Job ID = 10480724 sra ファイルのダウンロード中... Completed: 735860K bytes transferred in 21 seconds (282321K 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 11042944 spots for /home/okishinya/chipatlas/results/dm3/SRX3087200/SRR5926832.sra Written 11042944 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: 00:00:01 Multiseed full-index search: 00:28:18 11042944 reads; of these: 11042944 (100.00%) were paired; of these: 998031 (9.04%) aligned concordantly 0 times 7716145 (69.87%) aligned concordantly exactly 1 time 2328768 (21.09%) aligned concordantly >1 times ---- 998031 pairs aligned concordantly 0 times; of these: 10841 (1.09%) aligned discordantly 1 time ---- 987190 pairs aligned 0 times concordantly or discordantly; of these: 1974380 mates make up the pairs; of these: 1516845 (76.83%) aligned 0 times 287714 (14.57%) aligned exactly 1 time 169821 (8.60%) aligned >1 times 93.13% overall alignment rate Time searching: 00:28:19 Overall time: 00:28:19 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] 1749338 / 10048552 = 0.1741 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 08:19:57: # Command line: callpeak -t SRX3087200.bam -f BAM -g dm -n SRX3087200.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087200.05 # format = BAM # ChIP-seq file = ['SRX3087200.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 08:19:57: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:19:57: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:19:57: # Command line: callpeak -t SRX3087200.bam -f BAM -g dm -n SRX3087200.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087200.20 # format = BAM # ChIP-seq file = ['SRX3087200.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 08:19:57: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:19:57: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:19:57: # Command line: callpeak -t SRX3087200.bam -f BAM -g dm -n SRX3087200.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087200.10 # format = BAM # ChIP-seq file = ['SRX3087200.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 08:19:57: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:19:57: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:20:04: 1000000 INFO @ Fri, 16 Mar 2018 08:20:04: 1000000 INFO @ Fri, 16 Mar 2018 08:20:05: 1000000 INFO @ Fri, 16 Mar 2018 08:20:11: 2000000 INFO @ Fri, 16 Mar 2018 08:20:12: 2000000 INFO @ Fri, 16 Mar 2018 08:20:12: 2000000 INFO @ Fri, 16 Mar 2018 08:20:18: 3000000 INFO @ Fri, 16 Mar 2018 08:20:19: 3000000 INFO @ Fri, 16 Mar 2018 08:20:19: 3000000 INFO @ Fri, 16 Mar 2018 08:20:25: 4000000 INFO @ Fri, 16 Mar 2018 08:20:26: 4000000 INFO @ Fri, 16 Mar 2018 08:20:26: 4000000 INFO @ Fri, 16 Mar 2018 08:20:32: 5000000 INFO @ Fri, 16 Mar 2018 08:20:33: 5000000 INFO @ Fri, 16 Mar 2018 08:20:34: 5000000 INFO @ Fri, 16 Mar 2018 08:20:39: 6000000 INFO @ Fri, 16 Mar 2018 08:20:41: 6000000 INFO @ Fri, 16 Mar 2018 08:20:41: 6000000 INFO @ Fri, 16 Mar 2018 08:20:46: 7000000 INFO @ Fri, 16 Mar 2018 08:20:48: 7000000 INFO @ Fri, 16 Mar 2018 08:20:49: 7000000 INFO @ Fri, 16 Mar 2018 08:20:53: 8000000 INFO @ Fri, 16 Mar 2018 08:20:55: 8000000 INFO @ Fri, 16 Mar 2018 08:20:56: 8000000 INFO @ Fri, 16 Mar 2018 08:21:00: 9000000 INFO @ Fri, 16 Mar 2018 08:21:03: 9000000 INFO @ Fri, 16 Mar 2018 08:21:04: 9000000 INFO @ Fri, 16 Mar 2018 08:21:06: 10000000 INFO @ Fri, 16 Mar 2018 08:21:10: 10000000 INFO @ Fri, 16 Mar 2018 08:21:11: 10000000 INFO @ Fri, 16 Mar 2018 08:21:13: 11000000 INFO @ Fri, 16 Mar 2018 08:21:17: 11000000 INFO @ Fri, 16 Mar 2018 08:21:19: 11000000 INFO @ Fri, 16 Mar 2018 08:21:20: 12000000 INFO @ Fri, 16 Mar 2018 08:21:25: 12000000 INFO @ Fri, 16 Mar 2018 08:21:27: 12000000 INFO @ Fri, 16 Mar 2018 08:21:27: 13000000 INFO @ Fri, 16 Mar 2018 08:21:32: 13000000 INFO @ Fri, 16 Mar 2018 08:21:34: 14000000 INFO @ Fri, 16 Mar 2018 08:21:34: 13000000 INFO @ Fri, 16 Mar 2018 08:21:39: 14000000 INFO @ Fri, 16 Mar 2018 08:21:41: 15000000 INFO @ Fri, 16 Mar 2018 08:21:42: 14000000 INFO @ Fri, 16 Mar 2018 08:21:47: 15000000 INFO @ Fri, 16 Mar 2018 08:21:48: 16000000 INFO @ Fri, 16 Mar 2018 08:21:49: 15000000 INFO @ Fri, 16 Mar 2018 08:21:54: 16000000 INFO @ Fri, 16 Mar 2018 08:21:54: 17000000 INFO @ Fri, 16 Mar 2018 08:21:55: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:21:55: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:21:55: #1 total tags in treatment: 8297029 INFO @ Fri, 16 Mar 2018 08:21:55: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:21:55: #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 08:21:55: #1 tags after filtering in treatment: 7522591 INFO @ Fri, 16 Mar 2018 