Job ID = 9159813 sra ファイルのダウンロード中... Completed: 746275K bytes transferred in 10 seconds (602147K bits/sec), in 2 files, 3 directories. 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 3227173 spots for /home/okishinya/chipatlas/results/dm3/SRX699107/SRR1573145.sra Written 3227173 spots total Written 3278036 spots for /home/okishinya/chipatlas/results/dm3/SRX699107/SRR1573146.sra Written 3278036 spots total fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:20:08 6505209 reads; of these: 6505209 (100.00%) were paired; of these: 271207 (4.17%) aligned concordantly 0 times 5194451 (79.85%) aligned concordantly exactly 1 time 1039551 (15.98%) aligned concordantly >1 times ---- 271207 pairs aligned concordantly 0 times; of these: 32794 (12.09%) aligned discordantly 1 time ---- 238413 pairs aligned 0 times concordantly or discordantly; of these: 476826 mates make up the pairs; of these: 281997 (59.14%) aligned 0 times 129091 (27.07%) aligned exactly 1 time 65738 (13.79%) aligned >1 times 97.83% overall alignment rate Time searching: 00:20:09 Overall time: 00:20:09 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] 1574886 / 6259455 = 0.2516 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, 28 Jun 2017 00:13:53: # Command line: callpeak -t SRX699107.bam -f BAM -g dm -n SRX699107.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX699107.10 # format = BAM # ChIP-seq file = ['SRX699107.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, 28 Jun 2017 00:13:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:13:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:13:53: # Command line: callpeak -t SRX699107.bam -f BAM -g dm -n SRX699107.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX699107.05 # format = BAM # ChIP-seq file = ['SRX699107.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, 28 Jun 2017 00:13:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:13:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:13:53: # Command line: callpeak -t SRX699107.bam -f BAM -g dm -n SRX699107.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX699107.20 # format = BAM # ChIP-seq file = ['SRX699107.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, 28 Jun 2017 00:13:53: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:13:53: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:14:03: 1000000 INFO @ Wed, 28 Jun 2017 00:14:03: 1000000 INFO @ Wed, 28 Jun 2017 00:14:04: 1000000 INFO @ Wed, 28 Jun 2017 00:14:13: 2000000 INFO @ Wed, 28 Jun 2017 00:14:13: 2000000 INFO @ Wed, 28 Jun 2017 00:14:16: 2000000 INFO @ Wed, 28 Jun 2017 00:14:23: 3000000 INFO @ Wed, 28 Jun 2017 00:14:23: 3000000 INFO @ Wed, 28 Jun 2017 00:14:28: 3000000 INFO @ Wed, 28 Jun 2017 00:14:34: 4000000 INFO @ Wed, 28 Jun 2017 00:14:34: 4000000 INFO @ Wed, 28 Jun 2017 00:14:40: 4000000 INFO @ Wed, 28 Jun 2017 00:14:43: 5000000 INFO @ Wed, 28 Jun 2017 00:14:44: 5000000 INFO @ Wed, 28 Jun 2017 00:14:52: 5000000 INFO @ Wed, 28 Jun 2017 00:14:53: 6000000 INFO @ Wed, 28 Jun 2017 00:14:53: 6000000 INFO @ Wed, 28 Jun 2017 00:15:03: 7000000 INFO @ Wed, 28 Jun 2017 00:15:03: 7000000 INFO @ Wed, 28 Jun 2017 00:15:04: 6000000 INFO @ Wed, 28 Jun 2017 00:15:13: 8000000 INFO @ Wed, 28 Jun 2017 00:15:13: 8000000 INFO @ Wed, 28 Jun 2017 00:15:16: 7000000 INFO @ Wed, 28 Jun 2017 00:15:22: 9000000 INFO @ Wed, 28 Jun 2017 00:15:22: 9000000 INFO @ Wed, 28 Jun 2017 00:15:28: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:15:28: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:15:28: #1 total tags in treatment: 4667168 INFO @ Wed, 28 Jun 2017 00:15:28: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:15:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:15:28: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:15:28: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:15:28: #1 total tags in treatment: 4667168 INFO @ Wed, 28 Jun 2017 00:15:28: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:15:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:15:28: #1 tags after filtering in treatment: 4487123 INFO @ Wed, 28 Jun 2017 00:15:28: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 28 Jun 2017 00:15:28: #1 finished! INFO @ Wed, 28 Jun 2017 