Job ID = 9371934 sra ファイルのダウンロード中... Completed: 1253309K bytes transferred in 13 seconds (769043K 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 14059502 spots for /home/okishinya/chipatlas/results/dm3/SRX2548345/SRR5241489.sra Written 14059502 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: 02:00:39 14059502 reads; of these: 14059502 (100.00%) were paired; of these: 2859478 (20.34%) aligned concordantly 0 times 3994795 (28.41%) aligned concordantly exactly 1 time 7205229 (51.25%) aligned concordantly >1 times ---- 2859478 pairs aligned concordantly 0 times; of these: 538432 (18.83%) aligned discordantly 1 time ---- 2321046 pairs aligned 0 times concordantly or discordantly; of these: 4642092 mates make up the pairs; of these: 2087758 (44.97%) aligned 0 times 336153 (7.24%) aligned exactly 1 time 2218181 (47.78%) aligned >1 times 92.58% overall alignment rate Time searching: 02:00:39 Overall time: 02:00:39 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] 363334 / 11676814 = 0.0311 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 17:14:13: # Command line: callpeak -t SRX2548345.bam -f BAM -g dm -n SRX2548345.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2548345.10 # format = BAM # ChIP-seq file = ['SRX2548345.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 17:14:13: #1 read tag files... INFO @ Fri, 04 Aug 2017 17:14:13: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 17:14:13: # Command line: callpeak -t SRX2548345.bam -f BAM -g dm -n SRX2548345.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2548345.05 # format = BAM # ChIP-seq file = ['SRX2548345.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 17:14:13: #1 read tag files... INFO @ Fri, 04 Aug 2017 17:14:13: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 17:14:13: # Command line: callpeak -t SRX2548345.bam -f BAM -g dm -n SRX2548345.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2548345.20 # format = BAM # ChIP-seq file = ['SRX2548345.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 17:14:13: #1 read tag files... INFO @ Fri, 04 Aug 2017 17:14:13: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 17:14:21: 1000000 INFO @ Fri, 04 Aug 2017 17:14:21: 1000000 INFO @ Fri, 04 Aug 2017 17:14:21: 1000000 INFO @ Fri, 04 Aug 2017 17:14:28: 2000000 INFO @ Fri, 04 Aug 2017 17:14:29: 2000000 INFO @ Fri, 04 Aug 2017 17:14:29: 2000000 INFO @ Fri, 04 Aug 2017 17:14:36: 3000000 INFO @ Fri, 04 Aug 2017 17:14:37: 3000000 INFO @ Fri, 04 Aug 2017 17:14:37: 3000000 INFO @ Fri, 04 Aug 2017 17:14:44: 4000000 INFO @ Fri, 04 Aug 2017 17:14:44: 4000000 INFO @ Fri, 04 Aug 2017 17:14:44: 4000000 INFO @ Fri, 04 Aug 2017 17:14:52: 5000000 INFO @ Fri, 04 Aug 2017 17:14:52: 5000000 INFO @ Fri, 04 Aug 2017 17:14:52: 5000000 INFO @ Fri, 04 Aug 2017 17:15:00: 6000000 INFO @ Fri, 04 Aug 2017 17:15:00: 6000000 INFO @ Fri, 04 Aug 2017 17:15:00: 6000000 INFO @ Fri, 04 Aug 2017 17:15:08: 7000000 INFO @ Fri, 04 Aug 2017 17:15:08: 7000000 INFO @ Fri, 04 Aug 2017 17:15:08: 7000000 INFO @ Fri, 04 Aug 2017 17:15:16: 8000000 INFO @ Fri, 04 Aug 2017 17:15:16: 8000000 INFO @ Fri, 04 Aug 2017 17:15:16: 8000000 INFO @ Fri, 04 Aug 2017 17:15:24: 9000000 INFO @ Fri, 04 Aug 2017 17:15:24: 9000000 INFO @ Fri, 04 Aug 2017 17:15:24: 9000000 INFO @ Fri, 04 Aug 2017 17:15:32: 10000000 INFO @ Fri, 04 Aug 2017 17:15:32: 10000000 INFO @ Fri, 04 Aug 2017 17:15:32: 10000000 INFO @ Fri, 04 Aug 2017 17:15:40: 11000000 INFO @ Fri, 04 Aug 2017 17:15:40: 11000000 INFO @ Fri, 04 Aug 2017 17:15:40: 11000000 INFO @ Fri, 04 Aug 