Job ID = 9371916 sra ファイルのダウンロード中... Completed: 303366K bytes transferred in 12 seconds (196709K 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 14386095 spots for /home/okishinya/chipatlas/results/dm3/SRX2520640/SRR5206759.sra Written 14386095 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: 00:00:00 Multiseed full-index search: 00:05:32 14386095 reads; of these: 14386095 (100.00%) were unpaired; of these: 309255 (2.15%) aligned 0 times 10845721 (75.39%) aligned exactly 1 time 3231119 (22.46%) aligned >1 times 97.85% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 1817171 / 14076840 = 0.1291 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 14:58:37: # Command line: callpeak -t SRX2520640.bam -f BAM -g dm -n SRX2520640.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520640.10 # format = BAM # ChIP-seq file = ['SRX2520640.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 14:58:37: # Command line: callpeak -t SRX2520640.bam -f BAM -g dm -n SRX2520640.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520640.05 # format = BAM # ChIP-seq file = ['SRX2520640.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 14:58:37: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:58:37: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:58:37: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:58:37: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:58:37: # Command line: callpeak -t SRX2520640.bam -f BAM -g dm -n SRX2520640.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520640.20 # format = BAM # ChIP-seq file = ['SRX2520640.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 14:58:37: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:58:37: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:58:45: 1000000 INFO @ Fri, 04 Aug 2017 14:58:45: 1000000 INFO @ Fri, 04 Aug 2017 14:58:45: 1000000 INFO @ Fri, 04 Aug 2017 14:58:53: 2000000 INFO @ Fri, 04 Aug 2017 14:58:53: 2000000 INFO @ Fri, 04 Aug 2017 14:58:53: 2000000 INFO @ Fri, 04 Aug 2017 14:59:01: 3000000 INFO @ Fri, 04 Aug 2017 14:59:01: 3000000 INFO @ Fri, 04 Aug 2017 14:59:01: 3000000 INFO @ Fri, 04 Aug 2017 14:59:09: 4000000 INFO @ Fri, 04 Aug 2017 14:59:09: 4000000 INFO @ Fri, 04 Aug 2017 14:59:09: 4000000 INFO @ Fri, 04 Aug 2017 14:59:17: 5000000 INFO @ Fri, 04 Aug 2017 14:59:17: 5000000 INFO @ Fri, 04 Aug 2017 14:59:17: 5000000 INFO @ Fri, 04 Aug 2017 14:59:24: 6000000 INFO @ Fri, 04 Aug 2017 14:59:25: 6000000 INFO @ Fri, 04 Aug 2017 14:59:25: 6000000 INFO @ Fri, 04 Aug 2017 14:59:32: 7000000 INFO @ Fri, 04 Aug 2017 14:59:33: 7000000 INFO @ Fri, 04 Aug 2017 14:59:33: 7000000 INFO @ Fri, 04 Aug 2017 14:59:40: 8000000 INFO @ Fri, 04 Aug 2017 14:59:41: 8000000 INFO @ Fri, 04 Aug 2017 14:59:41: 8000000 INFO @ Fri, 04 Aug 2017 14:59:48: 9000000 INFO @ Fri, 04 Aug 2017 14:59:49: 9000000 INFO @ Fri, 04 Aug 2017 14:59:49: 9000000 INFO @ Fri, 04 Aug 2017 14:59:56: 10000000 INFO @ Fri, 04 Aug 2017 14:59:57: 10000000 INFO @ Fri, 04 Aug 2017 14:59:57: 10000000 INFO @ Fri, 04 Aug 2017 15:00:03: 11000000 INFO @ Fri, 04 Aug 2017 15:00:06: 11000000 INFO @ Fri, 04 Aug 2017 15:00:06: 11000000 INFO @ Fri, 04 Aug 2017 15:00:11: 12000000 INFO @ Fri, 04 Aug 2017 15:00:13: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:00:13: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:00:13: #1 total tags in treatment: 12259669 INFO @ Fri, 04 Aug 2017 15:00:13: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:00:13: #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 15:00:13: #1 tags after filtering in treatment: 12259669 INFO @ Fri, 04 Aug 2017 15:00:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:00:13: #1 finished! INFO @ Fri, 04 Aug 2017 15:00:13: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:00:14: 12000000 INFO @ Fri, 04 Aug 2017 15:00:14: #2 number of paired peaks: 288 WARNING @ Fri, 04 Aug 2017 15:00:14: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Fri, 04 Aug 2017 15:00:14: start model_add_line... INFO @ Fri, 04 Aug 2017 15:00:14: 12000000 INFO @ Fri, 04 Aug 2017 15:00:14: start X-correlation... INFO @ Fri, 04 Aug 2017 15:00:14: end of X-cor INFO @ Fri, 04 Aug 2017 15:00:14: #2 finished! INFO @ Fri, 04 Aug 2017 15:00:14: #2 predicted fragment length is 50 bps INFO @ Fri, 04 Aug 2017 15:00:14: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 04 Aug 2017 15:00:14: #2.2 Generate R script for model : SRX2520640.10_model.r WARNING @ Fri, 04 Aug 2017 15:00:14: #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 