Job ID = 10450763 sra ファイルのダウンロード中... Completed: 448257K bytes transferred in 17 seconds (210550K 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 23397826 spots for /home/okishinya/chipatlas/results/dm3/SRX3404025/SRR6303502.sra Written 23397826 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:23 23397826 reads; of these: 23397826 (100.00%) were unpaired; of these: 492733 (2.11%) aligned 0 times 17456254 (74.61%) aligned exactly 1 time 5448839 (23.29%) aligned >1 times 97.89% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 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] 2032823 / 22905093 = 0.0887 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 14:33:19: # Command line: callpeak -t SRX3404025.bam -f BAM -g dm -n SRX3404025.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404025.05 # format = BAM # ChIP-seq file = ['SRX3404025.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 14:33:19: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:33:19: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:33:19: # Command line: callpeak -t SRX3404025.bam -f BAM -g dm -n SRX3404025.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404025.20 # format = BAM # ChIP-seq file = ['SRX3404025.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 14:33:19: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:33:19: # Command line: callpeak -t SRX3404025.bam -f BAM -g dm -n SRX3404025.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404025.10 # format = BAM # ChIP-seq file = ['SRX3404025.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 14:33:19: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:33:19: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:33:19: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:33:26: 1000000 INFO @ Wed, 07 Feb 2018 14:33:26: 1000000 INFO @ Wed, 07 Feb 2018 14:33:26: 1000000 INFO @ Wed, 07 Feb 2018 14:33:32: 2000000 INFO @ Wed, 07 Feb 2018 14:33:32: 2000000 INFO @ Wed, 07 Feb 2018 14:33:33: 2000000 INFO @ Wed, 07 Feb 2018 14:33:39: 3000000 INFO @ Wed, 07 Feb 2018 14:33:39: 3000000 INFO @ Wed, 07 Feb 2018 14:33:39: 3000000 INFO @ Wed, 07 Feb 2018 14:33:45: 4000000 INFO @ Wed, 07 Feb 2018 14:33:45: 4000000 INFO @ Wed, 07 Feb 2018 14:33:46: 4000000 INFO @ Wed, 07 Feb 2018 14:33:51: 5000000 INFO @ Wed, 07 Feb 2018 14:33:52: 5000000 INFO @ Wed, 07 Feb 2018 14:33:53: 5000000 INFO @ Wed, 07 Feb 2018 14:33:58: 6000000 INFO @ Wed, 07 Feb 2018 14:33:58: 6000000 INFO @ Wed, 07 Feb 2018 14:33:59: 6000000 INFO @ Wed, 07 Feb 2018 14:34:04: 7000000 INFO @ Wed, 07 Feb 2018 14:34:05: 7000000 INFO @ Wed, 07 Feb 2018 14:34:06: 7000000 INFO @ Wed, 07 Feb 2018 14:34:11: 8000000 INFO @ Wed, 07 Feb 2018 14:34:12: 8000000 INFO @ Wed, 07 Feb 2018 14:34:12: 8000000 INFO @ Wed, 07 Feb 2018 14:34:18: 9000000 INFO @ Wed, 07 Feb 2018 14:34:18: 9000000 INFO @ Wed, 07 Feb 2018 14:34:19: 9000000 INFO @ Wed, 07 Feb 2018 14:34:24: 10000000 INFO @ Wed, 07 Feb 2018 14:34:25: 10000000 INFO @ Wed, 07 Feb 2018 14:34:26: 10000000 INFO @ Wed, 07 Feb 2018 14:34:31: 11000000 INFO @ Wed, 07 Feb 2018 14:34:32: 11000000 INFO @ Wed, 07 Feb 2018 14:34:32: 11000000 INFO @ Wed, 07 Feb 2018 14:34:38: 12000000 INFO @ Wed, 07 Feb 2018 14:34:39: 12000000 INFO @ Wed, 07 Feb 2018 14:34:39: 12000000 INFO @ Wed, 07 Feb 2018 14:34:44: 13000000 INFO @ Wed, 07 Feb 2018 14:34:45: 13000000 INFO @ Wed, 07 Feb 2018 14:34:46: 13000000 INFO @ Wed, 07 Feb 2018 14:34:51: 14000000 INFO @ Wed, 07 Feb 2018 14:34:52: 14000000 INFO @ Wed, 07 Feb 2018 14:34:52: 14000000 INFO @ Wed, 07 Feb 2018 14:34:58: 15000000 INFO @ Wed, 07 Feb 2018 14:34:59: 15000000 INFO @ Wed, 07 Feb 2018 14:34:59: 15000000 INFO @ Wed, 07 Feb 2018 14:35:04: 16000000 INFO @ Wed, 07 Feb 2018 14:35:05: 16000000 INFO @ Wed, 07 Feb 2018 14:35:06: 16000000 INFO @ Wed, 07 Feb 2018 14:35:11: 17000000 INFO @ Wed, 07 Feb 2018 14:35:12: 17000000 INFO @ Wed, 07 Feb 2018 14:35:13: 17000000 INFO @ Wed, 07 Feb 2018 14:35:18: 18000000 INFO @ Wed, 07 Feb 2018 14:35:19: 18000000 INFO @ Wed, 07 Feb 2018 14:35:20: 18000000 INFO @ Wed, 07 Feb 2018 14:35:25: 19000000 INFO @ Wed, 07 Feb 2018 14:35:26: 19000000 INFO @ Wed, 07 Feb 2018 14:35:27: 19000000 INFO @ Wed, 07 Feb 2018 14:35:31: 20000000 INFO @ Wed, 07 Feb 2018 14:35:32: 20000000 INFO @ Wed, 07 Feb 2018 14:35:34: 20000000 INFO @ Wed, 07 Feb 2018 14:35:38: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:35:38: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:35:38: #1 total tags in treatment: 20872270 INFO @ Wed, 07 Feb 2018 14:35:38: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:35:38: #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 14:35:38: #1 tags after filtering in treatment: 20872270 INFO @ Wed, 07 Feb 2018 14:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:35:38: #1 finished! INFO @ Wed, 07 Feb 2018 14:35:38: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:35:38: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:35:38: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:35:38: #1 total tags in treatment: 20872270 INFO @ Wed, 07 Feb 2018 14:35:38: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:35:38: #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 