Job ID = 10480728 sra ファイルのダウンロード中... Completed: 322853K bytes transferred in 11 seconds (226273K 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: SINGLE fastq に変換中... Written 19217803 spots for /home/okishinya/chipatlas/results/dm3/SRX3380787/SRR6278150.sra Written 19217803 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: 00:04:59 19217803 reads; of these: 19217803 (100.00%) were unpaired; of these: 1439462 (7.49%) aligned 0 times 16162470 (84.10%) aligned exactly 1 time 1615871 (8.41%) aligned >1 times 92.51% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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_rmdupse_core] 1614026 / 17778341 = 0.0908 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, 16 Mar 2018 07:53:43: # Command line: callpeak -t SRX3380787.bam -f BAM -g dm -n SRX3380787.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380787.20 # format = BAM # ChIP-seq file = ['SRX3380787.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, 16 Mar 2018 07:53:43: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:53:43: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:53:43: # Command line: callpeak -t SRX3380787.bam -f BAM -g dm -n SRX3380787.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380787.05 # format = BAM # ChIP-seq file = ['SRX3380787.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, 16 Mar 2018 07:53:43: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:53:43: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:53:43: # Command line: callpeak -t SRX3380787.bam -f BAM -g dm -n SRX3380787.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380787.10 # format = BAM # ChIP-seq file = ['SRX3380787.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, 16 Mar 2018 07:53:43: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:53:43: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:53:49: 1000000 INFO @ Fri, 16 Mar 2018 07:53:49: 1000000 INFO @ Fri, 16 Mar 2018 07:53:49: 1000000 INFO @ Fri, 16 Mar 2018 07:53:55: 2000000 INFO @ Fri, 16 Mar 2018 07:53:55: 2000000 INFO @ Fri, 16 Mar 2018 07:53:55: 2000000 INFO @ Fri, 16 Mar 2018 07:54:01: 3000000 INFO @ Fri, 16 Mar 2018 07:54:01: 3000000 INFO @ Fri, 16 Mar 2018 07:54:04: 3000000 INFO @ Fri, 16 Mar 2018 07:54:07: 4000000 INFO @ Fri, 16 Mar 2018 07:54:07: 4000000 INFO @ Fri, 16 Mar 2018 07:54:13: 4000000 INFO @ Fri, 16 Mar 2018 07:54:13: 5000000 INFO @ Fri, 16 Mar 2018 07:54:14: 5000000 INFO @ Fri, 16 Mar 2018 07:54:19: 6000000 INFO @ Fri, 16 Mar 2018 07:54:19: 5000000 INFO @ Fri, 16 Mar 2018 07:54:20: 6000000 INFO @ Fri, 16 Mar 2018 07:54:24: 7000000 INFO @ Fri, 16 Mar 2018 07:54:26: 6000000 INFO @ Fri, 16 Mar 2018 07:54:26: 7000000 INFO @ Fri, 16 Mar 2018 07:54:30: 8000000 INFO @ Fri, 16 Mar 2018 07:54:32: 7000000 INFO @ Fri, 16 Mar 2018 07:54:32: 8000000 INFO @ Fri, 16 Mar 2018 07:54:36: 9000000 INFO @ Fri, 16 Mar 2018 07:54:38: 9000000 INFO @ Fri, 16 Mar 2018 07:54:39: 8000000 INFO @ Fri, 16 Mar 2018 07:54:42: 10000000 INFO @ Fri, 16 Mar 2018 07:54:45: 10000000 INFO @ Fri, 16 Mar 2018 07:54:45: 9000000 INFO @ Fri, 16 Mar 2018 07:54:48: 11000000 INFO @ Fri, 16 Mar 2018 07:54:51: 11000000 INFO @ Fri, 16 Mar 2018 07:54:52: 10000000 INFO @ Fri, 16 Mar 2018 07:54:53: 12000000 INFO @ Fri, 16 Mar 2018 07:54:57: 12000000 INFO @ Fri, 16 Mar 2018 07:54:58: 11000000 INFO @ Fri, 16 Mar 2018 07:54:59: 13000000 INFO @ Fri, 16 Mar 2018 07:55:03: 13000000 INFO @ Fri, 16 Mar 2018 07:55:04: 12000000 INFO @ Fri, 16 Mar 2018 07:55:05: 14000000 INFO @ Fri, 16 Mar 2018 07:55:09: 14000000 INFO @ Fri, 16 Mar 2018 07:55:11: 13000000 INFO @ Fri, 16 Mar 2018 07:55:11: 15000000 INFO @ Fri, 16 Mar 2018 07:55:15: 15000000 INFO @ Fri, 16 Mar 2018 07:55:17: 14000000 INFO @ Fri, 16 Mar 2018 07:55:17: 16000000 INFO @ Fri, 16 Mar 2018 07:55:19: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:55:19: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:55:19: #1 total tags in treatment: 16164315 INFO @ Fri, 16 Mar 2018 07:55:19: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:55:19: #1 tags after filtering in treatment: 16164315 INFO @ Fri, 16 Mar 2018 07:55:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:19: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:19: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:20: #2 number of paired peaks: 769 WARNING @ Fri, 16 Mar 2018 07:55:20: Fewer paired peaks (769) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 769 pairs to build model! INFO @ Fri, 16 Mar 2018 07:55:20: start model_add_line... INFO @ Fri, 16 Mar 2018 07:55:20: start X-correlation... INFO @ Fri, 16 Mar 2018 07:55:20: end of X-cor INFO @ Fri, 16 Mar 2018 07:55:20: #2 finished! INFO @ Fri, 16 Mar 2018 07:55:20: #2 predicted fragment length is 198 bps INFO @ Fri, 16 Mar 2018 07:55:20: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 16 Mar 2018 07:55:20: #2.2 Generate R script for model : SRX3380787.10_model.r INFO @ Fri, 16 Mar 2018 07:55:20: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:55:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:55:20: 16000000 INFO @ Fri, 16 Mar 2018 07:55:22: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:55:22: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:55:22: #1 total tags in treatment: 16164315 INFO @ Fri, 16 Mar 2018 07:55:22: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:55:22: #1 tags after filtering in treatment: 16164315 INFO @ Fri, 16 Mar 2018 07:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:22: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:22: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:23: #2 number of paired peaks: 769 WARNING @ Fri, 16 Mar 2018 07:55:23: Fewer paired peaks (769) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 769 pairs to build model! INFO @ Fri, 16 Mar 2018 07:55:23: start model_add_line... INFO @ Fri, 16 Mar 2018 07:55:23: start X-correlation... INFO @ Fri, 16 Mar 2018 07:55:23: end of X-cor INFO @ Fri, 16 Mar 2018 07:55:23: #2 finished! INFO @ Fri, 16 Mar 2018 07:55:23: #2 predicted fragment length is 198 bps INFO @ Fri, 16 Mar 2018 07:55:23: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 16 Mar 2018 07:55:23: #2.2 Generate R script for model : SRX3380787.05_model.r INFO @ Fri, 16 Mar 2018 07:55:23: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:55:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:55:23: 15000000 INFO @ Fri, 16 Mar 2018 07:55:29: 16000000 INFO @ Fri, 16 Mar 2018 07:55:30: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:55:30: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:55:30: #1 total tags in treatment: 16164315 INFO @ Fri, 16 Mar 2018 07:55:30: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:55:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:55:31: #1 tags after filtering in treatment: 16164315 INFO @ Fri, 16 Mar 2018 07:55:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:55:31: #1 finished! INFO @ Fri, 16 Mar 2018 07:55:31: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:55:32: #2 number of paired peaks: 769 WARNING @ Fri, 16 Mar 2018 07:55:32: Fewer paired peaks (769) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 769 pairs to build model! INFO @ Fri, 16 Mar 2018 07:55:32: start model_add_line... INFO @ Fri, 16 Mar 2018 07:55:32: start X-correlation... INFO @ Fri, 16 Mar 2018 07:55:32: end of X-cor INFO @ Fri, 16 Mar 2018 07:55:32: #2 finished! INFO @ Fri, 16 Mar 2018 07:55:32: #2 predicted fragment length is 198 bps INFO @ Fri, 16 Mar 2018 07:55:32: #2 alternative fragment length(s) may be 198 bps INFO @ Fri, 16 Mar 2018 07:55:32: #2.2 Generate R script for model : SRX3380787.20_model.r INFO @ Fri, 16 Mar 2018 07:55:32: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:55:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:56:02: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:56:05: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:56:12: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:56:25: #4 Write output xls file... SRX3380787.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:25: #4 Write peak in narrowPeak format file... SRX3380787.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:25: #4 Write summits bed file... SRX3380787.10_summits.bed INFO @ Fri, 16 Mar 2018 07:56:25: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3163 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:56:27: #4 Write output xls file... SRX3380787.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:27: #4 Write peak in narrowPeak format file... SRX3380787.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:27: #4 Write summits bed file... SRX3380787.05_summits.bed INFO @ Fri, 16 Mar 2018 07:56:27: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5516 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:56:32: #4 Write output xls file... SRX3380787.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:56:32: #4 Write peak in narrowPeak format file... SRX3380787.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:56:32: #4 Write summits bed file... SRX3380787.20_summits.bed INFO @ Fri, 16 Mar 2018 07:56:32: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1123 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。