Job ID = 11171109 sra ファイルのダウンロード中... Completed: 1309025K bytes transferred in 17 seconds (605934K 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... Read 28337250 spots for /home/okishinya/chipatlas/results/dm3/SRX2000505/SRR4000132.sra Written 28337250 spots for /home/okishinya/chipatlas/results/dm3/SRX2000505/SRR4000132.sra 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:51:03 28337250 reads; of these: 28337250 (100.00%) were paired; of these: 8295847 (29.28%) aligned concordantly 0 times 15459071 (54.55%) aligned concordantly exactly 1 time 4582332 (16.17%) aligned concordantly >1 times ---- 8295847 pairs aligned concordantly 0 times; of these: 93711 (1.13%) aligned discordantly 1 time ---- 8202136 pairs aligned 0 times concordantly or discordantly; of these: 16404272 mates make up the pairs; of these: 15165366 (92.45%) aligned 0 times 754519 (4.60%) aligned exactly 1 time 484387 (2.95%) aligned >1 times 73.24% overall alignment rate Time searching: 00:51:04 Overall time: 00:51:04 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 20 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] 422494 / 20070112 = 0.0211 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 @ Sat, 08 Sep 2018 12:57:09: # Command line: callpeak -t SRX2000505.bam -f BAM -g dm -n SRX2000505.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2000505.20 # format = BAM # ChIP-seq file = ['SRX2000505.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 @ Sat, 08 Sep 2018 12:57:09: # Command line: callpeak -t SRX2000505.bam -f BAM -g dm -n SRX2000505.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2000505.10 # format = BAM # ChIP-seq file = ['SRX2000505.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 @ Sat, 08 Sep 2018 12:57:09: # Command line: callpeak -t SRX2000505.bam -f BAM -g dm -n SRX2000505.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2000505.05 # format = BAM # ChIP-seq file = ['SRX2000505.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 @ Sat, 08 Sep 2018 12:57:09: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:57:09: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:57:09: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:57:09: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:57:09: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:57:09: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:57:14: 1000000 INFO @ Sat, 08 Sep 2018 12:57:14: 1000000 INFO @ Sat, 08 Sep 2018 12:57:15: 1000000 INFO @ Sat, 08 Sep 2018 12:57:20: 2000000 INFO @ Sat, 08 Sep 2018 12:57:20: 2000000 INFO @ Sat, 08 Sep 2018 12:57:21: 2000000 INFO @ Sat, 08 Sep 2018 12:57:26: 3000000 INFO @ Sat, 08 Sep 2018 12:57:27: 3000000 INFO @ Sat, 08 Sep 2018 12:57:28: 3000000 INFO @ Sat, 08 Sep 2018 12:57:33: 4000000 INFO @ Sat, 08 Sep 2018 12:57:33: 4000000 INFO @ Sat, 08 Sep 2018 12:57:34: 4000000 INFO @ Sat, 08 Sep 2018 12:57:39: 5000000 INFO @ Sat, 08 Sep 2018 12:57:39: 5000000 INFO @ Sat, 08 Sep 2018 12:57:41: 5000000 INFO @ Sat, 08 Sep 2018 12:57:45: 6000000 INFO @ Sat, 08 Sep 2018 12:57:46: 6000000 INFO @ Sat, 08 Sep 2018 12:57:48: 6000000 INFO @ Sat, 08 Sep 2018 12:57:52: 