00:15:28: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:15:28: #1 tags after filtering in treatment: 4487123 INFO @ Wed, 28 Jun 2017 00:15:28: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 28 Jun 2017 00:15:28: #1 finished! INFO @ Wed, 28 Jun 2017 00:15:28: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:15:28: 8000000 INFO @ Wed, 28 Jun 2017 00:15:28: #2 number of paired peaks: 3832 INFO @ Wed, 28 Jun 2017 00:15:28: start model_add_line... INFO @ Wed, 28 Jun 2017 00:15:28: start X-correlation... INFO @ Wed, 28 Jun 2017 00:15:28: end of X-cor INFO @ Wed, 28 Jun 2017 00:15:28: #2 finished! INFO @ Wed, 28 Jun 2017 00:15:28: #2 predicted fragment length is 223 bps INFO @ Wed, 28 Jun 2017 00:15:28: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 28 Jun 2017 00:15:28: #2.2 Generate R script for model : SRX699107.05_model.r INFO @ Wed, 28 Jun 2017 00:15:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:15:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:15:28: #2 number of paired peaks: 3832 INFO @ Wed, 28 Jun 2017 00:15:28: start model_add_line... INFO @ Wed, 28 Jun 2017 00:15:28: start X-correlation... INFO @ Wed, 28 Jun 2017 00:15:28: end of X-cor INFO @ Wed, 28 Jun 2017 00:15:28: #2 finished! INFO @ Wed, 28 Jun 2017 00:15:28: #2 predicted fragment length is 223 bps INFO @ Wed, 28 Jun 2017 00:15:28: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 28 Jun 2017 00:15:28: #2.2 Generate R script for model : SRX699107.10_model.r INFO @ Wed, 28 Jun 2017 00:15:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:15:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:15:41: 9000000 INFO @ Wed, 28 Jun 2017 00:15:41: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:15:42: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:15:48: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 00:15:48: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 00:15:48: #1 total tags in treatment: 4667168 INFO @ Wed, 28 Jun 2017 00:15:48: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:15:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:15:48: #1 tags after filtering in treatment: 4487123 INFO @ Wed, 28 Jun 2017 00:15:48: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 28 Jun 2017 00:15:48: #1 finished! INFO @ Wed, 28 Jun 2017 00:15:48: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:15:48: #4 Write output xls file... SRX699107.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:15:48: #4 Write peak in narrowPeak format file... SRX699107.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:15:48: #2 number of paired peaks: 3832 INFO @ Wed, 28 Jun 2017 00:15:48: start model_add_line... INFO @ Wed, 28 Jun 2017 00:15:48: #4 Write summits bed file... SRX699107.10_summits.bed INFO @ Wed, 28 Jun 2017 00:15:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (746 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:15:49: start X-correlation... INFO @ Wed, 28 Jun 2017 00:15:49: end of X-cor INFO @ Wed, 28 Jun 2017 00:15:49: #2 finished! INFO @ Wed, 28 Jun 2017 00:15:49: #2 predicted fragment length is 223 bps INFO @ Wed, 28 Jun 2017 00:15:49: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 28 Jun 2017 00:15:49: #2.2 Generate R script for model : SRX699107.20_model.r INFO @ Wed, 28 Jun 2017 00:15:49: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:15:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:15:49: #4 Write output xls file... SRX699107.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:15:49: #4 Write peak in narrowPeak format file... SRX699107.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:15:49: #4 Write summits bed file... SRX699107.05_summits.bed INFO @ Wed, 28 Jun 2017 00:15:49: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1986 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:16:02: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:16:09: #4 Write output xls file... SRX699107.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:16:09: #4 Write peak in narrowPeak format file... SRX699107.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:16:09: #4 Write summits bed file... SRX699107.20_summits.bed INFO @ Wed, 28 Jun 2017 00:16:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。