2017 17:15:47: 12000000 INFO @ Fri, 04 Aug 2017 17:15:47: 12000000 INFO @ Fri, 04 Aug 2017 17:15:48: 12000000 INFO @ Fri, 04 Aug 2017 17:15:55: 13000000 INFO @ Fri, 04 Aug 2017 17:15:55: 13000000 INFO @ Fri, 04 Aug 2017 17:15:55: 13000000 INFO @ Fri, 04 Aug 2017 17:16:03: 14000000 INFO @ Fri, 04 Aug 2017 17:16:04: 14000000 INFO @ Fri, 04 Aug 2017 17:16:04: 14000000 INFO @ Fri, 04 Aug 2017 17:16:11: 15000000 INFO @ Fri, 04 Aug 2017 17:16:11: 15000000 INFO @ Fri, 04 Aug 2017 17:16:12: 15000000 INFO @ Fri, 04 Aug 2017 17:16:19: 16000000 INFO @ Fri, 04 Aug 2017 17:16:20: 16000000 INFO @ Fri, 04 Aug 2017 17:16:20: 16000000 INFO @ Fri, 04 Aug 2017 17:16:26: 17000000 INFO @ Fri, 04 Aug 2017 17:16:29: 17000000 INFO @ Fri, 04 Aug 2017 17:16:29: 17000000 INFO @ Fri, 04 Aug 2017 17:16:33: 18000000 INFO @ Fri, 04 Aug 2017 17:16:37: 18000000 INFO @ Fri, 04 Aug 2017 17:16:38: 18000000 INFO @ Fri, 04 Aug 2017 17:16:41: 19000000 INFO @ Fri, 04 Aug 2017 17:16:47: 19000000 INFO @ Fri, 04 Aug 2017 17:16:47: 19000000 INFO @ Fri, 04 Aug 2017 17:16:48: 20000000 INFO @ Fri, 04 Aug 2017 17:16:56: 20000000 INFO @ Fri, 04 Aug 2017 17:16:56: 21000000 INFO @ Fri, 04 Aug 2017 17:16:56: 20000000 INFO @ Fri, 04 Aug 2017 17:17:03: 22000000 INFO @ Fri, 04 Aug 2017 17:17:04: 21000000 INFO @ Fri, 04 Aug 2017 17:17:06: 21000000 INFO @ Fri, 04 Aug 2017 17:17:11: 23000000 INFO @ Fri, 04 Aug 2017 17:17:13: 22000000 INFO @ Fri, 04 Aug 2017 17:17:15: 22000000 INFO @ Fri, 04 Aug 2017 17:17:18: 24000000 INFO @ Fri, 04 Aug 2017 17:17:23: 23000000 INFO @ Fri, 04 Aug 2017 17:17:24: 23000000 INFO @ Fri, 04 Aug 2017 17:17:26: 25000000 INFO @ Fri, 04 Aug 2017 17:17:28: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 17:17:28: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 17:17:28: #1 total tags in treatment: 10839250 INFO @ Fri, 04 Aug 2017 17:17:28: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 17:17:28: #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 17:17:28: #1 tags after filtering in treatment: 9418687 INFO @ Fri, 04 Aug 2017 17:17:28: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 04 Aug 2017 17:17:28: #1 finished! INFO @ Fri, 04 Aug 2017 17:17:28: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 17:17:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 17:17:29: #2 number of paired peaks: 2861 INFO @ Fri, 04 Aug 2017 17:17:29: start model_add_line... INFO @ Fri, 04 Aug 2017 17:17:30: start X-correlation... INFO @ Fri, 04 Aug 2017 17:17:30: end of X-cor INFO @ Fri, 04 Aug 2017 17:17:30: #2 finished! INFO @ Fri, 04 Aug 2017 17:17:30: #2 predicted fragment length is 207 bps INFO @ Fri, 04 Aug 2017 17:17:30: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 04 Aug 2017 17:17:30: #2.2 Generate R script for model : SRX2548345.10_model.r INFO @ Fri, 04 Aug 2017 17:17:30: #3 Call peaks... INFO @ Fri, 04 Aug 2017 17:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 17:17:32: 24000000 INFO @ Fri, 04 Aug 2017 17:17:33: 24000000 INFO @ Fri, 04 Aug 2017 17:17:41: 25000000 INFO @ Fri, 04 Aug 2017 17:17:42: 25000000 INFO @ Fri, 04 Aug 2017 17:17:43: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 17:17:43: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 17:17:43: #1 total tags in treatment: 10839250 INFO @ Fri, 04 Aug 2017 17:17:43: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 17:17:43: #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 17:17:44: #1 tags after filtering in treatment: 9418687 INFO @ Fri, 04 Aug 2017 17:17:44: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 