7000000 INFO @ Sat, 08 Sep 2018 12:57:53: 7000000 INFO @ Sat, 08 Sep 2018 12:57:55: 7000000 INFO @ Sat, 08 Sep 2018 12:57:59: 8000000 INFO @ Sat, 08 Sep 2018 12:58:00: 8000000 INFO @ Sat, 08 Sep 2018 12:58:02: 8000000 INFO @ Sat, 08 Sep 2018 12:58:06: 9000000 INFO @ Sat, 08 Sep 2018 12:58:06: 9000000 INFO @ Sat, 08 Sep 2018 12:58:09: 9000000 INFO @ Sat, 08 Sep 2018 12:58:12: 10000000 INFO @ Sat, 08 Sep 2018 12:58:13: 10000000 INFO @ Sat, 08 Sep 2018 12:58:16: 10000000 INFO @ Sat, 08 Sep 2018 12:58:19: 11000000 INFO @ Sat, 08 Sep 2018 12:58:20: 11000000 INFO @ Sat, 08 Sep 2018 12:58:23: 11000000 INFO @ Sat, 08 Sep 2018 12:58:26: 12000000 INFO @ Sat, 08 Sep 2018 12:58:27: 12000000 INFO @ Sat, 08 Sep 2018 12:58:30: 12000000 INFO @ Sat, 08 Sep 2018 12:58:32: 13000000 INFO @ Sat, 08 Sep 2018 12:58:34: 13000000 INFO @ Sat, 08 Sep 2018 12:58:37: 13000000 INFO @ Sat, 08 Sep 2018 12:58:39: 14000000 INFO @ Sat, 08 Sep 2018 12:58:41: 14000000 INFO @ Sat, 08 Sep 2018 12:58:44: 14000000 INFO @ Sat, 08 Sep 2018 12:58:46: 15000000 INFO @ Sat, 08 Sep 2018 12:58:47: 15000000 INFO @ Sat, 08 Sep 2018 12:58:51: 15000000 INFO @ Sat, 08 Sep 2018 12:58:52: 16000000 INFO @ Sat, 08 Sep 2018 12:58:54: 16000000 INFO @ Sat, 08 Sep 2018 12:58:58: 16000000 INFO @ Sat, 08 Sep 2018 12:58:59: 17000000 INFO @ Sat, 08 Sep 2018 12:59:01: 17000000 INFO @ Sat, 08 Sep 2018 12:59:05: 17000000 INFO @ Sat, 08 Sep 2018 12:59:06: 18000000 INFO @ Sat, 08 Sep 2018 12:59:08: 18000000 INFO @ Sat, 08 Sep 2018 12:59:12: 18000000 INFO @ Sat, 08 Sep 2018 12:59:12: 19000000 INFO @ Sat, 08 Sep 2018 12:59:14: 19000000 INFO @ Sat, 08 Sep 2018 12:59:19: 20000000 INFO @ Sat, 08 Sep 2018 12:59:19: 19000000 INFO @ Sat, 08 Sep 2018 12:59:21: 20000000 INFO @ Sat, 08 Sep 2018 12:59:26: 21000000 INFO @ Sat, 08 Sep 2018 12:59:26: 20000000 INFO @ Sat, 08 Sep 2018 12:59:28: 21000000 INFO @ Sat, 08 Sep 2018 12:59:32: 22000000 INFO @ Sat, 08 Sep 2018 12:59:33: 21000000 INFO @ Sat, 08 Sep 2018 12:59:35: 22000000 INFO @ Sat, 08 Sep 2018 12:59:39: 23000000 INFO @ Sat, 08 Sep 2018 12:59:40: 22000000 INFO @ Sat, 08 Sep 2018 12:59:41: 23000000 INFO @ Sat, 08 Sep 2018 12:59:45: 24000000 INFO @ Sat, 08 Sep 2018 12:59:47: 23000000 INFO @ Sat, 08 Sep 2018 12:59:48: 24000000 INFO @ Sat, 08 Sep 2018 12:59:52: 25000000 INFO @ Sat, 08 Sep 2018 12:59:54: 24000000 INFO @ Sat, 08 Sep 2018 12:59:55: 25000000 INFO @ Sat, 08 Sep 2018 12:59:59: 26000000 INFO @ Sat, 08 Sep 2018 13:00:01: 25000000 INFO @ Sat, 08 Sep 2018 13:00:01: 26000000 INFO @ Sat, 08 Sep 2018 13:00:05: 27000000 INFO @ Sat, 08 Sep 2018 13:00:08: 26000000 INFO @ Sat, 08 Sep 2018 13:00:08: 27000000 INFO @ Sat, 08 Sep 2018 13:00:12: 28000000 INFO @ Sat, 08 Sep 2018 13:00:14: 27000000 INFO @ Sat, 08 Sep 2018 13:00:15: 28000000 INFO @ Sat, 08 Sep 2018 13:00:18: 29000000 INFO @ Sat, 08 Sep 2018 13:00:21: 28000000 INFO @ Sat, 08 Sep 2018 13:00:21: 29000000 INFO @ Sat, 08 Sep 2018 13:00:25: 30000000 INFO @ Sat, 08 Sep 2018 13:00:28: 30000000 INFO @ Sat, 08 Sep 2018 13:00:28: 29000000 INFO @ Sat, 08 Sep 2018 13:00:32: 31000000 INFO @ Sat, 08 Sep 2018 13:00:35: 31000000 INFO @ Sat, 08 Sep 2018 13:00:35: 30000000 INFO @ Sat, 08 Sep 2018 13:00:38: 32000000 INFO @ Sat, 08 Sep 2018 13:00:42: 32000000 INFO @ Sat, 08 Sep 2018 13:00:42: 31000000 INFO @ Sat, 08 Sep 2018 13:00:45: 33000000 INFO @ Sat, 08 Sep 2018 13:00:48: 33000000 INFO @ Sat, 08 Sep 2018 13:00:49: 32000000 INFO @ Sat, 08 Sep 2018 13:00:52: 34000000 INFO @ Sat, 08 Sep 2018 13:00:55: 34000000 INFO @ Sat, 08 Sep 2018 13:00:56: 33000000 INFO @ Sat, 08 Sep 2018 13:00:58: 35000000 INFO @ Sat, 08 Sep 2018 13:01:02: 35000000 INFO @ Sat, 08 Sep 2018 13:01:03: 34000000 INFO @ Sat, 08 Sep 2018 13:01:05: 36000000 INFO @ Sat, 08 Sep 2018 13:01:09: 36000000 INFO @ Sat, 08 Sep 2018 13:01:10: 35000000 INFO @ Sat, 08 Sep 2018 13:01:11: 37000000 INFO @ Sat, 08 Sep 2018 13:01:15: 37000000 INFO @ Sat, 08 Sep 2018 13:01:17: 36000000 INFO @ Sat, 08 Sep 2018 13:01:18: 38000000 INFO @ Sat, 08 Sep 2018 13:01:22: 38000000 INFO @ Sat, 08 Sep 2018 13:01:24: 37000000 INFO @ Sat, 08 Sep 2018 13:01:25: 39000000 INFO @ Sat, 08 Sep 2018 13:01:29: 39000000 INFO @ Sat, 08 Sep 2018 13:01:31: 38000000 INFO @ Sat, 08 Sep 2018 13:01:31: 40000000 INFO @ Sat, 08 Sep 2018 13:01:36: 40000000 INFO @ Sat, 08 Sep 2018 13:01:36: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:01:36: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:01:36: #1 total tags in treatment: 19619472 INFO @ Sat, 08 Sep 2018 13:01:36: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:01:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:01:36: #1 tags after filtering in treatment: 16307060 INFO @ Sat, 08 Sep 2018 13:01:36: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 08 Sep 2018 13:01:36: #1 finished! INFO @ Sat, 08 Sep 2018 13:01:36: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:01:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:01:37: 39000000 INFO @ Sat, 08 Sep 2018 13:01:38: #2 number of paired peaks: 2819 INFO @ Sat, 08 Sep 2018 13:01:38: start model_add_line... INFO @ Sat, 08 Sep 2018 13:01:38: start X-correlation... INFO @ Sat, 08 Sep 2018 13:01:38: end of X-cor INFO @ Sat, 08 Sep 2018 13:01:38: #2 finished! INFO @ Sat, 08 Sep 2018 13:01:38: #2 predicted fragment length is 196 bps INFO @ Sat, 08 Sep 2018 13:01:38: #2 alternative fragment length(s) may be 196 bps INFO @ Sat, 08 Sep 2018 13:01:38: #2.2 Generate R script for model : SRX2000505.20_model.r INFO @ Sat, 08 Sep 2018 13:01:38: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:01:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:01:40: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:01:40: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:01:40: #1 total tags in treatment: 19619472 INFO @ Sat, 08 Sep 2018 13:01:40: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:01:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:01:40: #1 tags after filtering in treatment: 16307060 INFO @ Sat, 08 Sep 2018 13:01:40: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 08 Sep 2018 13:01:40: #1 finished! INFO @ Sat, 08 Sep 2018 13:01:40: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:01:42: #2 number of paired peaks: 2819 INFO @ Sat, 08 Sep 2018 13:01:42: start model_add_line... INFO @ Sat, 08 Sep 