15:00:14: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 04 Aug 2017 15:00:14: #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 15:00:14: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:00:16: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:00:16: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:00:16: #1 total tags in treatment: 12259669 INFO @ Fri, 04 Aug 2017 15:00:16: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:00:16: #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 15:00:16: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:00:16: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:00:16: #1 total tags in treatment: 12259669 INFO @ Fri, 04 Aug 2017 15:00:16: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:00:16: #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 15:00:16: #1 tags after filtering in treatment: 12259669 INFO @ Fri, 04 Aug 2017 15:00:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:00:16: #1 finished! INFO @ Fri, 04 Aug 2017 15:00:16: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:00:16: #1 tags after filtering in treatment: 12259669 INFO @ Fri, 04 Aug 2017 15:00:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:00:16: #1 finished! INFO @ Fri, 04 Aug 2017 15:00:16: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:00:17: #2 number of paired peaks: 288 WARNING @ Fri, 04 Aug 2017 15:00:17: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Fri, 04 Aug 2017 15:00:17: start model_add_line... INFO @ Fri, 04 Aug 2017 15:00:17: start X-correlation... INFO @ Fri, 04 Aug 2017 15:00:17: end of X-cor INFO @ Fri, 04 Aug 2017 15:00:17: #2 finished! INFO @ Fri, 04 Aug 2017 15:00:17: #2 predicted fragment length is 50 bps INFO @ Fri, 04 Aug 2017 15:00:17: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 04 Aug 2017 15:00:17: #2.2 Generate R script for model : SRX2520640.20_model.r INFO @ Fri, 04 Aug 2017 15:00:17: #2 number of paired peaks: 288 WARNING @ Fri, 04 Aug 2017 15:00:17: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Fri, 04 Aug 2017 15:00:17: start model_add_line... WARNING @ Fri, 04 Aug 2017 15:00:17: #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 15:00:17: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 04 Aug 2017 15:00:17: #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 15:00:17: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:00:17: start X-correlation... INFO @ Fri, 04 Aug 2017 15:00:17: end of X-cor INFO @ Fri, 04 Aug 2017 15:00:17: #2 finished! INFO @ Fri, 04 Aug 2017 15:00:17: #2 predicted fragment length is 50 bps INFO @ Fri, 04 Aug 2017 15:00:17: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 04 Aug 2017 15:00:17: #2.2 Generate R script for model : SRX2520640.05_model.r WARNING @ Fri, 04 Aug 2017 15:00:17: #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 15:00:17: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 04 Aug 2017 15:00:17: #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 15:00:17: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:00:39: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:00:42: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:00:43: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:00:53: #4 Write output xls file... SRX2520640.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:00:53: #4 Write peak in narrowPeak format file... SRX2520640.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:00:53: #4 Write summits bed file... SRX2520640.10_summits.bed INFO @ Fri, 04 Aug 2017 15:00:53: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1147 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:00:57: #4 Write output xls file... SRX2520640.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:00:57: #4 Write peak in narrowPeak format file... SRX2520640.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:00:57: #4 Write summits bed file... SRX2520640.05_summits.bed INFO @ Fri, 04 Aug 2017 15:00:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1611 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:00:58: #4 Write output xls file... SRX2520640.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:00:58: #4 Write peak in narrowPeak format file... SRX2520640.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:00:58: #4 Write summits bed file... SRX2520640.20_summits.bed INFO @ Fri, 04 Aug 2017 15:00:58: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (828 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。