04 Aug 2017 17:17:44: #1 finished! INFO @ Fri, 04 Aug 2017 17:17:44: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 17:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 17:17:45: #2 number of paired peaks: 2861 INFO @ Fri, 04 Aug 2017 17:17:45: start model_add_line... INFO @ Fri, 04 Aug 2017 17:17:45: start X-correlation... INFO @ Fri, 04 Aug 2017 17:17:45: end of X-cor INFO @ Fri, 04 Aug 2017 17:17:45: #2 finished! INFO @ Fri, 04 Aug 2017 17:17:45: #2 predicted fragment length is 207 bps INFO @ Fri, 04 Aug 2017 17:17:45: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 04 Aug 2017 17:17:45: #2.2 Generate R script for model : SRX2548345.05_model.r INFO @ Fri, 04 Aug 2017 17:17:45: #3 Call peaks... INFO @ Fri, 04 Aug 2017 17:17:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 17:17:45: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 17:17:45: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 17:17:45: #1 total tags in treatment: 10839250 INFO @ Fri, 04 Aug 2017 17:17:45: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 17:17:45: #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 17:17:45: #1 tags after filtering in treatment: 9418687 INFO @ Fri, 04 Aug 2017 17:17:45: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 04 Aug 2017 17:17:45: #1 finished! INFO @ Fri, 04 Aug 2017 17:17:45: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 17:17:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 17:17:46: #2 number of paired peaks: 2861 INFO @ Fri, 04 Aug 2017 17:17:46: start model_add_line... INFO @ Fri, 04 Aug 2017 17:17:46: start X-correlation... INFO @ Fri, 04 Aug 2017 17:17:46: end of X-cor INFO @ Fri, 04 Aug 2017 17:17:46: #2 finished! INFO @ Fri, 04 Aug 2017 17:17:46: #2 predicted fragment length is 207 bps INFO @ Fri, 04 Aug 2017 17:17:46: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 04 Aug 2017 17:17:46: #2.2 Generate R script for model : SRX2548345.20_model.r INFO @ Fri, 04 Aug 2017 17:17:46: #3 Call peaks... INFO @ Fri, 04 Aug 2017 17:17:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 17:17:58: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 17:18:11: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 17:18:12: #4 Write output xls file... SRX2548345.10_peaks.xls INFO @ Fri, 04 Aug 2017 17:18:12: #4 Write peak in narrowPeak format file... SRX2548345.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 17:18:12: #4 Write summits bed file... SRX2548345.10_summits.bed INFO @ Fri, 04 Aug 2017 17:18:12: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6154 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 17:18:14: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 17:18:25: #4 Write output xls file... SRX2548345.05_peaks.xls INFO @ Fri, 04 Aug 2017 17:18:25: #4 Write peak in narrowPeak format file... SRX2548345.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 17:18:26: #4 Write summits bed file... SRX2548345.05_summits.bed INFO @ Fri, 04 Aug 2017 17:18:26: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9603 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 17:18:28: #4 Write output xls file... SRX2548345.20_peaks.xls INFO @ Fri, 04 Aug 2017 17:18:28: #4 Write peak in narrowPeak format file... SRX2548345.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 17:18:28: #4 Write summits bed file... SRX2548345.20_summits.bed INFO @ Fri, 04 Aug 2017 17:18:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3522 records, 4 fields): 35 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。