Job ID = 9159851 sra ファイルのダウンロード中... Completed: 891456K bytes transferred in 12 seconds (594583K bits/sec), in 1 file, 2 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 14446472 spots for /home/okishinya/chipatlas/results/dm3/SRX749044/SRR1636772.sra Written 14446472 spots total 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: 00:32:44 14446472 reads; of these: 14446472 (100.00%) were paired; of these: 786364 (5.44%) aligned concordantly 0 times 10691950 (74.01%) aligned concordantly exactly 1 time 2968158 (20.55%) aligned concordantly >1 times ---- 786364 pairs aligned concordantly 0 times; of these: 11287 (1.44%) aligned discordantly 1 time ---- 775077 pairs aligned 0 times concordantly or discordantly; of these: 1550154 mates make up the pairs; of these: 1137882 (73.40%) aligned 0 times 297340 (19.18%) aligned exactly 1 time 114932 (7.41%) aligned >1 times 96.06% overall alignment rate Time searching: 00:32:44 Overall time: 00:32:44 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] 9007262 / 13665132 = 0.6591 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 00:58:24: # Command line: callpeak -t SRX749044.bam -f BAM -g dm -n SRX749044.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749044.10 # format = BAM # ChIP-seq file = ['SRX749044.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 00:58:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:24: # Command line: callpeak -t SRX749044.bam -f BAM -g dm -n SRX749044.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749044.05 # format = BAM # ChIP-seq file = ['SRX749044.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 00:58:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:24: # Command line: callpeak -t SRX749044.bam -f BAM -g dm -n SRX749044.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749044.20 # format = BAM # ChIP-seq file = ['SRX749044.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 00:58:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:31: 1000000 INFO @ Wed, 28 Jun 2017 00:58:31: 1000000 INFO @ Wed, 28 Jun 2017 00:58:32: 1000000 INFO @ Wed, 28 Jun 2017 00:58:38: 2000000 INFO @ Wed, 28 Jun 2017 00:58:38: 2000000 INFO @ Wed, 28 Jun 2017 00:58:40: 2000000 INFO @ Wed, 28 Jun 2017 00:58:45: 3000000 INFO @ Wed, 28 Jun 2017 00:58:45: 3000000 INFO @ Wed, 28 Jun 2017 00:58:47: 3000000 INFO @ Wed, 28 Jun 2017 00:58:53: 4000000 INFO @ Wed, 28 Jun 2017 00:58:53: 4000000 INFO @ Wed, 28 Jun 2017 00:58:53: 4000000 INFO @ Wed, 28 Jun 2017 00:59:00: 5000000 INFO @ Wed, 28 Jun 2017 00:59:01: 5000000 INFO @ Wed, 28 Jun 2017 00:59:01: 5000000 INFO @ Wed, 28 Jun 2017 00:59:07: 6000000 INFO @ Wed, 28 Jun 2017 00:59:08: 6000000 INFO @ Wed, 28 Jun 2017 00:59:08: 6000000 INFO @ Wed, 28 Jun 2017 00:59:14: 7000000 INFO @ Wed, 28 Jun 2017 00:59:16: 7000000 INFO @ Wed, 28 Jun 2017 00:59:16: 7000000 INFO @ Wed, 28 Jun 2017 00:59:21: 8000000 INFO @ Wed, 28 Jun 2017 00:59:23: 8000000 INFO @ Wed, 28 Jun 2017 00:59:24: 8000000 INFO @ Wed, 28 Jun 2017 00:59:29: 9000000 INFO @ Wed, 28 Jun 2017 00:59:30: 9000000 INFO @ Wed, 28 Jun 2017 00:59:31: 9000000 INFO @ Wed, 28 Jun 2017 00:59:35: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:59:35: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:59:35: #1 total tags in treatment: 4658703 INFO @ Wed, 28 Jun 2017 00:59:35: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:59:35: #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 00:59:35: #1 tags after filtering in treatment: 4397153 INFO @ Wed, 28 Jun 2017 00:59:35: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 28 Jun 2017 00:59:35: #1 finished! INFO @ Wed, 28 Jun 2017 00:59:35: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:59:35: #2 number of paired peaks: 3374 INFO @ Wed, 28 Jun 2017 00:59:35: start model_add_line... INFO @ Wed, 28 Jun 2017 00:59:35: start X-correlation... INFO @ Wed, 28 Jun 2017 00:59:35: end of X-cor INFO @ Wed, 28 Jun 2017 00:59:35: #2 finished! INFO @ Wed, 28 Jun 2017 00:59:35: #2 predicted fragment length is 163 bps INFO @ Wed, 