Job ID = 9371929 sra ファイルのダウンロード中... Completed: 398285K bytes transferred in 16 seconds (200330K bits/sec), in 1 file, 2 directories. 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 18939179 spots for /home/okishinya/chipatlas/results/dm3/SRX2520631/SRR5206750.sra Written 18939179 spots total 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: 00:00:01 Multiseed full-index search: 00:07:43 18939179 reads; of these: 18939179 (100.00%) were unpaired; of these: 430269 (2.27%) aligned 0 times 14201506 (74.98%) aligned exactly 1 time 4307404 (22.74%) aligned >1 times 97.73% overall alignment rate Time searching: 00:07:44 Overall time: 00:07:44 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] 2521325 / 18508910 = 0.1362 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, 04 Aug 2017 15:02:08: # Command line: callpeak -t SRX2520631.bam -f BAM -g dm -n SRX2520631.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520631.10 # format = BAM # ChIP-seq file = ['SRX2520631.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, 04 Aug 2017 15:02:08: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:02:08: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:02:08: # Command line: callpeak -t SRX2520631.bam -f BAM -g dm -n SRX2520631.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520631.05 # format = BAM # ChIP-seq file = ['SRX2520631.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, 04 Aug 2017 15:02:08: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:02:08: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:02:08: # Command line: callpeak -t SRX2520631.bam -f BAM -g dm -n SRX2520631.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520631.20 # format = BAM # ChIP-seq file = ['SRX2520631.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, 04 Aug 2017 15:02:08: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:02:08: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:02:17: 1000000 INFO @ Fri, 04 Aug 2017 15:02:17: 1000000 INFO @ Fri, 04 Aug 2017 15:02:17: 1000000 INFO @ Fri, 04 Aug 2017 15:02:25: 2000000 INFO @ Fri, 04 Aug 2017 15:02:25: 2000000 INFO @ Fri, 04 Aug 2017 15:02:25: 2000000 INFO @ Fri, 04 Aug 2017 15:02:33: 3000000 INFO @ Fri, 04 Aug 2017 15:02:33: 3000000 INFO @ Fri, 04 Aug 2017 15:02:33: 3000000 INFO @ Fri, 04 Aug 2017 15:02:41: 4000000 INFO @ Fri, 04 Aug 2017 15:02:41: 4000000 INFO @ Fri, 04 Aug 2017 15:02:41: 4000000 INFO @ Fri, 04 Aug 2017 15:02:49: 5000000 INFO @ Fri, 04 Aug 2017 15:02:49: 5000000 INFO @ Fri, 04 Aug 2017 15:02:50: 5000000 INFO @ Fri, 04 Aug 2017 15:02:57: 6000000 INFO @ Fri, 04 Aug 2017 15:02:57: 6000000 INFO @ Fri, 04 Aug 2017 15:02:58: 6000000 INFO @ Fri, 04 Aug 2017 15:03:06: 7000000 INFO @ Fri, 04 Aug 2017 15:03:06: 7000000 INFO @ Fri, 04 Aug 2017 15:03:06: 7000000 INFO @ Fri, 04 Aug 2017 15:03:14: 8000000 INFO @ Fri, 04 Aug 2017 15:03:14: 8000000 INFO @ Fri, 04 Aug 2017 15:03:14: 8000000 INFO @ Fri, 04 Aug 2017 15:03:22: 9000000 INFO @ Fri, 04 Aug 2017 15:03:22: 9000000 INFO @ Fri, 04 Aug 2017 15:03:22: 9000000 INFO @ Fri, 04 Aug 2017 15:03:30: 10000000 INFO @ Fri, 04 Aug 2017 15:03:30: 10000000 INFO @ Fri, 04 Aug 2017 15:03:30: 10000000 INFO @ Fri, 04 Aug 2017 15:03:38: 11000000 INFO @ Fri, 04 Aug 2017 15:03:38: 11000000 INFO @ Fri, 04 Aug 2017 15:03:38: 11000000 INFO @ Fri, 04 Aug 2017 15:03:46: 12000000 INFO @ Fri, 04 Aug 2017 15:03:46: 12000000 INFO @ Fri, 04 Aug 2017 15:03:47: 12000000 INFO @ Fri, 04 Aug 2017 15:03:54: 13000000 INFO @ Fri, 04 Aug 2017 15:03:54: 13000000 INFO @ Fri, 04 Aug 2017 15:03:55: 13000000 INFO @ Fri, 04 Aug 2017 15:04:01: 14000000 INFO @ Fri, 04 Aug 2017 15:04:02: 14000000 INFO @ Fri, 04 Aug 2017 15:04:03: 14000000 INFO @ Fri, 04 Aug 2017 15:04:09: 15000000 INFO @ Fri, 04 Aug 2017 15:04:10: 15000000 INFO @ Fri, 04 Aug 2017 15:04:11: 15000000 INFO @ Fri, 04 Aug 2017 15:04:17: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:04:17: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:04:17: #1 total tags in treatment: 15987585 INFO @ Fri, 04 Aug 2017 15:04:17: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:04:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:04:17: #1 tags after filtering in treatment: 15987585 INFO @ Fri, 04 Aug 2017 15:04:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:04:17: #1 finished! INFO @ Fri, 04 Aug 2017 15:04:17: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:04:17: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:04:17: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:04:17: #1 total tags in treatment: 15987585 INFO @ Fri, 04 Aug 2017 15:04:17: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:04:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:04:18: #1 tags after filtering in treatment: 15987585 INFO @ Fri, 04 Aug 2017 