Fri, 16 Mar 2018 08:34:04: 6000000 INFO @ Fri, 16 Mar 2018 08:34:09: 6000000 INFO @ Fri, 16 Mar 2018 08:34:09: 6000000 INFO @ Fri, 16 Mar 2018 08:34:11: 7000000 INFO @ Fri, 16 Mar 2018 08:34:17: 7000000 INFO @ Fri, 16 Mar 2018 08:34:17: 7000000 INFO @ Fri, 16 Mar 2018 08:34:17: 8000000 INFO @ Fri, 16 Mar 2018 08:34:24: 9000000 INFO @ Fri, 16 Mar 2018 08:34:24: 8000000 INFO @ Fri, 16 Mar 2018 08:34:24: 8000000 INFO @ Fri, 16 Mar 2018 08:34:30: 10000000 INFO @ Fri, 16 Mar 2018 08:34:32: 9000000 INFO @ Fri, 16 Mar 2018 08:34:32: 9000000 INFO @ Fri, 16 Mar 2018 08:34:37: 11000000 INFO @ Fri, 16 Mar 2018 08:34:39: 10000000 INFO @ Fri, 16 Mar 2018 08:34:39: 10000000 INFO @ Fri, 16 Mar 2018 08:34:43: 12000000 INFO @ Fri, 16 Mar 2018 08:34:47: 11000000 INFO @ Fri, 16 Mar 2018 08:34:47: 11000000 INFO @ Fri, 16 Mar 2018 08:34:50: 13000000 INFO @ Fri, 16 Mar 2018 08:34:54: 12000000 INFO @ Fri, 16 Mar 2018 08:34:54: 12000000 INFO @ Fri, 16 Mar 2018 08:34:57: 14000000 INFO @ Fri, 16 Mar 2018 08:35:02: 13000000 INFO @ Fri, 16 Mar 2018 08:35:02: 13000000 INFO @ Fri, 16 Mar 2018 08:35:03: 15000000 INFO @ Fri, 16 Mar 2018 08:35:09: 14000000 INFO @ Fri, 16 Mar 2018 08:35:09: 14000000 INFO @ Fri, 16 Mar 2018 08:35:10: 16000000 INFO @ Fri, 16 Mar 2018 08:35:16: 17000000 INFO @ Fri, 16 Mar 2018 08:35:17: 15000000 INFO @ Fri, 16 Mar 2018 08:35:17: 15000000 INFO @ Fri, 16 Mar 2018 08:35:23: 18000000 INFO @ Fri, 16 Mar 2018 08:35:24: 16000000 INFO @ Fri, 16 Mar 2018 08:35:24: 16000000 INFO @ Fri, 16 Mar 2018 08:35:30: 19000000 INFO @ Fri, 16 Mar 2018 08:35:31: 17000000 INFO @ Fri, 16 Mar 2018 08:35:31: 17000000 INFO @ Fri, 16 Mar 2018 08:35:36: 20000000 INFO @ Fri, 16 Mar 2018 08:35:36: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:35:36: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:35:36: #1 total tags in treatment: 9763804 INFO @ Fri, 16 Mar 2018 08:35:36: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:35:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:35:37: #1 tags after filtering in treatment: 8884852 INFO @ Fri, 16 Mar 2018 08:35:37: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Mar 2018 08:35:37: #1 finished! INFO @ Fri, 16 Mar 2018 08:35:37: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:35:37: #2 number of paired peaks: 2643 INFO @ Fri, 16 Mar 2018 08:35:37: start model_add_line... INFO @ Fri, 16 Mar 2018 08:35:38: start X-correlation... INFO @ Fri, 16 Mar 2018 08:35:38: end of X-cor INFO @ Fri, 16 Mar 2018 08:35:38: #2 finished! INFO @ Fri, 16 Mar 2018 08:35:38: #2 predicted fragment length is 198 bps INFO @ Fri, 16 Mar 2018 08:35:38: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 16 Mar 2018 08:35:38: #2.2 Generate R script for model : SRX3087198.05_model.r INFO @ Fri, 16 Mar 2018 08:35:38: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:35:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:35:40: 18000000 INFO @ Fri, 16 Mar 2018 08:35:40: 18000000 INFO @ Fri, 16 Mar 2018 08:35:49: 19000000 INFO @ Fri, 16 Mar 2018 08:35:49: 19000000 INFO @ Fri, 16 Mar 2018 08:35:58: 20000000 INFO @ Fri, 16 Mar 2018 08:35:58: 20000000 INFO @ Fri, 16 Mar 2018 08:35:58: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:35:58: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:35:58: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:35:58: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:35:58: #1 total tags in treatment: 9763804 INFO @ Fri, 16 Mar 2018 08:35:58: #1 total