28 Jun 2017 00:59:35: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 28 Jun 2017 00:59:35: #2.2 Generate R script for model : SRX749044.10_model.r INFO @ Wed, 28 Jun 2017 00:59:35: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:59:36: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:59:36: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:59:36: #1 total tags in treatment: 4658703 INFO @ Wed, 28 Jun 2017 00:59:36: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:59:36: #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 00:59:36: #1 tags after filtering in treatment: 4397153 INFO @ Wed, 28 Jun 2017 00:59:36: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 28 Jun 2017 00:59:36: #1 finished! INFO @ Wed, 28 Jun 2017 00:59:36: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:59:36: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:59:36: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:59:36: #1 total tags in treatment: 4658703 INFO @ Wed, 28 Jun 2017 00:59:36: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:59:36: #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 00:59:36: #1 tags after filtering in treatment: 4397153 INFO @ Wed, 28 Jun 2017 00:59:36: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 28 Jun 2017 00:59:36: #1 finished! INFO @ Wed, 28 Jun 2017 00:59:36: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:59:36: #2 number of paired peaks: 3374 INFO @ Wed, 28 Jun 2017 00:59:36: start model_add_line... INFO @ Wed, 28 Jun 2017 00:59:36: start X-correlation... INFO @ Wed, 28 Jun 2017 00:59:36: end of X-cor INFO @ Wed, 28 Jun 2017 00:59:36: #2 finished! INFO @ Wed, 28 Jun 2017 00:59:36: #2 predicted fragment length is 163 bps INFO @ Wed, 28 Jun 2017 00:59:36: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 28 Jun 2017 00:59:36: #2.2 Generate R script for model : SRX749044.20_model.r INFO @ Wed, 28 Jun 2017 00:59:36: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:59:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:59:36: #2 number of paired peaks: 3374 INFO @ Wed, 28 Jun 2017 00:59:36: start model_add_line... INFO @ Wed, 28 Jun 2017 00:59:37: start X-correlation... INFO @ Wed, 28 Jun 2017 00:59:37: end of X-cor INFO @ Wed, 28 Jun 2017 00:59:37: #2 finished! INFO @ Wed, 28 Jun 2017 00:59:37: #2 predicted fragment length is 163 bps INFO @ Wed, 28 Jun 2017 00:59:37: #2 alternative fragment length(s) may be 163 bps INFO @ Wed, 28 Jun 2017 00:59:37: #2.2 Generate R script for model : SRX749044.05_model.r INFO @ Wed, 28 Jun 2017 00:59:37: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:59:48: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:59:48: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:59:49: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:59:54: #4 Write output xls file... SRX749044.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:59:55: #4 Write peak in narrowPeak format file... SRX749044.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:59:55: #4 Write summits bed file... SRX749044.20_summits.bed INFO @ Wed, 28 Jun 2017 00:59:55: Done! INFO @ Wed, 28 Jun 2017 00:59:55: #4 Write output xls file... SRX749044.10_peaks.xls pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1358 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:59:55: #4 Write peak in narrowPeak format file... SRX749044.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:59:55: #4 Write summits bed file... SRX749044.10_summits.bed INFO @ Wed, 28 Jun 2017 00:59:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3194 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:59:56: #4 Write output xls file... SRX749044.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:59:56: #4 Write peak in narrowPeak format file... SRX749044.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:59:56: #4 Write summits bed file... SRX749044.05_summits.bed INFO @ Wed, 28 Jun 2017 00:59:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6794 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。