Job ID = 11240768 sra ファイルのダウンロード中... Completed: 474084K bytes transferred in 11 seconds (344644K 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... Read 29694717 spots for /home/okishinya/chipatlas/results/dm3/SRX4669052/SRR7817577.sra Written 29694717 spots for /home/okishinya/chipatlas/results/dm3/SRX4669052/SRR7817577.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: 00:07:57 29694717 reads; of these: 29694717 (100.00%) were unpaired; of these: 4227357 (14.24%) aligned 0 times 21132130 (71.16%) aligned exactly 1 time 4335230 (14.60%) aligned >1 times 85.76% overall alignment rate Time searching: 00:07:58 Overall time: 00:07:58 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 12 files... [bam_rmdupse_core] 6674443 / 25467360 = 0.2621 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, 07 Oct 2018 20:44:23: # Command line: callpeak -t SRX4669052.bam -f BAM -g dm -n SRX4669052.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669052.05 # format = BAM # ChIP-seq file = ['SRX4669052.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, 07 Oct 2018 20:44:23: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:44:23: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:44:23: # Command line: callpeak -t SRX4669052.bam -f BAM -g dm -n SRX4669052.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669052.20 # format = BAM # ChIP-seq file = ['SRX4669052.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, 07 Oct 2018 20:44:23: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:44:23: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:44:23: # Command line: callpeak -t SRX4669052.bam -f BAM -g dm -n SRX4669052.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669052.10 # format = BAM # ChIP-seq file = ['SRX4669052.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, 07 Oct 2018 20:44:23: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:44:23: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:44:31: 1000000 INFO @ Sun, 07 Oct 2018 20:44:31: 1000000 INFO @ Sun, 07 Oct 2018 20:44:31: 1000000 INFO @ Sun, 07 Oct 2018 20:44:39: 2000000 INFO @ Sun, 07 Oct 2018 20:44:39: 2000000 INFO @ Sun, 07 Oct 2018 20:44:39: 2000000 INFO @ Sun, 07 Oct 2018 20:44:46: 3000000 INFO @ Sun, 07 Oct 2018 20:44:47: 3000000 INFO @ Sun, 07 Oct 2018 20:44:47: 3000000 INFO @ Sun, 07 Oct 2018 20:44:54: 4000000 INFO @ Sun, 07 Oct 2018 20:44:55: 4000000 INFO @ Sun, 07 Oct 2018 20:44:55: 4000000 INFO @ Sun, 07 Oct 2018 20:45:01: 5000000 INFO @ Sun, 07 Oct 2018 20:45:03: 5000000 INFO @ Sun, 07 Oct 2018 20:45:03: 5000000 INFO @ Sun, 07 Oct 2018 20:45:09: 6000000 INFO @ Sun, 07 Oct 2018 20:45:11: 6000000 INFO @ Sun, 07 Oct 2018 20:45:11: 6000000 INFO @ Sun, 07 Oct 2018 20:45:16: 7000000 INFO @ Sun, 07 Oct 2018 20:45:19: 7000000 INFO @ Sun, 07 Oct 2018 20:45:19: 7000000 INFO @ Sun, 07 Oct 2018 20:45:23: 8000000 INFO @ Sun, 07 Oct 2018 20:45:26: 8000000 INFO @ Sun, 07 Oct 2018 20:45:27: 8000000 INFO @ Sun, 07 Oct 2018 20:45:31: 9000000 INFO @ Sun, 07 Oct 2018 20:45:34: 9000000 INFO @ Sun, 07 Oct 2018 20:45:36: 9000000 INFO @ Sun, 07 Oct 2018 20:45:39: 10000000 INFO @ Sun, 07 Oct 2018 20:45:42: 10000000 INFO @ Sun, 07 Oct 2018 20:45:45: 10000000 INFO @ Sun, 07 Oct 2018 20:45:46: 11000000 INFO @ Sun, 07 Oct 2018 20:45:50: 11000000 INFO @ Sun, 07 Oct 2018 20:45:54: 11000000 INFO @ Sun, 07 Oct 2018 20:45:54: 12000000 INFO @ Sun, 07 Oct 2018 20:45:57: 12000000 INFO @ Sun, 07 Oct 2018 20:46:02: 13000000 INFO @ Sun, 07 Oct 2018 20:46:03: 12000000 INFO @ Sun, 07 Oct 2018 20:46:05: 13000000 INFO @ Sun, 07 Oct 2018 20:46:10: 14000000 INFO @ Sun, 07 Oct 2018 20:46:11: 13000000 INFO @ Sun, 07 Oct 2018 20:46:12: 14000000 INFO @ Sun, 07 Oct 2018 20:46:17: 15000000 INFO @ Sun, 07 Oct 2018 20:46:20: 15000000 INFO @ Sun, 07 Oct 2018 20:46:20: 14000000 INFO @ Sun, 07 Oct 2018 20:46:25: 16000000 INFO @ Sun, 07 Oct 2018 20:46:28: 16000000 INFO @ Sun, 07 Oct 2018 20:46:29: 15000000 INFO @ Sun, 07 Oct 2018 20:46:33: 17000000 INFO @ Sun, 07 Oct 2018 20:46:35: 17000000 INFO @ Sun, 07 Oct 2018 20:46:38: 16000000 INFO @ Sun, 07 Oct 2018 20:46:41: 18000000 INFO @ Sun, 07 Oct 2018 20:46:43: 18000000 INFO @ Sun, 07 Oct 2018 20:46:47: 17000000 INFO @ Sun, 07 Oct 2018 20:46:47: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:46:47: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:46:47: #1 total tags in treatment: 18792917 INFO @ Sun, 07 Oct 2018 20:46:47: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:46:47: #1 tags after filtering in treatment: 18792917 INFO @ Sun, 07 Oct 2018 20:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:47: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:47: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:48: #2 number of paired peaks: 158 WARNING @ Sun, 07 Oct 2018 20:46:48: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 07 Oct 2018 20:46:48: start model_add_line... INFO @ Sun, 07 Oct 2018 