Job ID = 10714533 sra ファイルのダウンロード中... Completed: 1709919K bytes transferred in 12 seconds (1084467K 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 28371180 spots for /home/okishinya/chipatlas/results/dm3/SRX1619256/SRR3211632.sra Written 28371180 spots for /home/okishinya/chipatlas/results/dm3/SRX1619256/SRR3211632.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:03:57 28371180 reads; of these: 28371180 (100.00%) were paired; of these: 8350244 (29.43%) aligned concordantly 0 times 15399956 (54.28%) aligned concordantly exactly 1 time 4620980 (16.29%) aligned concordantly >1 times ---- 8350244 pairs aligned concordantly 0 times; of these: 4678651 (56.03%) aligned discordantly 1 time ---- 3671593 pairs aligned 0 times concordantly or discordantly; of these: 7343186 mates make up the pairs; of these: 3393070 (46.21%) aligned 0 times 1727444 (23.52%) aligned exactly 1 time 2222672 (30.27%) aligned >1 times 94.02% overall alignment rate Time searching: 01:03:57 Overall time: 01:03:57 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 24 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] 5657107 / 24641802 = 0.2296 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 @ Sun, 03 Jun 2018 14:31:52: # Command line: callpeak -t SRX1619256.bam -f BAM -g dm -n SRX1619256.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1619256.20 # format = BAM # ChIP-seq file = ['SRX1619256.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 @ Sun, 03 Jun 2018 14:31:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:31:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:31:52: # Command line: callpeak -t SRX1619256.bam -f BAM -g dm -n SRX1619256.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1619256.05 # format = BAM # ChIP-seq file = ['SRX1619256.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 @ Sun, 03 Jun 2018 14:31:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:31:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:31:52: # Command line: callpeak -t SRX1619256.bam -f BAM -g dm -n SRX1619256.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1619256.10 # format = BAM # ChIP-seq file = ['SRX1619256.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 @ Sun, 03 Jun 2018 14:31:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 14:31:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 14:31:58: 1000000 INFO @ Sun, 03 Jun 2018 14:31:58: 1000000 INFO @ Sun, 03 Jun 2018 14:31:58: 1000000 INFO @ Sun, 03 Jun 2018 14:32:04: 2000000 INFO @ Sun, 03 Jun 2018 14:32:05: 2000000 INFO @ Sun, 03 Jun 2018 14:32:05: 2000000 INFO @ Sun, 03 Jun 2018 14:32:11: 3000000 INFO @ Sun, 03 Jun 2018 14:32:11: 3000000 INFO @ Sun, 03 Jun 2018 14:32:11: 3000000 INFO @ Sun, 03 Jun 2018 14:32:17: 4000000 INFO @ Sun, 03 Jun 2018 14:32:17: 4000000 INFO @ Sun, 03 Jun 2018 14:32:17: 4000000 INFO @ Sun, 03 Jun 2018 14:32:23: 5000000 INFO @ Sun, 03 Jun 2018 14:32:24: 5000000 INFO @ Sun, 03 Jun 2018 14:32:24: 5000000 INFO @ Sun, 03 Jun 2018 14:32:30: 6000000 INFO @ Sun, 03 Jun 2018 14:32:30: 6000000 INFO @ Sun, 03 Jun 2018 14:32:30: 6000000 INFO @ Sun, 03 Jun 2018 14:32:36: 7000000 INFO @ Sun, 03 Jun 2018 14:32:36: 7000000 INFO @ Sun, 03 Jun 2018 14:32:36: 7000000 INFO @ Sun, 03 Jun 2018 14:32:42: 8000000 INFO @ Sun, 03 Jun 