Job ID = 9371936 sra ファイルのダウンロード中... Completed: 1752308K bytes transferred in 45 seconds (314103K 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 18785501 spots for /home/okishinya/chipatlas/results/dm3/SRX2548343/SRR5241487.sra Written 18785501 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: 04:32:38 18785501 reads; of these: 18785501 (100.00%) were paired; of these: 7452381 (39.67%) aligned concordantly 0 times 4189055 (22.30%) aligned concordantly exactly 1 time 7144065 (38.03%) aligned concordantly >1 times ---- 7452381 pairs aligned concordantly 0 times; of these: 750116 (10.07%) aligned discordantly 1 time ---- 6702265 pairs aligned 0 times concordantly or discordantly; of these: 13404530 mates make up the pairs; of these: 10150657 (75.73%) aligned 0 times 451454 (3.37%) aligned exactly 1 time 2802419 (20.91%) aligned >1 times 72.98% overall alignment rate Time searching: 04:32:38 Overall time: 04:32:38 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] 300135 / 12030868 = 0.0249 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, 04 Aug 2017 19:53:30: # Command line: callpeak -t SRX2548343.bam -f BAM -g dm -n SRX2548343.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2548343.20 # format = BAM # ChIP-seq file = ['SRX2548343.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, 04 Aug 2017 19:53:30: #1 read tag files... INFO @ Fri, 04 Aug 2017 19:53:30: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 19:53:30: # Command line: callpeak -t SRX2548343.bam -f BAM -g dm -n SRX2548343.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2548343.10 # format = BAM # ChIP-seq file = ['SRX2548343.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, 04 Aug 2017 19:53:30: #1 read tag files... INFO @ Fri, 04 Aug 2017 19:53:30: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 19:53:30: # Command line: callpeak -t SRX2548343.bam -f BAM -g dm -n SRX2548343.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2548343.05 # format = BAM # ChIP-seq file = ['SRX2548343.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, 04 Aug 2017 19:53:30: #1 read tag files... INFO @ Fri, 04 Aug 2017 19:53:30: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 19:53:45: 1000000 INFO @ Fri, 04 Aug 2017 19:53:46: 1000000 INFO @ Fri, 04 Aug 2017 19:53:51: 1000000 INFO @ Fri, 04 Aug 2017 19:53:57: 2000000 INFO @ Fri, 04 Aug 2017 19:53:58: 2000000 INFO @ Fri, 04 Aug 2017 19:54:05: 2000000 INFO @ Fri, 04 Aug 2017 19:54:08: 3000000 INFO @ Fri, 04 Aug 2017 19:54:10: 3000000 INFO @ Fri, 04 Aug 2017 19:54:21: 3000000 INFO @ Fri, 04 Aug 2017 19:54:22: 4000000 INFO @ Fri, 04 Aug 2017 19:54:25: 4000000 INFO @ Fri, 04 Aug 2017 19:54:33: 5000000 INFO @ Fri, 04 Aug 2017 19:54:38: 4000000 INFO @ Fri, 04 Aug 2017 19:54:43: 5000000 INFO @ Fri, 04 Aug 2017 19:54:44: 6000000 INFO @ Fri, 04 Aug 2017 19:54:55: 7000000 INFO @ Fri, 04 Aug 2017 19:54:57: 5000000 INFO @ Fri, 04 Aug 2017 19:55:02: 6000000 INFO @ Fri, 04 Aug 2017 19:55:13: 8000000 INFO @ Fri, 04 Aug 2017 19:55:14: 6000000 INFO @ Fri, 04 Aug 2017 19:55:21: 7000000 INFO @ Fri, 04 Aug 2017 19:55:32: 7000000 INFO @ Fri, 04 Aug 2017 19:55:34: 9000000 INFO @ Fri, 04 Aug 2017 19:55:40: 8000000 INFO @ Fri, 04 Aug 2017 19:55:49: 8000000 INFO @ Fri, 04 Aug 2017 19:56:03: 10000000 INFO @ Fri, 04 Aug 2017 19:56:08: 9000000 INFO @ Fri, 04 Aug 2017 19:56:09: 9000000 INFO @ Fri, 04 Aug 2017 19:56:33: 11000000 INFO @ Fri, 04 Aug 2017 19:56:33: 10000000 INFO @ Fri, 04 Aug 2017 19:56:38: 10000000 INFO @ Fri, 04 Aug 2017 19:56:53: 11000000 INFO @ Fri, 04 Aug 2017 19:57:04: 12000000 INFO @ Fri, 04 Aug 