Job ID = 10480726 sra ファイルのダウンロード中... Completed: 978054K bytes transferred in 22 seconds (358373K 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 15128592 spots for /home/okishinya/chipatlas/results/dm3/SRX3087202/SRR5926834.sra Written 15128592 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: 00:42:46 15128592 reads; of these: 15128592 (100.00%) were paired; of these: 2236511 (14.78%) aligned concordantly 0 times 9512729 (62.88%) aligned concordantly exactly 1 time 3379352 (22.34%) aligned concordantly >1 times ---- 2236511 pairs aligned concordantly 0 times; of these: 25635 (1.15%) aligned discordantly 1 time ---- 2210876 pairs aligned 0 times concordantly or discordantly; of these: 4421752 mates make up the pairs; of these: 3725365 (84.25%) aligned 0 times 414378 (9.37%) aligned exactly 1 time 282009 (6.38%) aligned >1 times 87.69% overall alignment rate Time searching: 00:42:46 Overall time: 00:42:46 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 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] 5547526 / 12894094 = 0.4302 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 08:36:22: # Command line: callpeak -t SRX3087202.bam -f BAM -g dm -n SRX3087202.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087202.20 # format = BAM # ChIP-seq file = ['SRX3087202.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 08:36:22: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:36:22: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:36:22: # Command line: callpeak -t SRX3087202.bam -f BAM -g dm -n SRX3087202.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087202.05 # format = BAM # ChIP-seq file = ['SRX3087202.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 08:36:22: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:36:22: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:36:22: # Command line: callpeak -t SRX3087202.bam -f BAM -g dm -n SRX3087202.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087202.10 # format = BAM # ChIP-seq file = ['SRX3087202.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 08:36:22: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:36:22: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:36:29: 1000000 INFO @ Fri, 16 Mar 2018 08:36:30: 1000000 INFO @ Fri, 16 Mar 2018 08:36:30: 1000000 INFO @ Fri, 16 Mar 2018 08:36:36: 2000000 INFO @ Fri, 16 Mar 2018 08:36:39: 2000000 INFO @ Fri, 16 Mar 2018 08:36:39: 2000000 INFO @ Fri, 16 Mar 2018 08:36:43: 3000000 INFO @ Fri, 16 Mar 2018 08:36:48: 3000000 INFO @ Fri, 16 Mar 2018 08:36:49: 3000000 INFO @ Fri, 16 Mar 2018 08:36:51: 4000000 INFO @ Fri, 16 Mar 2018 08:36:56: 4000000 INFO @ Fri, 16 Mar 2018 08:36:56: 4000000 INFO @ Fri, 16 Mar 2018 08:36:59: 5000000 INFO @ Fri, 16 Mar 2018 08:37:04: 5000000 INFO @ Fri, 16 Mar 2018 08:37:05: 5000000 INFO @ Fri, 16 Mar 2018 08:37:07: 6000000 INFO @ Fri, 16 Mar 2018 08:37:11: 6000000 INFO @ Fri, 16 Mar 2018 08:37:13: 6000000 INFO @ Fri, 16 Mar 2018 08:37:15: 7000000 INFO @ Fri, 16 Mar 2018 08:37:19: 7000000 INFO @ Fri, 16 Mar 2018 08:37:21: 7000000 INFO @ Fri, 16 Mar 2018 08:37:23: 8000000 INFO @ Fri, 16 Mar 2018 08:37:28: 8000000 INFO @ Fri, 16 Mar 2018 08:37:30: 8000000 INFO @ Fri, 16 Mar 2018 08:37:32: 9000000 INFO @ Fri, 16 Mar 2018 08:37:36: 9000000 INFO @ Fri, 16 Mar 2018 08:37:39: 9000000 INFO @ Fri, 16 Mar 2018 08:37:41: 10000000 INFO @ Fri, 16 Mar 2018 08:37:45: 10000000 INFO @ Fri, 16 Mar 2018 08:37:49: 10000000 INFO @ Fri, 16 Mar 2018 08:37:50: 11000000 INFO @ Fri, 16 Mar 2018 08:37:53: 11000000 INFO @ Fri, 16 Mar 2018 08:37:58: 11000000 INFO @ Fri, 16 Mar 2018 08:37:59: 12000000 INFO @ Fri, 16 Mar 2018 08:38:01: 12000000 INFO @ Fri, 16 Mar 2018 08:38:05: 12000000 INFO @ Fri, 16 Mar 2018 08:38:06: 13000000 INFO @ Fri, 16 Mar 2018 08:38:08: 13000000 INFO @ Fri, 16 Mar 2018 08:38:13: 13000000 INFO @ Fri, 16 Mar 2018 08:38:13: 14000000 INFO @ Fri, 16 Mar 2018 08:38:16: 14000000 INFO @ Fri, 16 Mar 2018 08:38:20: 15000000 INFO @ Fri, 16 Mar 2018 08:38:20: 14000000 INFO @ Fri, 16 Mar 2018 08:38:23: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:38:23: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:38:23: #1 total tags in treatment: 7350120 INFO @ Fri, 16 Mar 2018 08:38:23: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:38:23: #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 08:38:23: 15000000 INFO @ Fri, 16 Mar 2018 08:38:23: #1 tags after filtering in treatment: 6308560 INFO @ Fri, 16 Mar 2018 08:38:23: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Mar 2018 08:38:23: #1 finished! INFO @ Fri, 16 Mar 2018 