2018 14:32:43: 8000000 INFO @ Sun, 03 Jun 2018 14:32:43: 8000000 INFO @ Sun, 03 Jun 2018 14:32:48: 9000000 INFO @ Sun, 03 Jun 2018 14:32:49: 9000000 INFO @ Sun, 03 Jun 2018 14:32:49: 9000000 INFO @ Sun, 03 Jun 2018 14:32:55: 10000000 INFO @ Sun, 03 Jun 2018 14:32:55: 10000000 INFO @ Sun, 03 Jun 2018 14:32:55: 10000000 INFO @ Sun, 03 Jun 2018 14:33:01: 11000000 INFO @ Sun, 03 Jun 2018 14:33:02: 11000000 INFO @ Sun, 03 Jun 2018 14:33:02: 11000000 INFO @ Sun, 03 Jun 2018 14:33:07: 12000000 INFO @ Sun, 03 Jun 2018 14:33:08: 12000000 INFO @ Sun, 03 Jun 2018 14:33:08: 12000000 INFO @ Sun, 03 Jun 2018 14:33:13: 13000000 INFO @ Sun, 03 Jun 2018 14:33:14: 13000000 INFO @ Sun, 03 Jun 2018 14:33:14: 13000000 INFO @ Sun, 03 Jun 2018 14:33:20: 14000000 INFO @ Sun, 03 Jun 2018 14:33:21: 14000000 INFO @ Sun, 03 Jun 2018 14:33:21: 14000000 INFO @ Sun, 03 Jun 2018 14:33:26: 15000000 INFO @ Sun, 03 Jun 2018 14:33:27: 15000000 INFO @ Sun, 03 Jun 2018 14:33:27: 15000000 INFO @ Sun, 03 Jun 2018 14:33:32: 16000000 INFO @ Sun, 03 Jun 2018 14:33:34: 16000000 INFO @ Sun, 03 Jun 2018 14:33:34: 16000000 INFO @ Sun, 03 Jun 2018 14:33:38: 17000000 INFO @ Sun, 03 Jun 2018 14:33:40: 17000000 INFO @ Sun, 03 Jun 2018 14:33:40: 17000000 INFO @ Sun, 03 Jun 2018 14:33:45: 18000000 INFO @ Sun, 03 Jun 2018 14:33:47: 18000000 INFO @ Sun, 03 Jun 2018 14:33:47: 18000000 INFO @ Sun, 03 Jun 2018 14:33:51: 19000000 INFO @ Sun, 03 Jun 2018 14:33:53: 19000000 INFO @ Sun, 03 Jun 2018 14:33:53: 19000000 INFO @ Sun, 03 Jun 2018 14:33:57: 20000000 INFO @ Sun, 03 Jun 2018 14:34:00: 20000000 INFO @ Sun, 03 Jun 2018 14:34:00: 20000000 INFO @ Sun, 03 Jun 2018 14:34:03: 21000000 INFO @ Sun, 03 Jun 2018 14:34:06: 21000000 INFO @ Sun, 03 Jun 2018 14:34:06: 21000000 INFO @ Sun, 03 Jun 2018 14:34:09: 22000000 INFO @ Sun, 03 Jun 2018 14:34:12: 22000000 INFO @ Sun, 03 Jun 2018 14:34:12: 22000000 INFO @ Sun, 03 Jun 2018 14:34:16: 23000000 INFO @ Sun, 03 Jun 2018 14:34:19: 23000000 INFO @ Sun, 03 Jun 2018 14:34:19: 23000000 INFO @ Sun, 03 Jun 2018 14:34:22: 24000000 INFO @ Sun, 03 Jun 2018 14:34:25: 24000000 INFO @ Sun, 03 Jun 2018 14:34:25: 24000000 INFO @ Sun, 03 Jun 2018 14:34:28: 25000000 INFO @ Sun, 03 Jun 2018 14:34:31: 25000000 INFO @ Sun, 03 Jun 2018 14:34:32: 25000000 INFO @ Sun, 03 Jun 2018 14:34:35: 26000000 INFO @ Sun, 03 Jun 2018 14:34:38: 26000000 INFO @ Sun, 03 Jun 2018 14:34:38: 26000000 INFO @ Sun, 03 Jun 2018 14:34:41: 27000000 INFO @ Sun, 03 Jun 2018 14:34:44: 27000000 INFO @ Sun, 03 Jun 2018 14:34:44: 27000000 INFO @ Sun, 03 Jun 2018 14:34:48: 28000000 INFO @ Sun, 03 Jun 2018 14:34:50: 28000000 INFO @ Sun, 03 Jun 2018 14:34:50: 28000000 INFO @ Sun, 03 Jun 2018 14:34:54: 29000000 INFO @ Sun, 03 Jun 2018 14:34:56: 29000000 INFO @ Sun, 03 Jun 2018 14:34:57: 29000000 INFO @ Sun, 03 Jun 2018 14:35:01: 30000000 INFO @ Sun, 03 Jun 2018 14:35:02: 30000000 INFO @ Sun, 03 Jun 2018 14:35:03: 30000000 INFO @ Sun, 03 Jun 2018 14:35:07: 31000000 INFO @ Sun, 03 Jun 2018 14:35:08: 31000000 INFO @ Sun, 03 Jun 2018 14:35:09: 31000000 INFO @ Sun, 03 Jun 2018 14:35:14: 32000000 INFO @ Sun, 03 Jun 2018 14:35:14: 32000000 INFO @ Sun, 03 Jun 2018 14:35:16: 32000000 INFO @ Sun, 03 Jun 2018 14:35:20: 33000000 INFO @ Sun, 03 Jun 2018 14:35:21: 33000000 INFO @ Sun, 03 Jun 2018 