2017 19:57:10: 11000000 INFO @ Fri, 04 Aug 2017 19:57:12: 12000000 INFO @ Fri, 04 Aug 2017 19:57:30: 13000000 INFO @ Fri, 04 Aug 2017 19:57:37: 13000000 INFO @ Fri, 04 Aug 2017 19:57:43: 12000000 INFO @ Fri, 04 Aug 2017 19:57:44: 14000000 INFO @ Fri, 04 Aug 2017 19:57:58: 15000000 INFO @ Fri, 04 Aug 2017 19:58:07: 14000000 INFO @ Fri, 04 Aug 2017 19:58:16: 13000000 INFO @ Fri, 04 Aug 2017 19:58:17: 16000000 INFO @ Fri, 04 Aug 2017 19:58:28: 15000000 INFO @ Fri, 04 Aug 2017 19:58:32: 17000000 INFO @ Fri, 04 Aug 2017 19:58:46: 16000000 INFO @ Fri, 04 Aug 2017 19:58:48: 14000000 INFO @ Fri, 04 Aug 2017 19:58:50: 18000000 INFO @ Fri, 04 Aug 2017 19:59:04: 17000000 INFO @ Fri, 04 Aug 2017 19:59:09: 19000000 INFO @ Fri, 04 Aug 2017 19:59:19: 15000000 INFO @ Fri, 04 Aug 2017 19:59:22: 18000000 INFO @ Fri, 04 Aug 2017 19:59:27: 20000000 INFO @ Fri, 04 Aug 2017 19:59:38: 19000000 INFO @ Fri, 04 Aug 2017 19:59:43: 21000000 INFO @ Fri, 04 Aug 2017 19:59:50: 16000000 INFO @ Fri, 04 Aug 2017 19:59:54: 20000000 INFO @ Fri, 04 Aug 2017 19:59:58: 22000000 INFO @ Fri, 04 Aug 2017 20:00:08: 21000000 INFO @ Fri, 04 Aug 2017 20:00:13: 23000000 INFO @ Fri, 04 Aug 2017 20:00:21: 17000000 INFO @ Fri, 04 Aug 2017 20:00:21: 22000000 INFO @ Fri, 04 Aug 2017 20:00:28: 24000000 INFO @ Fri, 04 Aug 2017 20:00:35: 23000000 INFO @ Fri, 04 Aug 2017 20:00:44: 25000000 INFO @ Fri, 04 Aug 2017 20:00:48: 24000000 INFO @ Fri, 04 Aug 2017 20:00:49: 18000000 INFO @ Fri, 04 Aug 2017 20:00:59: 26000000 INFO @ Fri, 04 Aug 2017 20:01:03: 25000000 INFO @ Fri, 04 Aug 2017 20:01:11: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 20:01:11: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 20:01:11: #1 total tags in treatment: 11040142 INFO @ Fri, 04 Aug 2017 20:01:11: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 20:01:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 20:01:12: #1 tags after filtering in treatment: 9622728 INFO @ Fri, 04 Aug 2017 20:01:12: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 04 Aug 2017 20:01:12: #1 finished! INFO @ Fri, 04 Aug 2017 20:01:12: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 20:01:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 20:01:13: #2 number of paired peaks: 3039 INFO @ Fri, 04 Aug 2017 20:01:13: start model_add_line... INFO @ Fri, 04 Aug 2017 20:01:13: start X-correlation... INFO @ Fri, 04 Aug 2017 20:01:13: end of X-cor INFO @ Fri, 04 Aug 2017 20:01:13: #2 finished! INFO @ Fri, 04 Aug 2017 20:01:13: #2 predicted fragment length is 225 bps INFO @ Fri, 04 Aug 2017 20:01:13: #2 alternative fragment length(s) may be 225 bps INFO @ Fri, 04 Aug 2017 20:01:13: #2.2 Generate R script for model : SRX2548343.10_model.r INFO @ Fri, 04 Aug 2017 20:01:13: #3 Call peaks... INFO @ Fri, 04 Aug 2017 20:01:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 20:01:15: 19000000 INFO @ Fri, 04 Aug 2017 20:01:15: 26000000 INFO @ Fri, 04 Aug 2017 20:01:24: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 20:01:24: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 20:01:24: #1 total tags in treatment: 11040142 INFO @ Fri, 04 Aug 2017 20:01:24: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 20:01:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 20:01:24: #1 tags after filtering in treatment: 9622728 INFO @ Fri, 04 Aug 2017 20:01:24: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 04 Aug 2017 20:01:24: #1 finished! INFO @ Fri, 04 Aug 2017 20:01:24: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 20:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 20:01:26: #2 number of paired peaks: 