20:46:49: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:46:49: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:46:49: #1 total tags in treatment: 18792917 INFO @ Sun, 07 Oct 2018 20:46:49: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:46:49: start X-correlation... INFO @ Sun, 07 Oct 2018 20:46:49: end of X-cor INFO @ Sun, 07 Oct 2018 20:46:49: #2 finished! INFO @ Sun, 07 Oct 2018 20:46:49: #2 predicted fragment length is 53 bps INFO @ Sun, 07 Oct 2018 20:46:49: #2 alternative fragment length(s) may be 2,53,573 bps INFO @ Sun, 07 Oct 2018 20:46:49: #2.2 Generate R script for model : SRX4669052.20_model.r WARNING @ Sun, 07 Oct 2018 20:46:49: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:46:49: #2 You may need to consider one of the other alternative d(s): 2,53,573 WARNING @ Sun, 07 Oct 2018 20:46:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:46:49: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:46:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:46:49: #1 tags after filtering in treatment: 18792917 INFO @ Sun, 07 Oct 2018 20:46:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:49: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:49: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:50: #2 number of paired peaks: 158 WARNING @ Sun, 07 Oct 2018 20:46:50: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 07 Oct 2018 20:46:50: start model_add_line... INFO @ Sun, 07 Oct 2018 20:46:50: start X-correlation... INFO @ Sun, 07 Oct 2018 20:46:50: end of X-cor INFO @ Sun, 07 Oct 2018 20:46:50: #2 finished! INFO @ Sun, 07 Oct 2018 20:46:50: #2 predicted fragment length is 53 bps INFO @ Sun, 07 Oct 2018 20:46:50: #2 alternative fragment length(s) may be 2,53,573 bps INFO @ Sun, 07 Oct 2018 20:46:50: #2.2 Generate R script for model : SRX4669052.05_model.r WARNING @ Sun, 07 Oct 2018 20:46:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:46:50: #2 You may need to consider one of the other alternative d(s): 2,53,573 WARNING @ Sun, 07 Oct 2018 20:46:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:46:50: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:46:53: 18000000 INFO @ Sun, 07 Oct 2018 20:46:59: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:46:59: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:46:59: #1 total tags in treatment: 18792917 INFO @ Sun, 07 Oct 2018 20:46:59: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:46:59: #1 tags after filtering in treatment: 18792917 INFO @ Sun, 07 Oct 2018 20:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:59: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:59: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:00: #2 number of paired peaks: 158 WARNING @ Sun, 07 Oct 2018 20:47:00: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 07 Oct 2018 20:47:00: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:00: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:00: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:00: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:00: #2 predicted fragment length is 53 bps INFO @ Sun, 07 Oct 2018 20:47:00: #2 alternative fragment length(s) may be 2,53,573 bps INFO @ Sun, 07 Oct 2018 20:47:00: #2.2 Generate R script for model : SRX4669052.10_model.r WARNING @ Sun, 07 Oct 2018 20:47:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:47:00: #2 You may need to consider one of the other alternative d(s): 2,53,573 WARNING @ Sun, 07 Oct 2018 20:47:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:47:00: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:28: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:31: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:39: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:49: #4 Write output xls file... SRX4669052.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:49: #4 Write peak in narrowPeak format file... SRX4669052.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:49: #4 Write summits bed file... SRX4669052.20_summits.bed INFO @ Sun, 07 Oct 2018 20:47:49: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:47:51: #4 Write output xls file... SRX4669052.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:51: #4 Write peak in narrowPeak format file... SRX4669052.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:51: #4 Write summits bed file... SRX4669052.05_summits.bed INFO @ Sun, 07 Oct 2018 20:47:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6954 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:47:59: #4 Write output xls file... SRX4669052.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:59: #4 Write peak in narrowPeak format file... SRX4669052.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:59: #4 Write summits bed file... SRX4669052.10_summits.bed INFO @ Sun, 07 Oct 2018 20:47:59: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1690 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。