Job ID = 10320355 sra ファイルのダウンロード中... Completed: 271736K bytes transferred in 42 seconds (52126K 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 12640689 spots for /home/okishinya/chipatlas/results/dm3/SRX3293407/SRR6183234.sra Written 12640689 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: 00:30:37 12640689 reads; of these: 12640689 (100.00%) were paired; of these: 1095872 (8.67%) aligned concordantly 0 times 7362592 (58.25%) aligned concordantly exactly 1 time 4182225 (33.09%) aligned concordantly >1 times ---- 1095872 pairs aligned concordantly 0 times; of these: 174050 (15.88%) aligned discordantly 1 time ---- 921822 pairs aligned 0 times concordantly or discordantly; of these: 1843644 mates make up the pairs; of these: 850225 (46.12%) aligned 0 times 516889 (28.04%) aligned exactly 1 time 476530 (25.85%) aligned >1 times 96.64% overall alignment rate Time searching: 00:30:37 Overall time: 00:30:37 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 8 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] 1646415 / 11573147 = 0.1423 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 @ Thu, 11 Jan 2018 02:43:04: # Command line: callpeak -t SRX3293407.bam -f BAM -g dm -n SRX3293407.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3293407.10 # format = BAM # ChIP-seq file = ['SRX3293407.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 @ Thu, 11 Jan 2018 02:43:04: # Command line: callpeak -t SRX3293407.bam -f BAM -g dm -n SRX3293407.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3293407.05 # format = BAM # ChIP-seq file = ['SRX3293407.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 @ Thu, 11 Jan 2018 02:43:04: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:43:04: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:43:04: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:43:04: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:43:04: # Command line: callpeak -t SRX3293407.bam -f BAM -g dm -n SRX3293407.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3293407.20 # format = BAM # ChIP-seq file = ['SRX3293407.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 @ Thu, 11 Jan 2018 02:43:04: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:43:04: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:43:09: 1000000 INFO @ Thu, 11 Jan 2018 02:43:10: 1000000 INFO @ Thu, 11 Jan 2018 02:43:10: 1000000 INFO @ Thu, 11 Jan 2018 02:43:14: 2000000 INFO @ Thu, 11 Jan 2018 02:43:15: 2000000 INFO @ Thu, 11 Jan 2018 02:43:16: 2000000 INFO @ Thu, 11 Jan 2018 02:43:19: 3000000 INFO @ Thu, 11 Jan 2018 02:43:21: 3000000 INFO @ Thu, 11 Jan 2018 02:43:22: 3000000 INFO @ Thu, 11 Jan 2018 02:43:24: 4000000 INFO @ Thu, 11 Jan 2018 02:43:27: 4000000 INFO @ Thu, 11 Jan 2018 02:43:29: 4000000 INFO @ Thu, 11 Jan 2018 02:43:29: 5000000 INFO @ Thu, 11 Jan 2018 02:43:33: 5000000 INFO @ Thu, 11 Jan 2018 02:43:34: 6000000 INFO @ Thu, 11 Jan 2018 02:43:35: 5000000 INFO @ Thu, 11 Jan 2018 02:43:39: 6000000 INFO @ Thu, 11 Jan 2018 02:43:39: 7000000 INFO @ Thu, 11 Jan 2018 02:43:42: 6000000 INFO @ Thu, 11 Jan 2018 02:43:44: 8000000 INFO @ Thu, 11 Jan 2018 02:43:44: 7000000 INFO @ Thu, 11 Jan 2018 02:43:48: 7000000 INFO @ Thu, 11 Jan 2018 02:43:49: 9000000 INFO @ Thu, 11 Jan 2018 02:43:50: 8000000 INFO @ Thu, 11 Jan 2018 02:43:54: 10000000 INFO @ Thu, 11 Jan 2018 02:43:55: 8000000 INFO @ Thu, 11 Jan 2018 02:43:56: 9000000 INFO @ Thu, 11 Jan 2018 02:43:58: 11000000 INFO @ Thu, 11 Jan 2018 02:44:01: 9000000 INFO @ Thu, 11 Jan 2018 02:44:02: 10000000 INFO @ Thu, 11 Jan 2018 02:44:03: 12000000 INFO @ Thu, 11 Jan 2018 02:44:07: 10000000 INFO @ Thu, 11 Jan 2018 02:44:08: 11000000 INFO @ Thu, 11 Jan 2018 02:44:08: 13000000 INFO @ Thu, 11 Jan 2018 02:44:13: 14000000 INFO @ Thu, 11 Jan 2018 02:44:13: 12000000 INFO @ Thu, 11 Jan 2018 02:44:14: 11000000 INFO @ Thu, 11 Jan 2018 02:44:18: 15000000 INFO @ Thu, 11 Jan 2018 02:44:19: 13000000 INFO @ Thu, 11 Jan 2018 02:44:20: 12000000 INFO @ Thu, 11 Jan 2018 02:44:23: 16000000 INFO @ Thu, 11 Jan 2018 02:44:25: 14000000 INFO @ Thu, 11 Jan 2018 02:44:27: 13000000 INFO @ Thu, 11 Jan 2018 02:44:28: 17000000 INFO @ Thu, 11 Jan 2018 02:44:31: 15000000 INFO @ Thu, 11 Jan 2018 02:44:33: 18000000 INFO @ Thu, 11 Jan 2018 02:44:33: 14000000 INFO @ Thu, 11 Jan 2018 02:44:36: 16000000 INFO @ Thu, 11 Jan 2018 02:44:38: 19000000 INFO @ Thu, 11 Jan 2018 02:44:39: 15000000 INFO @ Thu, 11 Jan 2018 02:44:42: 17000000 INFO @ Thu, 11 Jan 2018 02:44:43: 20000000 INFO @ Thu, 11 Jan 2018 02:44:46: 16000000 INFO @ Thu, 11 Jan 2018 02:44:48: 21000000 INFO @ Thu, 11 Jan 2018 02:44:49: 18000000 INFO @ Thu, 11 Jan 2018 02:44:49: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 02:44:49: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 02:44:49: #1 total tags in treatment: 9899654 INFO @ Thu, 11 Jan 2018 02:44:49: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:44:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:44:49: #1 tags after filtering in treatment: 8484504 INFO @ Thu, 11 Jan 2018 02:44:49: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 11 Jan 