Job ID = 10845209 sra ファイルのダウンロード中... Completed: 180092K bytes transferred in 4 seconds (307777K bits/sec), in 1 file. Completed: 268674K bytes transferred in 5 seconds (421354K 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... Read 3074260 spots for /home/okishinya/chipatlas/results/dm3/SRX3632905/SRR6655545.sra Written 3074260 spots for /home/okishinya/chipatlas/results/dm3/SRX3632905/SRR6655545.sra Read 4850204 spots for /home/okishinya/chipatlas/results/dm3/SRX3632905/SRR6655546.sra Written 4850204 spots for /home/okishinya/chipatlas/results/dm3/SRX3632905/SRR6655546.sra 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 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: 00:00:01 Multiseed full-index search: 00:14:01 7924464 reads; of these: 7924464 (100.00%) were paired; of these: 1102289 (13.91%) aligned concordantly 0 times 6078514 (76.71%) aligned concordantly exactly 1 time 743661 (9.38%) aligned concordantly >1 times ---- 1102289 pairs aligned concordantly 0 times; of these: 577468 (52.39%) aligned discordantly 1 time ---- 524821 pairs aligned 0 times concordantly or discordantly; of these: 1049642 mates make up the pairs; of these: 592797 (56.48%) aligned 0 times 279341 (26.61%) aligned exactly 1 time 177504 (16.91%) aligned >1 times 96.26% overall alignment rate Time searching: 00:14:02 Overall time: 00:14:02 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] 322915 / 7331418 = 0.0440 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 @ Wed, 04 Jul 2018 09:46:21: # Command line: callpeak -t SRX3632905.bam -f BAM -g dm -n SRX3632905.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3632905.10 # format = BAM # ChIP-seq file = ['SRX3632905.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 @ Wed, 04 Jul 2018 09:46:21: # Command line: callpeak -t SRX3632905.bam -f BAM -g dm -n SRX3632905.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3632905.05 # format = BAM # ChIP-seq file = ['SRX3632905.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 @ Wed, 04 Jul 2018 09:46:21: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:46:21: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:46:21: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:46:21: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:46:21: # Command line: callpeak -t SRX3632905.bam -f BAM -g dm -n SRX3632905.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3632905.20 # format = BAM # ChIP-seq file = ['SRX3632905.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 @ Wed, 04 Jul 2018 09:46:21: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:46:21: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:46:29: 1000000 INFO @ Wed, 04 Jul 2018 09:46:29: 1000000 INFO @ Wed, 04 Jul 2018 09:46:29: 1000000 INFO @ Wed, 04 Jul 2018 09:46:37: 2000000 INFO @ Wed, 04 Jul 2018 09:46:37: 2000000 INFO @ Wed, 04 Jul 2018 09:46:37: 2000000 INFO @ Wed, 04 Jul 2018 09:46:44: 3000000 INFO @ Wed, 04 Jul 2018 09:46:44: 3000000 INFO @ Wed, 04 Jul 2018 09:46:45: 3000000 INFO @ Wed, 04 Jul 2018 09:46:52: 4000000 INFO @ Wed, 04 Jul 2018 09:46:52: 4000000 INFO @ Wed, 04 Jul 2018 09:46:53: 4000000 INFO @ Wed, 04 Jul 2018 09:47:00: 5000000 INFO @ Wed, 04 Jul 2018 09:47:00: 5000000 INFO @ Wed, 04 Jul 2018 09:47:01: 5000000 INFO @ Wed, 04 Jul 2018 09:47:08: 6000000 INFO @ Wed, 04 Jul 2018 09:47:08: 6000000 INFO @ Wed, 04 Jul 2018 09:47:09: 6000000 INFO @ Wed, 04 Jul 2018 09:47:16: 7000000 INFO @ Wed, 04 Jul 2018 09:47:16: 7000000 INFO @ Wed, 04 Jul 2018 09:47:17: 7000000 INFO @ Wed, 04 Jul 2018 09:47:25: 8000000 INFO @ Wed, 04 Jul 2018 09:47:25: 8000000 INFO @ Wed, 04 Jul 2018 09:47:25: 8000000 INFO @ Wed, 04 Jul 2018 09:47:33: 9000000 INFO @ Wed, 04 Jul 2018 09:47:33: 9000000 INFO @ Wed, 04 Jul 2018 09:47:33: 9000000 INFO @ Wed, 04 Jul 2018 09:47:41: 10000000 INFO @ Wed, 04 Jul 2018 09:47:41: 10000000 INFO @ Wed, 04 Jul 2018 09:47:41: 10000000 INFO @ Wed, 04 Jul 2018 09:47:49: 11000000 INFO @ Wed, 04 Jul 2018 09:47:49: 11000000 INFO @ Wed, 04 Jul 2018 09:47:49: 11000000 INFO @ Wed, 04 Jul 2018 09:47:57: 12000000 INFO @ Wed, 04 Jul 2018 09:47:57: 12000000 INFO @ Wed, 04 Jul 2018 09:47:57: 12000000 INFO @ Wed, 04 Jul 2018 09:48:05: 13000000 INFO @ Wed, 04 Jul 2018 09:48:05: 13000000 INFO @ Wed, 04 Jul 2018 09:48:05: 13000000 INFO @ Wed, 04 Jul 2018 09:48:13: 14000000 INFO @ Wed, 04 Jul 2018 09:48:13: 14000000 INFO @ Wed, 04 Jul 2018 09:48:14: 14000000 INFO @ Wed, 04 Jul 2018 09:48:17: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:48:17: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:48:17: #1 total tags in treatment: 6520629 INFO @ Wed, 04 Jul 2018 09:48:17: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:48:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:48:17: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:48:17: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:48:17: #1 total tags in treatment: 6520629 INFO @ Wed, 04 Jul 2018 09:48:17: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:48:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:48:17: #1 tags after filtering in treatment: 5758518 INFO @ Wed, 04 Jul 2018 09:48:17: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 04 Jul 2018 09:48:17: #1 finished! INFO @ Wed, 04 Jul 2018 09:48:17: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:48:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:48:17: #1 tags after filtering in treatment: 5758518 INFO @ Wed, 04 Jul 2018 09:48:17: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 04 Jul 2018 09:48:17: #1 finished! INFO @ Wed, 04 Jul 2018 09:48:17: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:48:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:48:18: #2 number of paired peaks: 3610 INFO @ Wed, 04 Jul 2018 09:48:18: start model_add_line... INFO @ Wed, 04 Jul 2018 09:48:18: #2 number of paired peaks: 3610 INFO @ Wed, 04 Jul 2018 09:48:18: start model_add_line... INFO @ Wed, 04 Jul 2018 09:48:18: start X-correlation... INFO @ Wed, 04 Jul 2018 09:48:18: start X-correlation... INFO @ Wed, 04 Jul 2018 09:48:18: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:48:18: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:48:18: #1 total tags in treatment: 6520629 INFO @ Wed, 04 Jul 2018 09:48:18: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:48:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:48:18: end of X-cor INFO @ Wed, 04 Jul 2018 09:48:18: end of X-cor INFO @ Wed, 04 Jul 2018 09:48:18: #2 finished! INFO @ Wed, 04 Jul 2018 09:48:18: #2 finished! INFO @ Wed, 04 Jul 2018 09:48:18: #2 predicted fragment length is 268 bps INFO @ Wed, 04 Jul 2018 09:48:18: #2 alternative fragment length(s) may be 3,268 bps INFO @ Wed, 04 Jul 2018 09:48:18: #2.2 Generate R script for model : SRX3632905.20_model.r INFO @ Wed, 04 Jul 2018 09:48:18: #2 predicted fragment length is 268 bps INFO @ Wed, 04 Jul 2018 09:48:18: #2 alternative fragment length(s) may be 3,268 bps INFO @ Wed, 04 Jul 2018 09:48:18: #2.2 Generate R script for model : SRX3632905.10_model.r INFO @ Wed, 04 Jul 2018 09:48:18: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:48:18: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:48:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:48:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:48:18: #1 tags after filtering in treatment: 5758518 INFO @ Wed, 04 Jul 2018 09:48:18: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 04 Jul 2018 09:48:18: #1 finished! INFO @ Wed, 04 Jul 2018 09:48:18: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:48:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:48:19: #2 number of paired peaks: 3610 INFO @ Wed, 04 Jul 2018 09:48:19: start model_add_line... INFO @ Wed, 04 Jul 2018 09:48:19: start X-correlation... INFO @ Wed, 04 Jul 2018 09:48:19: end of X-cor INFO @ Wed, 04 Jul 2018 09:48:19: #2 finished! INFO @ Wed, 04 Jul 2018 09:48:19: #2 predicted fragment length is 268 bps INFO @ Wed, 04 Jul 2018 09:48:19: #2 alternative fragment length(s) may be 3,268 bps INFO @ Wed, 04 Jul 2018 09:48:19: #2.2 Generate R script for model : SRX3632905.05_model.r INFO @ Wed, 04 Jul 2018 09:48:19: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:48:33: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:48:33: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:48:34: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:48:42: #4 Write output xls file... SRX3632905.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:48:42: #4 Write peak in narrowPeak format file... SRX3632905.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:48:42: #4 Write summits bed file... SRX3632905.05_summits.bed INFO @ Wed, 04 Jul 2018 09:48:42: Done! pass1 - making usageList (14 chroms): 9 millis pass2 - checking and writing primary data (3815 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:48:42: #4 Write output xls file... SRX3632905.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:48:42: #4 Write peak in narrowPeak format file... SRX3632905.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:48:42: #4 Write summits bed file... SRX3632905.20_summits.bed INFO @ Wed, 04 Jul 2018 09:48:42: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (266 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:48:42: #4 Write output xls file... SRX3632905.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:48:42: #4 Write peak in narrowPeak format file... SRX3632905.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:48:42: #4 Write summits bed file... SRX3632905.10_summits.bed INFO @ Wed, 04 Jul 2018 09:48:42: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1324 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。