08:38:23: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:38:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:38:24: #2 number of paired peaks: 4688 INFO @ Fri, 16 Mar 2018 08:38:24: start model_add_line... INFO @ Fri, 16 Mar 2018 08:38:24: start X-correlation... INFO @ Fri, 16 Mar 2018 08:38:24: end of X-cor INFO @ Fri, 16 Mar 2018 08:38:24: #2 finished! INFO @ Fri, 16 Mar 2018 08:38:24: #2 predicted fragment length is 209 bps INFO @ Fri, 16 Mar 2018 08:38:24: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 16 Mar 2018 08:38:24: #2.2 Generate R script for model : SRX3087202.20_model.r INFO @ Fri, 16 Mar 2018 08:38:24: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:38:26: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:38:26: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:38:26: #1 total tags in treatment: 7350120 INFO @ Fri, 16 Mar 2018 08:38:26: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:38:26: #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 08:38:26: #1 tags after filtering in treatment: 6308560 INFO @ Fri, 16 Mar 2018 08:38:26: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Mar 2018 08:38:26: #1 finished! INFO @ Fri, 16 Mar 2018 08:38:26: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:38:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:38:27: #2 number of paired peaks: 4688 INFO @ Fri, 16 Mar 2018 08:38:27: start model_add_line... INFO @ Fri, 16 Mar 2018 08:38:27: start X-correlation... INFO @ Fri, 16 Mar 2018 08:38:27: end of X-cor INFO @ Fri, 16 Mar 2018 08:38:27: #2 finished! INFO @ Fri, 16 Mar 2018 08:38:27: #2 predicted fragment length is 209 bps INFO @ Fri, 16 Mar 2018 08:38:27: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 16 Mar 2018 08:38:27: #2.2 Generate R script for model : SRX3087202.10_model.r INFO @ Fri, 16 Mar 2018 08:38:27: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:38:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:38:27: 15000000 INFO @ Fri, 16 Mar 2018 08:38:30: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:38:30: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:38:30: #1 total tags in treatment: 7350120 INFO @ Fri, 16 Mar 2018 08:38:30: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:38:30: #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 08:38:30: #1 tags after filtering in treatment: 6308560 INFO @ Fri, 16 Mar 2018 08:38:30: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Mar 2018 08:38:30: #1 finished! INFO @ Fri, 16 Mar 2018 08:38:30: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:38:31: #2 number of paired peaks: 4688 INFO @ Fri, 16 Mar 2018 08:38:31: start model_add_line... INFO @ Fri, 16 Mar 2018 08:38:32: start X-correlation... INFO @ Fri, 16 Mar 2018 08:38:32: end of X-cor INFO @ Fri, 16 Mar 2018 08:38:32: #2 finished! INFO @ Fri, 16 Mar 2018 08:38:32: #2 predicted fragment length is 209 bps INFO @ Fri, 16 Mar 2018 08:38:32: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 16 Mar 2018 08:38:32: #2.2 Generate R script for model : SRX3087202.05_model.r INFO @ Fri, 16 Mar 2018 08:38:32: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:38:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:38:45: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:38:47: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:38:53: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:38:55: #4 Write output xls file... SRX3087202.20_peaks.xls INFO @ Fri, 16 Mar 2018 08:38:55: #4 Write peak in narrowPeak format file... SRX3087202.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:38:55: #4 Write summits bed file... SRX3087202.20_summits.bed INFO @ Fri, 16 Mar 2018 08:38:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3226 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:38:57: #4 Write output xls file... SRX3087202.10_peaks.xls INFO @ Fri, 16 Mar 2018 08:38:57: #4 Write peak in narrowPeak format file... SRX3087202.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:38:57: #4 Write summits bed file... SRX3087202.10_summits.bed INFO @ Fri, 16 Mar 2018 08:38:57: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5094 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:39:01: #4 Write output xls file... SRX3087202.05_peaks.xls INFO @ Fri, 16 Mar 2018 08:39:01: #4 Write peak in narrowPeak format file... SRX3087202.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:39:02: #4 Write summits bed file... SRX3087202.05_summits.bed INFO @ Fri, 16 Mar 2018 08:39:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7336 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。