2018 02:44:49: #1 finished! INFO @ Thu, 11 Jan 2018 02:44:49: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:44:50: #2 number of paired peaks: 106 WARNING @ Thu, 11 Jan 2018 02:44:50: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Thu, 11 Jan 2018 02:44:50: start model_add_line... INFO @ Thu, 11 Jan 2018 02:44:50: start X-correlation... INFO @ Thu, 11 Jan 2018 02:44:50: end of X-cor INFO @ Thu, 11 Jan 2018 02:44:50: #2 finished! INFO @ Thu, 11 Jan 2018 02:44:50: #2 predicted fragment length is 67 bps INFO @ Thu, 11 Jan 2018 02:44:50: #2 alternative fragment length(s) may be 67 bps INFO @ Thu, 11 Jan 2018 02:44:50: #2.2 Generate R script for model : SRX3293407.20_model.r INFO @ Thu, 11 Jan 2018 02:44:50: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:44:53: 17000000 INFO @ Thu, 11 Jan 2018 02:44:55: 19000000 INFO @ Thu, 11 Jan 2018 02:44:59: 18000000 INFO @ Thu, 11 Jan 2018 02:45:00: 20000000 INFO @ Thu, 11 Jan 2018 02:45:06: 19000000 INFO @ Thu, 11 Jan 2018 02:45:06: 21000000 INFO @ Thu, 11 Jan 2018 02:45:07: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 02:45:07: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 02:45:07: #1 total tags in treatment: 9899654 INFO @ Thu, 11 Jan 2018 02:45:07: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:45:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:45:07: #1 tags after filtering in treatment: 8484504 INFO @ Thu, 11 Jan 2018 02:45:07: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 11 Jan 2018 02:45:07: #1 finished! INFO @ Thu, 11 Jan 2018 02:45:07: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:45:08: #2 number of paired peaks: 106 WARNING @ Thu, 11 Jan 2018 02:45:08: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Thu, 11 Jan 2018 02:45:08: start model_add_line... INFO @ Thu, 11 Jan 2018 02:45:08: start X-correlation... INFO @ Thu, 11 Jan 2018 02:45:08: end of X-cor INFO @ Thu, 11 Jan 2018 02:45:08: #2 finished! INFO @ Thu, 11 Jan 2018 02:45:08: #2 predicted fragment length is 67 bps INFO @ Thu, 11 Jan 2018 02:45:08: #2 alternative fragment length(s) may be 67 bps INFO @ Thu, 11 Jan 2018 02:45:08: #2.2 Generate R script for model : SRX3293407.05_model.r INFO @ Thu, 11 Jan 2018 02:45:08: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:45:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:45:09: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:45:13: 20000000 INFO @ Thu, 11 Jan 2018 02:45:18: 21000000 INFO @ Thu, 11 Jan 2018 02:45:18: #1 tag size is determined as 25 bps INFO @ Thu, 11 Jan 2018 02:45:18: #1 tag size = 25 INFO @ Thu, 11 Jan 2018 02:45:18: #1 total tags in treatment: 9899654 INFO @ Thu, 11 Jan 2018 02:45:18: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:45:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:45:19: #1 tags after filtering in treatment: 8484504 INFO @ Thu, 11 Jan 2018 02:45:19: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 11 Jan 2018 02:45:19: #1 finished! INFO @ Thu, 11 Jan 2018 02:45:19: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:45:19: #2 number of paired peaks: 106 WARNING @ Thu, 11 Jan 2018 02:45:19: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Thu, 11 Jan 2018 02:45:19: start model_add_line... INFO @ Thu, 11 Jan 2018 02:45:19: start X-correlation... INFO @ Thu, 11 Jan 2018 02:45:19: end of X-cor INFO @ Thu, 11 Jan 2018 02:45:19: #2 finished! INFO @ Thu, 11 Jan 2018 02:45:19: #2 predicted fragment length is 67 bps INFO @ Thu, 11 Jan 2018 02:45:19: #2 alternative fragment length(s) may be 67 bps INFO @ Thu, 11 Jan 2018 02:45:19: #2.2 Generate R script for model : SRX3293407.10_model.r INFO @ Thu, 11 Jan 2018 02:45:19: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:45:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:45:20: #4 Write output xls file... SRX3293407.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:45:20: #4 Write peak in narrowPeak format file... SRX3293407.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:45:20: #4 Write summits bed file... SRX3293407.20_summits.bed INFO @ Thu, 11 Jan 2018 02:45:20: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (81 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:45:26: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:45:36: #4 Write output xls file... SRX3293407.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:45:36: #4 Write peak in narrowPeak format file... SRX3293407.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:45:36: #4 Write summits bed file... SRX3293407.05_summits.bed INFO @ Thu, 11 Jan 2018 02:45:36: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (919 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:45:38: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:45:48: #4 Write output xls file... SRX3293407.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:45:48: #4 Write peak in narrowPeak format file... SRX3293407.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:45:48: #4 Write summits bed file... SRX3293407.10_summits.bed INFO @ Thu, 11 Jan 2018 02:45:48: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。