Job ID = 10450987 sra ファイルのダウンロード中... Completed: 376081K bytes transferred in 22 seconds (137208K 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 19585467 spots for /home/okishinya/chipatlas/results/dm3/SRX3404044/SRR6303521.sra Written 19585467 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:15:19 19585467 reads; of these: 19585467 (100.00%) were unpaired; of these: 539954 (2.76%) aligned 0 times 13487215 (68.86%) aligned exactly 1 time 5558298 (28.38%) aligned >1 times 97.24% overall alignment rate Time searching: 00:15:19 Overall time: 00:15:19 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] 1349505 / 19045513 = 0.0709 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 @ Wed, 07 Feb 2018 14:46:28: # Command line: callpeak -t SRX3404044.bam -f BAM -g dm -n SRX3404044.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404044.10 # format = BAM # ChIP-seq file = ['SRX3404044.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 @ Wed, 07 Feb 2018 14:46:28: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:46:28: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:46:28: # Command line: callpeak -t SRX3404044.bam -f BAM -g dm -n SRX3404044.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404044.05 # format = BAM # ChIP-seq file = ['SRX3404044.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 @ Wed, 07 Feb 2018 14:46:28: # Command line: callpeak -t SRX3404044.bam -f BAM -g dm -n SRX3404044.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404044.20 # format = BAM # ChIP-seq file = ['SRX3404044.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 @ Wed, 07 Feb 2018 14:46:28: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:46:28: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:46:28: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:46:28: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:46:46: 1000000 INFO @ Wed, 07 Feb 2018 14:46:48: 1000000 INFO @ Wed, 07 Feb 2018 14:46:50: 1000000 INFO @ Wed, 07 Feb 2018 14:47:03: 2000000 INFO @ Wed, 07 Feb 2018 14:47:10: 2000000 INFO @ Wed, 07 Feb 2018 14:47:11: 2000000 INFO @ Wed, 07 Feb 2018 14:47:20: 3000000 INFO @ Wed, 07 Feb 2018 14:47:20: 3000000 INFO @ Wed, 07 Feb 2018 14:47:30: 4000000 INFO @ Wed, 07 Feb 2018 14:47:31: 3000000 INFO @ Wed, 07 Feb 2018 14:47:36: 4000000 INFO @ Wed, 07 Feb 2018 14:47:39: 5000000 INFO @ Wed, 07 Feb 2018 14:47:50: 6000000 INFO @ Wed, 07 Feb 2018 14:47:52: 4000000 INFO @ Wed, 07 Feb 2018 14:47:52: 5000000 INFO @ Wed, 07 Feb 2018 14:48:00: 7000000 INFO @ Wed, 07 Feb 2018 14:48:09: 6000000 INFO @ Wed, 07 Feb 2018 14:48:11: 8000000 INFO @ Wed, 07 Feb 2018 14:48:12: 5000000 INFO @ Wed, 07 Feb 2018 14:48:22: 9000000 INFO @ Wed, 07 Feb 2018 14:48:27: 7000000 INFO @ Wed, 07 Feb 2018 14:48:30: 6000000 INFO @ Wed, 07 Feb 2018 14:48:32: 10000000 INFO @ Wed, 07 Feb 2018 14:48:43: 11000000 INFO @ Wed, 07 Feb 2018 14:48:43: 8000000 INFO @ Wed, 07 Feb 2018 14:48:50: 7000000 INFO @ Wed, 07 Feb 2018 14:48:53: 12000000 INFO @ Wed, 07 Feb 2018 14:48:59: 9000000 INFO @ Wed, 07 Feb 2018 14:49:04: 13000000 INFO @ Wed, 07 Feb 2018 14:49:12: 8000000 INFO @ Wed, 07 Feb 2018 14:49:14: 14000000 INFO @ Wed, 07 Feb 2018 14:49:15: 10000000 INFO @ Wed, 07 Feb 2018 14:49:25: 15000000 INFO @ Wed, 07 Feb 2018 14:49:31: 11000000 INFO @ Wed, 07 Feb 2018 14:49:33: 9000000 INFO @ Wed, 07 Feb 2018 14:49:35: 16000000 INFO @ Wed, 07 Feb 2018 14:49:46: 17000000 INFO @ Wed, 07 Feb 2018 14:49:49: 12000000 INFO @ Wed, 07 Feb 2018 14:49:53: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:49:53: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:49:53: #1 total tags in treatment: 17696008 INFO @ Wed, 07 Feb 2018 14:49:53: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:49:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 14:49:54: #1 tags after filtering in treatment: 17696008 INFO @ Wed, 07 Feb 2018 14:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:49:54: #1 finished! INFO @ Wed, 07 Feb 2018 14:49:54: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:49:55: 10000000 INFO @ Wed, 07 Feb 2018 14:49:55: #2 number of paired peaks: 264 WARNING @ Wed, 07 Feb 2018 14:49:55: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Wed, 07 Feb 2018 14:49:55: start model_add_line... INFO @ Wed, 07 Feb 2018 14:49:56: start X-correlation... INFO @ Wed, 07 Feb 2018 14:49:56: end of X-cor INFO @ Wed, 07 Feb 2018 14:49:56: #2 finished! INFO @ Wed, 07 Feb 2018 14:49:56: #2 predicted fragment length is 51 bps INFO @ Wed, 07 Feb 2018 14:49:56: #2 alternative fragment length(s) may be 2,51 bps INFO @ Wed, 07 Feb 2018 14:49:56: #2.2 Generate R script for model : SRX3404044.05_model.r WARNING @ Wed, 07 Feb 2018 14:49:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 14:49:56: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Wed, 07 Feb 2018 14:49:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 14:49:56: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:49:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:50:06: 13000000 INFO @ Wed, 07 Feb 2018 14:50:16: 11000000 INFO @ Wed, 07 Feb 2018 14:50:23: 14000000 INFO @ Wed, 07 Feb 2018 14:50:37: 12000000 INFO @ Wed, 07 Feb 2018 14:50:41: 15000000 INFO @ Wed, 07 Feb 2018 14:50:41: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:50:58: 16000000 INFO @ Wed, 07 Feb 2018 14:50:59: 13000000 INFO @ Wed, 07 Feb 2018 14:51:09: #4 Write output xls file... SRX3404044.05_peaks.xls INFO @ Wed, 07 Feb 2018 14:51:09: #4 Write peak in narrowPeak format file... SRX3404044.