15:04:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:04:18: #1 finished! INFO @ Fri, 04 Aug 2017 15:04:18: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:04:19: #2 number of paired peaks: 455 WARNING @ Fri, 04 Aug 2017 15:04:19: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Fri, 04 Aug 2017 15:04:19: start model_add_line... INFO @ Fri, 04 Aug 2017 15:04:19: start X-correlation... INFO @ Fri, 04 Aug 2017 15:04:19: end of X-cor INFO @ Fri, 04 Aug 2017 15:04:19: #2 finished! INFO @ Fri, 04 Aug 2017 15:04:19: #2 predicted fragment length is 50 bps INFO @ Fri, 04 Aug 2017 15:04:19: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 04 Aug 2017 15:04:19: #2.2 Generate R script for model : SRX2520631.20_model.r WARNING @ Fri, 04 Aug 2017 15:04:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:04:19: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 04 Aug 2017 15:04:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:04:19: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:04:19: #2 number of paired peaks: 455 WARNING @ Fri, 04 Aug 2017 15:04:19: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Fri, 04 Aug 2017 15:04:19: start model_add_line... INFO @ Fri, 04 Aug 2017 15:04:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:04:19: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:04:19: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:04:19: #1 total tags in treatment: 15987585 INFO @ Fri, 04 Aug 2017 15:04:19: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:04:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:04:19: start X-correlation... INFO @ Fri, 04 Aug 2017 15:04:19: end of X-cor INFO @ Fri, 04 Aug 2017 15:04:19: #2 finished! INFO @ Fri, 04 Aug 2017 15:04:19: #2 predicted fragment length is 50 bps INFO @ Fri, 04 Aug 2017 15:04:19: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 04 Aug 2017 15:04:19: #2.2 Generate R script for model : SRX2520631.10_model.r WARNING @ Fri, 04 Aug 2017 15:04:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:04:19: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 04 Aug 2017 15:04:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:04:19: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:04:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:04:19: #1 tags after filtering in treatment: 15987585 INFO @ Fri, 04 Aug 2017 15:04:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:04:19: #1 finished! INFO @ Fri, 04 Aug 2017 15:04:19: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:04:20: #2 number of paired peaks: 455 WARNING @ Fri, 04 Aug 2017 15:04:20: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Fri, 04 Aug 2017 15:04:20: start model_add_line... INFO @ Fri, 04 Aug 2017 15:04:21: start X-correlation... INFO @ Fri, 04 Aug 2017 15:04:21: end of X-cor INFO @ Fri, 04 Aug 2017 15:04:21: #2 finished! INFO @ Fri, 04 Aug 2017 15:04:21: #2 predicted fragment length is 50 bps INFO @ Fri, 04 Aug 2017 15:04:21: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 04 Aug 2017 15:04:21: #2.2 Generate R script for model : SRX2520631.05_model.r WARNING @ Fri, 04 Aug 2017 15:04:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:04:21: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 04 Aug 2017 15:04:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:04:21: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:04:52: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:04:54: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:04:55: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:05:09: #4 Write output xls file... SRX2520631.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:05:09: #4 Write peak in narrowPeak format file... SRX2520631.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:05:09: #4 Write summits bed file... SRX2520631.10_summits.bed INFO @ Fri, 04 Aug 2017 15:05:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2116 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:05:11: #4 Write output xls file... SRX2520631.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:05:11: #4 Write peak in narrowPeak format file... SRX2520631.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:05:11: #4 Write summits bed file... SRX2520631.05_summits.bed INFO @ Fri, 04 Aug 2017 15:05:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3300 records, 4 fields): 72 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:05:13: #4 Write output xls file... SRX2520631.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:05:13: #4 Write peak in narrowPeak format file... SRX2520631.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:05:13: #4 Write summits bed file... SRX2520631.20_summits.bed INFO @ Fri, 04 Aug 2017 15:05:13: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1092 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。