08:21:55: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Mar 2018 08:21:55: #1 finished! INFO @ Fri, 16 Mar 2018 08:21:55: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:21:56: #2 number of paired peaks: 3467 INFO @ Fri, 16 Mar 2018 08:21:56: start model_add_line... INFO @ Fri, 16 Mar 2018 08:21:56: start X-correlation... INFO @ Fri, 16 Mar 2018 08:21:56: end of X-cor INFO @ Fri, 16 Mar 2018 08:21:56: #2 finished! INFO @ Fri, 16 Mar 2018 08:21:56: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Mar 2018 08:21:56: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 16 Mar 2018 08:21:56: #2.2 Generate R script for model : SRX3087200.10_model.r INFO @ Fri, 16 Mar 2018 08:21:56: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:21:57: 16000000 INFO @ Fri, 16 Mar 2018 08:22:01: 17000000 INFO @ Fri, 16 Mar 2018 08:22:02: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:22:02: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:22:02: #1 total tags in treatment: 8297029 INFO @ Fri, 16 Mar 2018 08:22:02: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:22:02: #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 08:22:02: #1 tags after filtering in treatment: 7522591 INFO @ Fri, 16 Mar 2018 08:22:02: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Mar 2018 08:22:02: #1 finished! INFO @ Fri, 16 Mar 2018 08:22:02: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:22:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:22:03: #2 number of paired peaks: 3467 INFO @ Fri, 16 Mar 2018 08:22:03: start model_add_line... INFO @ Fri, 16 Mar 2018 08:22:03: start X-correlation... INFO @ Fri, 16 Mar 2018 08:22:03: end of X-cor INFO @ Fri, 16 Mar 2018 08:22:03: #2 finished! INFO @ Fri, 16 Mar 2018 08:22:03: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Mar 2018 08:22:03: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 16 Mar 2018 08:22:03: #2.2 Generate R script for model : SRX3087200.20_model.r INFO @ Fri, 16 Mar 2018 08:22:03: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:22:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:22:04: 17000000 INFO @ Fri, 16 Mar 2018 08:22:04: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:22:04: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:22:04: #1 total tags in treatment: 8297029 INFO @ Fri, 16 Mar 2018 08:22:04: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:22:04: #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 08:22:04: #1 tags after filtering in treatment: 7522591 INFO @ Fri, 16 Mar 2018 08:22:04: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Mar 2018 08:22:04: #1 finished! INFO @ Fri, 16 Mar 2018 08:22:04: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:22:05: #2 number of paired peaks: 3467 INFO @ Fri, 16 Mar 2018 08:22:05: start model_add_line... INFO @ Fri, 16 Mar 2018 08:22:05: start X-correlation... INFO @ Fri, 16 Mar 2018 08:22:05: end of X-cor INFO @ Fri, 16 Mar 2018 08:22:05: #2 finished! INFO @ Fri, 16 Mar 2018 08:22:05: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Mar 2018 08:22:05: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 16 Mar 2018 08:22:05: #2.2 Generate R script for model : SRX3087200.05_model.r INFO @ Fri, 16 Mar 2018 08:22:05: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:22:21: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:22:27: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:22:30: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:22:32: #4 Write output xls file... SRX3087200.10_peaks.xls INFO @ Fri, 16 Mar 2018 08:22:32: #4 Write peak in narrowPeak format file... SRX3087200.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:22:32: #4 Write summits bed file... SRX3087200.10_summits.bed INFO @ Fri, 16 Mar 2018 08:22:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4103 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:22:38: #4 Write output xls file... SRX3087200.20_peaks.xls INFO @ Fri, 16 Mar 2018 08:22:38: #4 Write peak in narrowPeak format file... SRX3087200.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:22:38: #4 Write summits bed file... SRX3087200.20_summits.bed INFO @ Fri, 16 Mar 2018 08:22:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2545 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:22:41: #4 Write output xls file... SRX3087200.05_peaks.xls INFO @ Fri, 16 Mar 2018 08:22:41: #4 Write peak in narrowPeak format file... SRX3087200.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:22:41: #4 Write summits bed file... SRX3087200.05_summits.bed INFO @ Fri, 16 Mar 2018 08:22:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6009 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。