Job ID = 11171258 sra ファイルのダウンロード中... Completed: 1797085K bytes transferred in 65 seconds (224805K 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 27302331 spots for /home/okishinya/chipatlas/results/dm3/SRX2982445/SRR5803100.sra Written 27302331 spots for /home/okishinya/chipatlas/results/dm3/SRX2982445/SRR5803100.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: 01:06:12 27302331 reads; of these: 27302331 (100.00%) were paired; of these: 3214371 (11.77%) aligned concordantly 0 times 19057490 (69.80%) aligned concordantly exactly 1 time 5030470 (18.43%) aligned concordantly >1 times ---- 3214371 pairs aligned concordantly 0 times; of these: 29487 (0.92%) aligned discordantly 1 time ---- 3184884 pairs aligned 0 times concordantly or discordantly; of these: 6369768 mates make up the pairs; of these: 5167163 (81.12%) aligned 0 times 787778 (12.37%) aligned exactly 1 time 414827 (6.51%) aligned >1 times 90.54% overall alignment rate Time searching: 01:06:13 Overall time: 01:06:13 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] 9872546 / 24089083 = 0.4098 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 14:43:08: # Command line: callpeak -t SRX2982445.bam -f BAM -g dm -n SRX2982445.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2982445.20 # format = BAM # ChIP-seq file = ['SRX2982445.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 14:43:08: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:43:08: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:43:08: # Command line: callpeak -t SRX2982445.bam -f BAM -g dm -n SRX2982445.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2982445.05 # format = BAM # ChIP-seq file = ['SRX2982445.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 14:43:08: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:43:08: # Command line: callpeak -t SRX2982445.bam -f BAM -g dm -n SRX2982445.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2982445.10 # format = BAM # ChIP-seq file = ['SRX2982445.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 14:43:08: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:43:08: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:43:08: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:43:15: 1000000 INFO @ Sat, 08 Sep 2018 14:43:15: 1000000 INFO @ Sat, 08 Sep 2018 14:43:15: 1000000 INFO @ Sat, 08 Sep 2018 14:43:22: 2000000 INFO @ Sat, 08 Sep 2018 14:43:22: 2000000 INFO @ Sat, 08 Sep 2018 14:43:23: 2000000 INFO @ Sat, 08 Sep 2018 14:43:29: 3000000 INFO @ Sat, 08 Sep 2018 14:43:29: 3000000 INFO @ Sat, 08 Sep 2018 14:43:30: 3000000 INFO @ Sat, 08 Sep 2018 14:43:36: 4000000 INFO @ Sat, 08 Sep 2018 14:43:36: 4000000 INFO @ Sat, 08 Sep 2018 14:43:38: 4000000 INFO @ Sat, 08 Sep 2018 14:43:43: 5000000 INFO @ Sat, 08 Sep 2018 14:43:44: 5000000 INFO @ Sat, 08 Sep 2018 14:43:45: 5000000 INFO @ Sat, 08 Sep 2018 14:43:50: 6000000 INFO @ Sat, 08 Sep 2018 14:43:51: 6000000 INFO @ Sat, 08 Sep 2018 14:43:52: 6000000 INFO @ Sat, 08 Sep 2018 14:43:57: 7000000 INFO @ Sat, 08 Sep 2018 14:43:58: 7000000 INFO @ Sat, 08 Sep 2018 14:44:00: 7000000 INFO @ Sat, 08 Sep 2018 14:44:04: 8000000 INFO @ Sat, 08 Sep 2018 14:44:05: 8000000 INFO @ Sat, 08 Sep 2018 14:44:07: 8000000 INFO @ Sat, 08 Sep 2018 14:44:11: 9000000 INFO @ Sat, 08 Sep 2018 14:44:12: 9000000 INFO @ Sat, 08 Sep 2018 14:44:15: 9000000 INFO @ Sat, 08 Sep 2018 14:44:18: 10000000 INFO @ Sat, 08 Sep 2018 14:44:19: 10000000 INFO @ Sat, 08 Sep 2018 14:44:23: 10000000 INFO @ Sat, 08 Sep 2018 14:44:25: 11000000 INFO @ Sat, 08 Sep 2018 14:44:27: 11000000 INFO @ Sat, 08 Sep 2018 14:44:31: 12000000 INFO @ Sat, 08 Sep 2018 14:44:32: 11000000 INFO @ Sat, 08 Sep 2018 14:44:35: 12000000 INFO @ Sat, 08 Sep 2018 14:44:38: 13000000 INFO @ Sat, 08 Sep 2018 14:44:41: 12000000 