3039 INFO @ Fri, 04 Aug 2017 20:01:26: start model_add_line... INFO @ Fri, 04 Aug 2017 20:01:26: start X-correlation... INFO @ Fri, 04 Aug 2017 20:01:26: end of X-cor INFO @ Fri, 04 Aug 2017 20:01:26: #2 finished! INFO @ Fri, 04 Aug 2017 20:01:26: #2 predicted fragment length is 225 bps INFO @ Fri, 04 Aug 2017 20:01:26: #2 alternative fragment length(s) may be 225 bps INFO @ Fri, 04 Aug 2017 20:01:26: #2.2 Generate R script for model : SRX2548343.20_model.r INFO @ Fri, 04 Aug 2017 20:01:26: #3 Call peaks... INFO @ Fri, 04 Aug 2017 20:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 20:01:39: 20000000 INFO @ Fri, 04 Aug 2017 20:01:52: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 20:01:59: 21000000 INFO @ Fri, 04 Aug 2017 20:02:04: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 20:02:11: #4 Write output xls file... SRX2548343.10_peaks.xls INFO @ Fri, 04 Aug 2017 20:02:12: #4 Write peak in narrowPeak format file... SRX2548343.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 20:02:12: #4 Write summits bed file... SRX2548343.10_summits.bed INFO @ Fri, 04 Aug 2017 20:02:12: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6097 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 20:02:21: 22000000 INFO @ Fri, 04 Aug 2017 20:02:23: #4 Write output xls file... SRX2548343.20_peaks.xls INFO @ Fri, 04 Aug 2017 20:02:23: #4 Write peak in narrowPeak format file... SRX2548343.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 20:02:23: #4 Write summits bed file... SRX2548343.20_summits.bed INFO @ Fri, 04 Aug 2017 20:02:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3730 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 20:02:43: 23000000 INFO @ Fri, 04 Aug 2017 20:03:03: 24000000 INFO @ Fri, 04 Aug 2017 20:03:16: 25000000 INFO @ Fri, 04 Aug 2017 20:03:27: 26000000 INFO @ Fri, 04 Aug 2017 20:03:37: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 20:03:37: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 20:03:37: #1 total tags in treatment: 11040142 INFO @ Fri, 04 Aug 2017 20:03:37: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 20:03:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 20:03:37: #1 tags after filtering in treatment: 9622728 INFO @ Fri, 04 Aug 2017 20:03:37: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 04 Aug 2017 20:03:37: #1 finished! INFO @ Fri, 04 Aug 2017 20:03:37: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 20:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 20:03:38: #2 number of paired peaks: 3039 INFO @ Fri, 04 Aug 2017 20:03:38: start model_add_line... INFO @ Fri, 04 Aug 2017 20:03:39: start X-correlation... INFO @ Fri, 04 Aug 2017 20:03:39: end of X-cor INFO @ Fri, 04 Aug 2017 20:03:39: #2 finished! INFO @ Fri, 04 Aug 2017 20:03:39: #2 predicted fragment length is 225 bps INFO @ Fri, 04 Aug 2017 20:03:39: #2 alternative fragment length(s) may be 225 bps INFO @ Fri, 04 Aug 2017 20:03:39: #2.2 Generate R script for model : SRX2548343.05_model.r INFO @ Fri, 04 Aug 2017 20:03:39: #3 Call peaks... INFO @ Fri, 04 Aug 2017 20:03:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 20:04:16: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 20:04:37: #4 Write output xls file... SRX2548343.05_peaks.xls INFO @ Fri, 04 Aug 2017 20:04:37: #4 Write peak in narrowPeak format file... SRX2548343.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 20:04:37: #4 Write summits bed file... SRX2548343.05_summits.bed INFO @ Fri, 04 Aug 2017 20:04:37: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9103 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。