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:51:09: #4 Write summits bed file... SRX3404044.05_summits.bed INFO @ Wed, 07 Feb 2018 14:51:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2576 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 14:51:15: 17000000 INFO @ Wed, 07 Feb 2018 14:51:19: 14000000 INFO @ Wed, 07 Feb 2018 14:51:27: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:51:27: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:51:27: #1 total tags in treatment: 17696008 INFO @ Wed, 07 Feb 2018 14:51:27: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:51:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 14:51:27: #1 tags after filtering in treatment: 17696008 INFO @ Wed, 07 Feb 2018 14:51:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:51:27: #1 finished! INFO @ Wed, 07 Feb 2018 14:51:27: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:51:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:51:29: #2 number of paired peaks: 264 WARNING @ Wed, 07 Feb 2018 14:51:29: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Wed, 07 Feb 2018 14:51:29: start model_add_line... INFO @ Wed, 07 Feb 2018 14:51:29: start X-correlation... INFO @ Wed, 07 Feb 2018 14:51:29: end of X-cor INFO @ Wed, 07 Feb 2018 14:51:29: #2 finished! INFO @ Wed, 07 Feb 2018 14:51:29: #2 predicted fragment length is 51 bps INFO @ Wed, 07 Feb 2018 14:51:29: #2 alternative fragment length(s) may be 2,51 bps INFO @ Wed, 07 Feb 2018 14:51:29: #2.2 Generate R script for model : SRX3404044.10_model.r WARNING @ Wed, 07 Feb 2018 14:51:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 14:51:29: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Wed, 07 Feb 2018 14:51:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 14:51:29: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:51:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:51:37: 15000000 INFO @ Wed, 07 Feb 2018 14:51:59: 16000000 INFO @ Wed, 07 Feb 2018 14:52:17: 17000000 INFO @ Wed, 07 Feb 2018 14:52:20: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:52:29: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:52:29: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:52:29: #1 total tags in treatment: 17696008 INFO @ Wed, 07 Feb 2018 14:52:29: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:52:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 14:52:30: #1 tags after filtering in treatment: 17696008 INFO @ Wed, 07 Feb 2018 14:52:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:52:30: #1 finished! INFO @ Wed, 07 Feb 2018 14:52:30: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:52:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:52:31: #2 number of paired peaks: 264 WARNING @ Wed, 07 Feb 2018 14:52:31: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Wed, 07 Feb 2018 14:52:31: start model_add_line... INFO @ Wed, 07 Feb 2018 14:52:32: start X-correlation... INFO @ Wed, 07 Feb 2018 14:52:32: end of X-cor INFO @ Wed, 07 Feb 2018 14:52:32: #2 finished! INFO @ Wed, 07 Feb 2018 14:52:32: #2 predicted fragment length is 51 bps INFO @ Wed, 07 Feb 2018 14:52:32: #2 alternative fragment length(s) may be 2,51 bps INFO @ Wed, 07 Feb 2018 14:52:32: #2.2 Generate R script for model : SRX3404044.20_model.r WARNING @ Wed, 07 Feb 2018 14:52:32: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 14:52:32: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Wed, 07 Feb 2018 14:52:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 14:52:32: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:52:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:52:53: #4 Write output xls file... SRX3404044.10_peaks.xls INFO @ Wed, 07 Feb 2018 14:52:53: #4 Write peak in narrowPeak format file... SRX3404044.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:52:53: #4 Write summits bed file... SRX3404044.10_summits.bed INFO @ Wed, 07 Feb 2018 14:52:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1357 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 14:53:18: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:53:47: #4 Write output xls file... SRX3404044.20_peaks.xls INFO @ Wed, 07 Feb 2018 14:53:47: #4 Write peak in narrowPeak format file... SRX3404044.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:53:47: #4 Write summits bed file... SRX3404044.20_summits.bed INFO @ Wed, 07 Feb 2018 14:53:47: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (452 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。