14:35:39: #1 tags after filtering in treatment: 20872270 INFO @ Wed, 07 Feb 2018 14:35:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:35:39: #1 finished! INFO @ Wed, 07 Feb 2018 14:35:39: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:35:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:35:39: #2 number of paired peaks: 251 WARNING @ Wed, 07 Feb 2018 14:35:39: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Wed, 07 Feb 2018 14:35:39: start model_add_line... INFO @ Wed, 07 Feb 2018 14:35:39: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:35:39: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:35:39: #1 total tags in treatment: 20872270 INFO @ Wed, 07 Feb 2018 14:35:39: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:35:39: #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 14:35:40: start X-correlation... INFO @ Wed, 07 Feb 2018 14:35:40: end of X-cor INFO @ Wed, 07 Feb 2018 14:35:40: #2 finished! INFO @ Wed, 07 Feb 2018 14:35:40: #2 predicted fragment length is 56 bps INFO @ Wed, 07 Feb 2018 14:35:40: #2 alternative fragment length(s) may be 2,56,70,568,573 bps INFO @ Wed, 07 Feb 2018 14:35:40: #2.2 Generate R script for model : SRX3404025.20_model.r WARNING @ Wed, 07 Feb 2018 14:35:40: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 14:35:40: #2 You may need to consider one of the other alternative d(s): 2,56,70,568,573 WARNING @ Wed, 07 Feb 2018 14:35:40: #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 14:35:40: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:35:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:35:40: #1 tags after filtering in treatment: 20872270 INFO @ Wed, 07 Feb 2018 14:35:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:35:40: #1 finished! INFO @ Wed, 07 Feb 2018 14:35:40: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:35:40: #2 number of paired peaks: 251 WARNING @ Wed, 07 Feb 2018 14:35:40: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Wed, 07 Feb 2018 14:35:40: start model_add_line... INFO @ Wed, 07 Feb 2018 14:35:40: start X-correlation... INFO @ Wed, 07 Feb 2018 14:35:40: end of X-cor INFO @ Wed, 07 Feb 2018 14:35:40: #2 finished! INFO @ Wed, 07 Feb 2018 14:35:40: #2 predicted fragment length is 56 bps INFO @ Wed, 07 Feb 2018 14:35:40: #2 alternative fragment length(s) may be 2,56,70,568,573 bps INFO @ Wed, 07 Feb 2018 14:35:40: #2.2 Generate R script for model : SRX3404025.05_model.r WARNING @ Wed, 07 Feb 2018 14:35:40: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 14:35:40: #2 You may need to consider one of the other alternative d(s): 2,56,70,568,573 WARNING @ Wed, 07 Feb 2018 14:35:40: #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 14:35:40: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:35:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:35:41: #2 number of paired peaks: 251 WARNING @ Wed, 07 Feb 2018 14:35:41: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Wed, 07 Feb 2018 14:35:41: start model_add_line... INFO @ Wed, 07 Feb 2018 14:35:41: start X-correlation... INFO @ Wed, 07 Feb 2018 14:35:41: end of X-cor INFO @ Wed, 07 Feb 2018 14:35:41: #2 finished! INFO @ Wed, 07 Feb 2018 14:35:41: #2 predicted fragment length is 56 bps INFO @ Wed, 07 Feb 2018 14:35:41: #2 alternative fragment length(s) may be 2,56,70,568,573 bps INFO @ Wed, 07 Feb 2018 14:35:41: #2.2 Generate R script for model : SRX3404025.10_model.r WARNING @ Wed, 07 Feb 2018 14:35:41: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 14:35:41: #2 You may need to consider one of the other alternative d(s): 2,56,70,568,573 WARNING @ Wed, 07 Feb 2018 14:35:41: #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 14:35:41: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:36:22: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:36:22: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:36:23: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:36:45: #4 Write output xls file... SRX3404025.20_peaks.xls INFO @ Wed, 07 Feb 2018 14:36:45: #4 Write peak in narrowPeak format file... SRX3404025.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:36:45: #4 Write summits bed file... SRX3404025.20_summits.bed INFO @ Wed, 07 Feb 2018 14:36:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (664 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 14:36:47: #4 Write output xls file... SRX3404025.05_peaks.xls INFO @ Wed, 07 Feb 2018 14:36:47: #4 Write peak in narrowPeak format file... SRX3404025.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:36:47: #4 Write summits bed file... SRX3404025.05_summits.bed INFO @ Wed, 07 Feb 2018 14:36:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2974 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 14:36:48: #4 Write output xls file... SRX3404025.10_peaks.xls INFO @ Wed, 07 Feb 2018 14:36:48: #4 Write peak in narrowPeak format file... SRX3404025.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:36:48: #4 Write summits bed file... SRX3404025.10_summits.bed INFO @ Wed, 07 Feb 2018 14:36:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1602 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。