INFO @ Sat, 08 Sep 2018 14:44:43: 13000000 INFO @ Sat, 08 Sep 2018 14:44:44: 14000000 INFO @ Sat, 08 Sep 2018 14:44:50: 13000000 INFO @ Sat, 08 Sep 2018 14:44:50: 15000000 INFO @ Sat, 08 Sep 2018 14:44:51: 14000000 INFO @ Sat, 08 Sep 2018 14:44:57: 16000000 INFO @ Sat, 08 Sep 2018 14:44:58: 14000000 INFO @ Sat, 08 Sep 2018 14:44:59: 15000000 INFO @ Sat, 08 Sep 2018 14:45:03: 17000000 INFO @ Sat, 08 Sep 2018 14:45:07: 16000000 INFO @ Sat, 08 Sep 2018 14:45:07: 15000000 INFO @ Sat, 08 Sep 2018 14:45:09: 18000000 INFO @ Sat, 08 Sep 2018 14:45:15: 17000000 INFO @ Sat, 08 Sep 2018 14:45:16: 19000000 INFO @ Sat, 08 Sep 2018 14:45:16: 16000000 INFO @ Sat, 08 Sep 2018 14:45:22: 20000000 INFO @ Sat, 08 Sep 2018 14:45:22: 18000000 INFO @ Sat, 08 Sep 2018 14:45:24: 17000000 INFO @ Sat, 08 Sep 2018 14:45:28: 21000000 INFO @ Sat, 08 Sep 2018 14:45:30: 19000000 INFO @ Sat, 08 Sep 2018 14:45:33: 18000000 INFO @ Sat, 08 Sep 2018 14:45:34: 22000000 INFO @ Sat, 08 Sep 2018 14:45:38: 20000000 INFO @ Sat, 08 Sep 2018 14:45:41: 23000000 INFO @ Sat, 08 Sep 2018 14:45:42: 19000000 INFO @ Sat, 08 Sep 2018 14:45:46: 21000000 INFO @ Sat, 08 Sep 2018 14:45:47: 24000000 INFO @ Sat, 08 Sep 2018 14:45:51: 20000000 INFO @ Sat, 08 Sep 2018 14:45:54: 22000000 INFO @ Sat, 08 Sep 2018 14:45:54: 25000000 INFO @ Sat, 08 Sep 2018 14:45:59: 21000000 INFO @ Sat, 08 Sep 2018 14:46:00: 26000000 INFO @ Sat, 08 Sep 2018 14:46:02: 23000000 INFO @ Sat, 08 Sep 2018 14:46:07: 27000000 INFO @ Sat, 08 Sep 2018 14:46:08: 22000000 INFO @ Sat, 08 Sep 2018 14:46:10: 24000000 INFO @ Sat, 08 Sep 2018 14:46:13: 28000000 INFO @ Sat, 08 Sep 2018 14:46:17: 23000000 INFO @ Sat, 08 Sep 2018 14:46:18: 25000000 INFO @ Sat, 08 Sep 2018 14:46:19: 29000000 INFO @ Sat, 08 Sep 2018 14:46:24: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:46:24: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:46:24: #1 total tags in treatment: 14223507 INFO @ Sat, 08 Sep 2018 14:46:24: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:46:24: #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 14:46:24: #1 tags after filtering in treatment: 13044218 INFO @ Sat, 08 Sep 2018 14:46:24: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Sep 2018 14:46:24: #1 finished! INFO @ Sat, 08 Sep 2018 14:46:24: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:46:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:46:25: #2 number of paired peaks: 171 WARNING @ Sat, 08 Sep 2018 14:46:25: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 08 Sep 2018 14:46:25: start model_add_line... INFO @ Sat, 08 Sep 2018 14:46:25: start X-correlation... INFO @ Sat, 08 Sep 2018 14:46:25: end of X-cor INFO @ Sat, 08 Sep 2018 14:46:25: #2 finished! INFO @ Sat, 08 Sep 2018 14:46:25: #2 predicted fragment length is 180 bps INFO @ Sat, 08 Sep 2018 14:46:25: #2 alternative fragment length(s) may be 1,112,161,180,304,595 bps INFO @ Sat, 08 Sep 2018 14:46:25: #2.2 Generate R script for model : SRX2982445.10_model.r INFO @ Sat, 08 Sep 2018 14:46:25: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:46:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:46:26: 24000000 INFO @ Sat, 08 Sep 2018 14:46:26: 26000000 INFO @ Sat, 08 Sep 2018 14:46:34: 27000000 INFO @ Sat, 08 Sep 2018 14:46:35: 25000000 INFO @ Sat, 08 Sep 2018 14:46:42: 28000000 INFO @ Sat, 08 Sep 2018 14:46:43: 26000000 INFO @ Sat, 08 Sep 2018 14:46:50: 29000000 INFO @ Sat, 08 Sep 2018 14:46:52: 27000000 INFO @ Sat, 08 Sep 2018 14:46:54: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:46:55: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:46:55: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:46:55: #1 total tags in treatment: 14223507 INFO @ Sat, 08 Sep 2018 14:46:55: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:46:55: #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 14:46:56: #1 tags after filtering in treatment: 13044218 INFO @ Sat, 08 Sep 2018 14:46:56: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Sep 2018 14:46:56: #1 finished! INFO @ Sat, 08 Sep 2018 14:46:56: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:46:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:46:57: #2 number of paired peaks: 171 WARNING @ Sat, 08 Sep 2018 14:46:57: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 08 Sep 2018 14:46:57: start model_add_line... INFO @ Sat, 08 Sep 2018 14:46:57: start X-correlation... INFO @ Sat, 08 Sep 2018 14:46:57: end of X-cor INFO @ Sat, 08 Sep 2018 14:46:57: #2 finished! INFO @ Sat, 08 Sep 2018 14:46:57: #2 predicted fragment length is 180 bps INFO @ Sat, 08 Sep 2018 14:46:57: #2 alternative fragment length(s) may be 1,112,161,180,304,595 bps INFO @ Sat, 08 Sep 2018 14:46:57: #2.2 Generate R script for model : SRX2982445.05_model.r INFO @ Sat, 08 Sep 2018 14:46:57: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:47:00: 28000000 INFO @ Sat, 08 Sep 2018 14:47:06: 29000000 INFO @ Sat, 08 Sep 2018 14:47:10: #4 Write output xls file... SRX2982445.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:47:10: #4 Write peak in narrowPeak format file... SRX2982445.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:47:10: #4 Write summits bed file... SRX2982445.10_summits.bed INFO @ Sat, 08 Sep 2018 14:47:10: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (505 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:47:11: #1 tag size is determined as 78 bps INFO @ Sat, 08 Sep 2018 14:47:11: #1 tag size = 78 INFO @ Sat, 08 Sep 2018 14:47:11: #1 total tags in treatment: 14223507 INFO @ Sat, 08 Sep 2018 14:47:11: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:47:11: #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 14:47:11: #1 tags after filtering in treatment: 13044218 INFO @ Sat, 08 Sep 2018 14:47:11: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Sep 2018 14:47:11: #1 finished! INFO @ Sat, 08 Sep 2018 14:47:11: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:47:12: #2 number of paired peaks: 171 WARNING @ Sat, 08 Sep 2018 14:47:12: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 08 Sep 2018 14:47:12: start model_add_line... INFO @ Sat, 08 Sep 2018 14:47:12: start X-correlation... INFO @ Sat, 08 Sep 2018 14:47:12: end of X-cor INFO @ Sat, 08 Sep 2018 14:47:12: #2 finished! INFO @ Sat, 08 Sep 2018 14:47:12: #2 predicted fragment length is 180 bps INFO @ Sat, 08 Sep 2018 14:47:12: #2 alternative fragment length(s) may be 1,112,161,180,304,595 bps INFO @ Sat, 08 Sep 2018 14:47:12: #2.2 Generate R script for model : SRX2982445.20_model.r INFO @ Sat, 08 Sep 2018 14:47:12: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:47:25: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:47:41: #4 Write output xls file... SRX2982445.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:47:41: #4 Write peak in narrowPeak format file... SRX2982445.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:47:41: #4 Write summits bed file... SRX2982445.05_summits.bed INFO @ Sat, 08 Sep 2018 14:47:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1255 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:47:43: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:47:58: #4 Write output xls file... SRX2982445.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:47:58: #4 Write peak in narrowPeak format file... SRX2982445.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:47:58: #4 Write summits bed file... SRX2982445.20_summits.bed INFO @ Sat, 08 Sep 2018 14:47:58: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (147 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。