2018 13:01:42: start X-correlation... INFO @ Sat, 08 Sep 2018 13:01:42: end of X-cor INFO @ Sat, 08 Sep 2018 13:01:42: #2 finished! INFO @ Sat, 08 Sep 2018 13:01:42: #2 predicted fragment length is 196 bps INFO @ Sat, 08 Sep 2018 13:01:42: #2 alternative fragment length(s) may be 196 bps INFO @ Sat, 08 Sep 2018 13:01:42: #2.2 Generate R script for model : SRX2000505.10_model.r INFO @ Sat, 08 Sep 2018 13:01:42: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:01:43: 40000000 INFO @ Sat, 08 Sep 2018 13:01:47: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:01:47: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:01:47: #1 total tags in treatment: 19619472 INFO @ Sat, 08 Sep 2018 13:01:47: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:01:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:01:48: #1 tags after filtering in treatment: 16307060 INFO @ Sat, 08 Sep 2018 13:01:48: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 08 Sep 2018 13:01:48: #1 finished! INFO @ Sat, 08 Sep 2018 13:01:48: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:01:49: #2 number of paired peaks: 2819 INFO @ Sat, 08 Sep 2018 13:01:49: start model_add_line... INFO @ Sat, 08 Sep 2018 13:01:49: start X-correlation... INFO @ Sat, 08 Sep 2018 13:01:49: end of X-cor INFO @ Sat, 08 Sep 2018 13:01:49: #2 finished! INFO @ Sat, 08 Sep 2018 13:01:49: #2 predicted fragment length is 196 bps INFO @ Sat, 08 Sep 2018 13:01:49: #2 alternative fragment length(s) may be 196 bps INFO @ Sat, 08 Sep 2018 13:01:49: #2.2 Generate R script for model : SRX2000505.05_model.r INFO @ Sat, 08 Sep 2018 13:01:49: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:01:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:02:30: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:02:30: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:02:40: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:02:54: #4 Write output xls file... SRX2000505.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:02:54: #4 Write peak in narrowPeak format file... SRX2000505.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:02:54: #4 Write summits bed file... SRX2000505.20_summits.bed INFO @ Sat, 08 Sep 2018 13:02:54: Done! INFO @ Sat, 08 Sep 2018 13:02:55: #4 Write output xls file... SRX2000505.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:02:55: #4 Write peak in narrowPeak format file... SRX2000505.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:02:55: #4 Write summits bed file... SRX2000505.10_summits.bed INFO @ Sat, 08 Sep 2018 13:02:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5012 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7139 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:03:06: #4 Write output xls file... SRX2000505.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:03:06: #4 Write peak in narrowPeak format file... SRX2000505.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:03:06: #4 Write summits bed file... SRX2000505.05_summits.bed INFO @ Sat, 08 Sep 2018 13:03:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9101 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。