tags in treatment: 9763804 INFO @ Fri, 16 Mar 2018 08:35:58: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:35:58: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:35:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:35:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 08:35:58: #1 tags after filtering in treatment: 8884852 INFO @ Fri, 16 Mar 2018 08:35:58: #1 tags after filtering in treatment: 8884852 INFO @ Fri, 16 Mar 2018 08:35:58: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Mar 2018 08:35:58: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Mar 2018 08:35:58: #1 finished! INFO @ Fri, 16 Mar 2018 08:35:58: #1 finished! INFO @ Fri, 16 Mar 2018 08:35:58: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:35:58: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:35:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:35:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:35:59: #2 number of paired peaks: 2643 INFO @ Fri, 16 Mar 2018 08:35:59: start model_add_line... INFO @ Fri, 16 Mar 2018 08:35:59: #2 number of paired peaks: 2643 INFO @ Fri, 16 Mar 2018 08:35:59: start model_add_line... INFO @ Fri, 16 Mar 2018 08:35:59: start X-correlation... INFO @ Fri, 16 Mar 2018 08:35:59: end of X-cor INFO @ Fri, 16 Mar 2018 08:35:59: #2 finished! INFO @ Fri, 16 Mar 2018 08:35:59: #2 predicted fragment length is 198 bps INFO @ Fri, 16 Mar 2018 08:35:59: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 16 Mar 2018 08:35:59: #2.2 Generate R script for model : SRX3087198.20_model.r INFO @ Fri, 16 Mar 2018 08:35:59: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:35:59: start X-correlation... INFO @ Fri, 16 Mar 2018 08:35:59: end of X-cor INFO @ Fri, 16 Mar 2018 08:35:59: #2 finished! INFO @ Fri, 16 Mar 2018 08:35:59: #2 predicted fragment length is 198 bps INFO @ Fri, 16 Mar 2018 08:35:59: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 16 Mar 2018 08:35:59: #2.2 Generate R script for model : SRX3087198.10_model.r INFO @ Fri, 16 Mar 2018 08:35:59: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:36:04: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:36:17: #4 Write output xls file... SRX3087198.05_peaks.xls INFO @ Fri, 16 Mar 2018 08:36:17: #4 Write peak in narrowPeak format file... SRX3087198.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:36:17: #4 Write summits bed file... SRX3087198.05_summits.bed INFO @ Fri, 16 Mar 2018 08:36:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5615 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:36:25: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:36:26: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:36:37: #4 Write output xls file... SRX3087198.20_peaks.xls INFO @ Fri, 16 Mar 2018 08:36:37: #4 Write peak in narrowPeak format file... SRX3087198.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:36:37: #4 Write summits bed file... SRX3087198.20_summits.bed INFO @ Fri, 16 Mar 2018 08:36:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2399 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:36:38: #4 Write output xls file... SRX3087198.10_peaks.xls INFO @ Fri, 16 Mar 2018 08:36:38: #4 Write peak in narrowPeak format file... SRX3087198.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:36:38: #4 Write summits bed file... SRX3087198.10_summits.bed INFO @ Fri, 16 Mar 2018 08:36:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3836 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。