14:35:22: 33000000 INFO @ Sun, 03 Jun 2018 14:35:27: 34000000 INFO @ Sun, 03 Jun 2018 14:35:27: 34000000 INFO @ Sun, 03 Jun 2018 14:35:28: 34000000 INFO @ Sun, 03 Jun 2018 14:35:33: 35000000 INFO @ Sun, 03 Jun 2018 14:35:33: 35000000 INFO @ Sun, 03 Jun 2018 14:35:35: 35000000 INFO @ Sun, 03 Jun 2018 14:35:39: 36000000 INFO @ Sun, 03 Jun 2018 14:35:40: 36000000 INFO @ Sun, 03 Jun 2018 14:35:41: 36000000 INFO @ Sun, 03 Jun 2018 14:35:45: 37000000 INFO @ Sun, 03 Jun 2018 14:35:47: 37000000 INFO @ Sun, 03 Jun 2018 14:35:47: 37000000 INFO @ Sun, 03 Jun 2018 14:35:52: 38000000 INFO @ Sun, 03 Jun 2018 14:35:53: 38000000 INFO @ Sun, 03 Jun 2018 14:35:54: 38000000 INFO @ Sun, 03 Jun 2018 14:35:58: 39000000 INFO @ Sun, 03 Jun 2018 14:36:00: 39000000 INFO @ Sun, 03 Jun 2018 14:36:00: 39000000 INFO @ Sun, 03 Jun 2018 14:36:04: 40000000 INFO @ Sun, 03 Jun 2018 14:36:06: 40000000 INFO @ Sun, 03 Jun 2018 14:36:06: 40000000 INFO @ Sun, 03 Jun 2018 14:36:10: 41000000 INFO @ Sun, 03 Jun 2018 14:36:12: 41000000 INFO @ Sun, 03 Jun 2018 14:36:13: 41000000 INFO @ Sun, 03 Jun 2018 14:36:16: 42000000 INFO @ Sun, 03 Jun 2018 14:36:17: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:36:17: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:36:17: #1 total tags in treatment: 14910705 INFO @ Sun, 03 Jun 2018 14:36:17: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:36:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:36:17: #1 tags after filtering in treatment: 11843641 INFO @ Sun, 03 Jun 2018 14:36:17: #1 Redundant rate of treatment: 0.21 INFO @ Sun, 03 Jun 2018 14:36:17: #1 finished! INFO @ Sun, 03 Jun 2018 14:36:17: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:36:18: #2 number of paired peaks: 195 WARNING @ Sun, 03 Jun 2018 14:36:18: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sun, 03 Jun 2018 14:36:18: start model_add_line... INFO @ Sun, 03 Jun 2018 14:36:18: start X-correlation... INFO @ Sun, 03 Jun 2018 14:36:18: end of X-cor INFO @ Sun, 03 Jun 2018 14:36:18: #2 finished! INFO @ Sun, 03 Jun 2018 14:36:18: #2 predicted fragment length is 238 bps INFO @ Sun, 03 Jun 2018 14:36:18: #2 alternative fragment length(s) may be 220,238 bps INFO @ Sun, 03 Jun 2018 14:36:18: #2.2 Generate R script for model : SRX1619256.05_model.r INFO @ Sun, 03 Jun 2018 14:36:18: #3 Call peaks... INFO @ Sun, 03 Jun 2018 14:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 14:36:19: 42000000 INFO @ Sun, 03 Jun 2018 14:36:19: 42000000 INFO @ Sun, 03 Jun 2018 14:36:19: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:36:19: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:36:19: #1 total tags in treatment: 14910705 INFO @ Sun, 03 Jun 2018 14:36:19: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:36:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:36:19: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 14:36:19: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 14:36:19: #1 total tags in treatment: 14910705 INFO @ Sun, 03 Jun 2018 14:36:19: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 14:36:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 14:36:19: #1 tags after filtering in treatment: 11843641 INFO @ Sun, 03 Jun 2018 14:36:19: #1 Redundant rate of treatment: 0.21 INFO @ Sun, 03 Jun 2018 14:36:19: #1 finished! INFO @ Sun, 03 Jun 2018 14:36:19: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:36:19: #1 tags after filtering in treatment: 11843641 INFO @ Sun, 03 Jun 2018 14:36:19: #1 Redundant rate of treatment: 0.21 INFO @ Sun, 03 Jun 2018 14:36:19: #1 finished! INFO @ Sun, 03 Jun 2018 14:36:19: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 14:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 14:36:20: #2 number of paired peaks: 195 WARNING @ Sun, 03 Jun 2018 14:36:20: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sun, 03 Jun 2018 14:36:20: start model_add_line... INFO @ Sun, 03 Jun 2018 14:36:20: #2 number of paired peaks: 195 WARNING @ Sun, 03 Jun 2018 14:36:20: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sun, 03 Jun 2018 14:36:20: start model_add_line... INFO @ Sun, 03 Jun 2018 14:36:20: start X-correlation... INFO @ Sun, 03 Jun 2018 14:36:20: end of X-cor INFO @ Sun, 03 Jun 2018 14:36:20: #2 finished! INFO @ Sun, 03 Jun 2018 14:36:20: #2 predicted fragment length is 238 bps INFO @ Sun, 03 Jun 2018 14:36:20: #2 alternative fragment length(s) may be 220,238 bps INFO @ Sun, 03 Jun 2018 14:36:20: #2.2 Generate R script for model : SRX1619256.20_model.r INFO @ Sun, 03 Jun 2018 14:36:20: start X-correlation... INFO @ Sun, 03 Jun 2018 14:36:20: #3 Call peaks... INFO @ Sun, 03 Jun 2018 14:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 14:36:20: end of X-cor INFO @ Sun, 03 Jun 2018 14:36:20: #2 finished! INFO @ Sun, 03 Jun 2018 14:36:20: #2 predicted fragment length is 238 bps INFO @ Sun, 03 Jun 2018 14:36:20: #2 alternative fragment length(s) may be 220,238 bps INFO @ Sun, 03 Jun 2018 14:36:20: #2.2 Generate R script for model : SRX1619256.10_model.r INFO @ Sun, 03 Jun 2018 14:36:20: #3 Call peaks... INFO @ Sun, 03 Jun 2018 14:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 14:36:44: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 14:36:46: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 14:36:48: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 14:36:58: #4 Write output xls file... SRX1619256.05_peaks.xls INFO @ Sun, 03 Jun 2018 14:36:58: #4 Write peak in narrowPeak format file... SRX1619256.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 14:36:58: #4 Write summits bed file... SRX1619256.05_summits.bed INFO @ Sun, 03 Jun 2018 14:36:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2257 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 14:36:59: #4 Write output xls file... SRX1619256.20_peaks.xls INFO @ Sun, 03 Jun 2018 14:36:59: #4 Write peak in narrowPeak format file... SRX1619256.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 14:36:59: #4 Write summits bed file... SRX1619256.20_summits.bed INFO @ Sun, 03 Jun 2018 14:36:59: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (445 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 14:37:03: #4 Write output xls file... SRX1619256.10_peaks.xls INFO @ Sun, 03 Jun 2018 14:37:03: #4 Write peak in narrowPeak format file... SRX1619256.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 14:37:03: #4 Write summits bed file... SRX1619256.10_summits.bed INFO @ Sun, 03 Jun 2018 14:37:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (983 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。