Job ID = 10480723 sra ファイルのダウンロード中... Completed: 986910K bytes transferred in 26 seconds (301935K 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 15543585 spots for /home/okishinya/chipatlas/results/dm3/SRX3087199/SRR5926831.sra Written 15543585 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: 00:43:29 15543585 reads; of these: 15543585 (100.00%) were paired; of these: 1758529 (11.31%) aligned concordantly 0 times 10277514 (66.12%) aligned concordantly exactly 1 time 3507542 (22.57%) aligned concordantly >1 times ---- 1758529 pairs aligned concordantly 0 times; of these: 11608 (0.66%) aligned discordantly 1 time ---- 1746921 pairs aligned 0 times concordantly or discordantly; of these: 3493842 mates make up the pairs; of these: 2971021 (85.04%) aligned 0 times 334795 (9.58%) aligned exactly 1 time 188026 (5.38%) aligned >1 times 90.44% overall alignment rate Time searching: 00:43:29 Overall time: 00:43:29 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] 3377414 / 13786676 = 0.2450 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 08:37:45: # Command line: callpeak -t SRX3087199.bam -f BAM -g dm -n SRX3087199.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087199.20 # format = BAM # ChIP-seq file = ['SRX3087199.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 08:37:45: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:37:45: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:37:45: # Command line: callpeak -t SRX3087199.bam -f BAM -g dm -n SRX3087199.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087199.05 # format = BAM # ChIP-seq file = ['SRX3087199.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 08:37:45: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:37:45: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:37:45: # Command line: callpeak -t SRX3087199.bam -f BAM -g dm -n SRX3087199.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087199.10 # format = BAM # ChIP-seq file = ['SRX3087199.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 08:37:45: #1 read tag files... INFO @ Fri, 16 Mar 2018 08:37:45: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 08:37:52: 1000000 INFO @ Fri, 16 Mar 2018 08:37:52: 1000000 INFO @ Fri, 16 Mar 2018 08:37:52: 1000000 INFO @ Fri, 16 Mar 2018 08:37:59: 2000000 INFO @ Fri, 16 Mar 2018 08:37:59: 2000000 INFO @ Fri, 16 Mar 2018 08:37:59: 2000000 INFO @ Fri, 16 Mar 2018 08:38:06: 3000000 INFO @ Fri, 16 Mar 2018 08:38:06: 3000000 INFO @ Fri, 16 Mar 2018 08:38:06: 3000000 INFO @ Fri, 16 Mar 2018 08:38:12: 4000000 INFO @ Fri, 16 Mar 2018 08:38:13: 4000000 INFO @ Fri, 16 Mar 2018 08:38:13: 4000000 INFO @ Fri, 16 Mar 2018 08:38:19: 5000000 INFO @ Fri, 16 Mar 2018 08:38:20: 5000000 INFO @ Fri, 16 Mar 2018 08:38:20: 5000000 INFO @ Fri, 16 Mar 2018 08:38:26: 6000000 INFO @ Fri, 16 Mar 2018 08:38:27: 6000000 INFO @ Fri, 16 Mar 2018 08:38:27: 6000000 INFO @ Fri, 16 Mar 2018 08:38:32: 7000000 INFO @ Fri, 16 Mar 2018 08:38:35: 7000000 INFO @ Fri, 16 Mar 2018 08:38:35: 7000000 INFO @ Fri, 16 Mar 2018 08:38:39: 8000000 INFO @ Fri, 16 Mar 2018 08:38:41: 8000000 INFO @ Fri, 16 Mar 2018 08:38:42: 8000000 INFO @ Fri, 16 Mar 2018 08:38:46: 9000000 INFO @ Fri, 16 Mar 2018 08:38:49: 9000000 INFO @ Fri, 16 Mar 2018 08:38:49: 9000000 INFO @ Fri, 16 Mar 2018 08:38:53: 10000000 INFO @ Fri, 16 Mar 2018 08:38:56: 10000000 INFO @ Fri, 16 Mar 2018 08:38:56: 10000000 INFO @ Fri, 16 Mar 2018 08:39:00: 11000000 INFO @ Fri, 16 Mar 2018 08:39:03: 11000000 INFO @ Fri, 16 Mar 2018 08:39:03: 11000000 INFO @ Fri, 16 Mar 2018 08:39:06: 12000000 INFO @ Fri, 16 Mar 2018 08:39:10: 12000000 INFO @ Fri, 16 Mar 2018 08:39:10: 12000000 INFO @ Fri, 16 Mar 2018 08:39:13: 13000000 INFO @ Fri, 16 Mar 2018 08:39:17: 13000000 INFO @ Fri, 16 Mar 2018 08:39:17: 13000000 INFO @ Fri, 16 Mar 2018 08:39:19: 14000000 INFO @ Fri, 16 Mar 2018 08:39:24: 14000000 INFO @ Fri, 16 Mar 2018 08:39:24: 14000000 INFO @ Fri, 16 Mar 2018 08:39:26: 15000000 INFO @ Fri, 16 Mar 2018 08:39:31: 15000000 INFO @ Fri, 16 Mar 2018 08:39:31: 15000000 INFO @ Fri, 16 Mar 2018 08:39:33: 16000000 INFO @ Fri, 16 Mar 2018 08:39:38: 16000000 INFO @ Fri, 16 Mar 2018 08:39:39: 16000000 INFO @ Fri, 16 Mar 2018 08:39:39: 17000000 INFO @ Fri, 16 Mar 2018 08:39:45: 17000000 INFO @ Fri, 16 Mar 2018 08:39:46: 18000000 INFO @ Fri, 16 Mar 2018 08:39:46: 17000000 INFO @ Fri, 16 Mar 2018 08:39:52: 18000000 INFO @ Fri, 16 Mar 2018 08:39:52: 19000000 INFO @ Fri, 16 Mar 2018 08:39:53: 18000000 INFO @ Fri, 16 Mar 2018 08:39:59: 20000000 INFO @ Fri, 16 Mar 2018 08:39:59: 19000000 INFO @ Fri, 16 Mar 2018 08:40:00: 19000000 INFO @ Fri, 16 Mar 2018 08:40:05: 21000000 INFO @ Fri, 16 Mar 2018 08:40:06: 20000000 INFO @ Fri, 16 Mar 2018 08:40:08: 20000000 INFO @ Fri, 16 Mar 2018 08:40:08: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:40:08: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:40:08: #1 total tags in treatment: 10409938 INFO @ Fri, 16 Mar 2018 08:40:08: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:40:08: #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 08:40:08: #1 tags after filtering in treatment: 9334381 INFO @ Fri, 16 Mar 2018 08:40:08: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Mar 2018 08:40:08: #1 finished! INFO @ Fri, 16 Mar 2018 08:40:08: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:40:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:40:09: #2 number of paired peaks: 2893 INFO @ Fri, 16 Mar 2018 08:40:09: start model_add_line... INFO @ Fri, 16 Mar 2018 08:40:09: start X-correlation... INFO @ Fri, 16 Mar 2018 08:40:09: end of X-cor INFO @ Fri, 16 Mar 2018 08:40:09: #2 finished! INFO @ Fri, 16 Mar 2018 08:40:09: #2 predicted fragment length is 193 bps INFO @ Fri, 16 Mar 2018 08:40:09: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 16 Mar 2018 08:40:09: #2.2 Generate R script for model : SRX3087199.10_model.r INFO @ Fri, 16 Mar 2018 08:40:09: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:40:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:40:14: 21000000 INFO @ Fri, 16 Mar 2018 08:40:15: 21000000 INFO @ Fri, 16 Mar 2018 08:40:16: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:40:16: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:40:16: #1 total tags in treatment: 10409938 INFO @ Fri, 16 Mar 2018 08:40:16: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:40:16: #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 08:40:16: #1 tags after filtering in treatment: 9334381 INFO @ Fri, 16 Mar 2018 08:40:16: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Mar 2018 08:40:16: #1 finished! INFO @ Fri, 16 Mar 2018 08:40:16: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:40:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:40:17: #2 number of paired peaks: 2893 INFO @ Fri, 16 Mar 2018 08:40:17: start model_add_line... INFO @ Fri, 16 Mar 2018 08:40:17: #1 tag size is determined as 72 bps INFO @ Fri, 16 Mar 2018 08:40:17: #1 tag size = 72 INFO @ Fri, 16 Mar 2018 08:40:17: #1 total tags in treatment: 10409938 INFO @ Fri, 16 Mar 2018 08:40:17: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:40:17: #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 08:40:17: start X-correlation... INFO @ Fri, 16 Mar 2018 08:40:17: end of X-cor INFO @ Fri, 16 Mar 2018 08:40:17: #2 finished! INFO @ Fri, 16 Mar 2018 08:40:17: #2 predicted fragment length is 193 bps INFO @ Fri, 16 Mar 2018 08:40:17: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 16 Mar 2018 08:40:17: #2.2 Generate R script for model : SRX3087199.20_model.r INFO @ Fri, 16 Mar 2018 08:40:17: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:40:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:40:18: #1 tags after filtering in treatment: 9334381 INFO @ Fri, 16 Mar 2018 08:40:18: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Mar 2018 08:40:18: #1 finished! INFO @ Fri, 16 Mar 2018 08:40:18: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:40:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:40:18: #2 number of paired peaks: 2893 INFO @ Fri, 16 Mar 2018 08:40:18: start model_add_line... INFO @ Fri, 16 Mar 2018 08:40:19: start X-correlation... INFO @ Fri, 16 Mar 2018 08:40:19: end of X-cor INFO @ Fri, 16 Mar 2018 08:40:19: #2 finished! INFO @ Fri, 16 Mar 2018 08:40:19: #2 predicted fragment length is 193 bps INFO @ Fri, 16 Mar 2018 08:40:19: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 16 Mar 2018 08:40:19: #2.2 Generate R script for model : SRX3087199.05_model.r INFO @ Fri, 16 Mar 2018 08:40:19: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:40:38: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:40:46: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:40:47: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:40:50: #4 Write output xls file... SRX3087199.10_peaks.xls INFO @ Fri, 16 Mar 2018 08:40:50: #4 Write peak in narrowPeak format file... SRX3087199.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:40:50: #4 Write summits bed file... SRX3087199.10_summits.bed INFO @ Fri, 16 Mar 2018 08:40:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4522 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:40:58: #4 Write output xls file... SRX3087199.20_peaks.xls INFO @ Fri, 16 Mar 2018 08:40:58: #4 Write peak in narrowPeak format file... SRX3087199.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:40:58: #4 Write summits bed file... SRX3087199.20_summits.bed INFO @ Fri, 16 Mar 2018 08:40:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2897 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:41:00: #4 Write output xls file... SRX3087199.05_peaks.xls INFO @ Fri, 16 Mar 2018 08:41:00: #4 Write peak in narrowPeak format file... SRX3087199.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:41:01: #4 Write summits bed file... SRX3087199.05_summits.bed INFO @ Fri, 16 Mar 2018 08:41:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6465 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。