Job ID = 9297502 sra ファイルのダウンロード中... Completed: 1120653K bytes transferred in 38 seconds (237248K 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: PAIRED fastq に変換中... Written 8779876 spots for /home/okishinya/chipatlas/results/dm3/SRX1929540/SRR3845160.sra Written 8779876 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: 00:16:02 8779876 reads; of these: 8779876 (100.00%) were paired; of these: 820177 (9.34%) aligned concordantly 0 times 7292520 (83.06%) aligned concordantly exactly 1 time 667179 (7.60%) aligned concordantly >1 times ---- 820177 pairs aligned concordantly 0 times; of these: 63508 (7.74%) aligned discordantly 1 time ---- 756669 pairs aligned 0 times concordantly or discordantly; of these: 1513338 mates make up the pairs; of these: 1396645 (92.29%) aligned 0 times 84589 (5.59%) aligned exactly 1 time 32104 (2.12%) aligned >1 times 92.05% overall alignment rate Time searching: 00:16:02 Overall time: 00:16:02 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 819881 / 8015291 = 0.1023 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 @ Thu, 27 Jul 2017 15:50:51: # Command line: callpeak -t SRX1929540.bam -f BAM -g dm -n SRX1929540.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1929540.10 # format = BAM # ChIP-seq file = ['SRX1929540.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 @ Thu, 27 Jul 2017 15:50:51: #1 read tag files... INFO @ Thu, 27 Jul 2017 15:50:51: #1 read treatment tags... INFO @ Thu, 27 Jul 2017 15:50:51: # Command line: callpeak -t SRX1929540.bam -f BAM -g dm -n SRX1929540.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1929540.20 # format = BAM # ChIP-seq file = ['SRX1929540.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 @ Thu, 27 Jul 2017 15:50:51: #1 read tag files... INFO @ Thu, 27 Jul 2017 15:50:51: #1 read treatment tags... INFO @ Thu, 27 Jul 2017 15:50:51: # Command line: callpeak -t SRX1929540.bam -f BAM -g dm -n SRX1929540.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1929540.05 # format = BAM # ChIP-seq file = ['SRX1929540.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 @ Thu, 27 Jul 2017 15:50:51: #1 read tag files... INFO @ Thu, 27 Jul 2017 15:50:51: #1 read treatment tags... INFO @ Thu, 27 Jul 2017 15:50:59: 1000000 INFO @ Thu, 27 Jul 2017 15:50:59: 1000000 INFO @ Thu, 27 Jul 2017 15:51:00: 1000000 INFO @ Thu, 27 Jul 2017 15:51:08: 2000000 INFO @ Thu, 27 Jul 2017 15:51:08: 2000000 INFO @ Thu, 27 Jul 2017 15:51:10: 2000000 INFO @ Thu, 27 Jul 2017 15:51:16: 3000000 INFO @ Thu, 27 Jul 2017 15:51:16: 3000000 INFO @ Thu, 27 Jul 2017 15:51:19: 3000000 INFO @ Thu, 27 Jul 2017 15:51:24: 4000000 INFO @ Thu, 27 Jul 2017 15:51:24: 4000000 INFO @ Thu, 27 Jul 2017 15:51:28: 4000000 INFO @ Thu, 27 Jul 2017 15:51:33: 5000000 INFO @ Thu, 27 Jul 2017 15:51:33: 5000000 INFO @ Thu, 27 Jul 2017 15:51:38: 5000000 INFO @ Thu, 27 Jul 2017 15:51:41: 6000000 INFO @ Thu, 27 Jul 2017 15:51:41: 6000000 INFO @ Thu, 27 Jul 2017 15:51:47: 6000000 INFO @ Thu, 27 Jul 2017 15:51:50: 7000000 INFO @ Thu, 27 Jul 2017 15:51:50: 7000000 INFO @ Thu, 27 Jul 2017 15:51:56: 7000000 INFO @ Thu, 27 Jul 2017 15:51:58: 8000000 INFO @ Thu, 27 Jul 2017 15:51:58: 8000000 INFO @ Thu, 27 Jul 2017 15:52:06: 9000000 INFO @ Thu, 27 Jul 2017 15:52:06: 9000000 INFO @ Thu, 27 Jul 2017 15:52:06: 8000000 INFO @ Thu, 27 Jul 2017 15:52:14: 9000000 INFO @ Thu, 27 Jul 2017 15:52:15: 10000000 INFO @ Thu, 27 Jul 2017 15:52:15: 10000000 INFO @ Thu, 27 Jul 2017 15:52:23: 10000000 INFO @ Thu, 27 Jul 2017 15:52:24: 11000000 INFO @ Thu, 27 Jul 2017 15:52:24: 11000000 INFO @ Thu, 27 Jul 2017 15:52:31: 11000000 INFO @ Thu, 27 Jul 2017 15:52:32: 12000000 INFO @ Thu, 27 Jul 2017 15:52:32: 12000000 INFO @ Thu, 27 Jul 2017 15:52:38: 12000000 INFO @ Thu, 27 Jul 2017 15:52:39: 13000000 INFO @ Thu, 27 Jul 2017 15:52:39: 13000000 INFO @ Thu, 27 Jul 2017 15:52:45: 13000000 INFO @ Thu, 27 Jul 2017 15:52:46: 14000000 INFO @ Thu, 27 Jul 2017 15:52:46: 14000000 INFO @ Thu, 27 Jul 2017 15:52:50: #1 tag size is determined as 101 bps INFO @ Thu, 27 Jul 2017 15:52:50: #1 tag size = 101 INFO @ Thu, 27 Jul 2017 15:52:50: #1 total tags in treatment: 7140488 INFO @ Thu, 27 Jul 2017 15:52:50: #1 user defined the maximum tags... INFO @ Thu, 27 Jul 2017 15:52:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 27 Jul 2017 15:52:50: #1 tags after filtering in treatment: 6386771 INFO @ Thu, 27 Jul 2017 15:52:50: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 27 Jul 2017 15:52:50: #1 finished! INFO @ Thu, 27 Jul 2017 15:52:50: #2 Build Peak Model... INFO @ Thu, 27 Jul 2017 15:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 27 Jul 2017 15:52:50: #1 tag size is determined as 101 bps INFO @ Thu, 27 Jul 2017 15:52:50: #1 tag size = 101 INFO @ Thu, 27 Jul 2017 15:52:50: #1 total tags in treatment: 7140488 INFO @ Thu, 27 Jul 2017 15:52:50: #1 user defined the maximum tags... INFO @ Thu, 27 Jul 2017 15:52:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 27 Jul 2017 15:52:51: #1 tags after filtering in treatment: 6386771 INFO @ Thu, 27 Jul 2017 15:52:51: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 27 Jul 2017 15:52:51: #1 finished! INFO @ Thu, 27 Jul 2017 15:52:51: #2 Build Peak Model... INFO @ Thu, 27 Jul 2017 15:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 27 Jul 2017 15:52:51: #2 number of paired peaks: 562 WARNING @ Thu, 27 Jul 2017 15:52:51: Fewer paired peaks (562) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 562 pairs to build model! INFO @ Thu, 27 Jul 2017 15:52:51: start model_add_line... INFO @ Thu, 27 Jul 2017 15:52:51: start X-correlation... INFO @ Thu, 27 Jul 2017 15:52:51: end of X-cor INFO @ Thu, 27 Jul 2017 15:52:51: #2 finished! INFO @ Thu, 27 Jul 2017 15:52:51: #2 predicted fragment length is 180 bps INFO @ Thu, 27 Jul 2017 15:52:51: #2 alternative fragment length(s) may be 180 bps INFO @ Thu, 27 Jul 2017 15:52:51: #2.2 Generate R script for model : SRX1929540.20_model.r WARNING @ Thu, 27 Jul 2017 15:52:51: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 27 Jul 2017 15:52:51: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Thu, 27 Jul 2017 15:52:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 27 Jul 2017 15:52:51: #3 Call peaks... INFO @ Thu, 27 Jul 2017 15:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 27 Jul 2017 15:52:51: #2 number of paired peaks: 562 WARNING @ Thu, 27 Jul 2017 15:52:51: Fewer paired peaks (562) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 562 pairs to build model! INFO @ Thu, 27 Jul 2017 15:52:51: start model_add_line... INFO @ Thu, 27 Jul 2017 15:52:51: start X-correlation... INFO @ Thu, 27 Jul 2017 15:52:51: end of X-cor INFO @ Thu, 27 Jul 2017 15:52:51: #2 finished! INFO @ Thu, 27 Jul 2017 15:52:51: #2 predicted fragment length is 180 bps INFO @ Thu, 27 Jul 2017 15:52:51: #2 alternative fragment length(s) may be 180 bps INFO @ Thu, 27 Jul 2017 15:52:51: #2.2 Generate R script for model : SRX1929540.10_model.r WARNING @ Thu, 27 Jul 2017 15:52:51: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 27 Jul 2017 15:52:51: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Thu, 27 Jul 2017 15:52:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 27 Jul 2017 15:52:51: #3 Call peaks... INFO @ Thu, 27 Jul 2017 15:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 27 Jul 2017 15:52:52: 14000000 INFO @ Thu, 27 Jul 2017 15:52:56: #1 tag size is determined as 101 bps INFO @ Thu, 27 Jul 2017 15:52:56: #1 tag size = 101 INFO @ Thu, 27 Jul 2017 15:52:56: #1 total tags in treatment: 7140488 INFO @ Thu, 27 Jul 2017 15:52:56: #1 user defined the maximum tags... INFO @ Thu, 27 Jul 2017 15:52:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 27 Jul 2017 15:52:56: #1 tags after filtering in treatment: 6386771 INFO @ Thu, 27 Jul 2017 15:52:56: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 27 Jul 2017 15:52:56: #1 finished! INFO @ Thu, 27 Jul 2017 15:52:56: #2 Build Peak Model... INFO @ Thu, 27 Jul 2017 15:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 27 Jul 2017 15:52:57: #2 number of paired peaks: 562 WARNING @ Thu, 27 Jul 2017 15:52:57: Fewer paired peaks (562) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 562 pairs to build model! INFO @ Thu, 27 Jul 2017 15:52:57: start model_add_line... INFO @ Thu, 27 Jul 2017 15:52:57: start X-correlation... INFO @ Thu, 27 Jul 2017 15:52:57: end of X-cor INFO @ Thu, 27 Jul 2017 15:52:57: #2 finished! INFO @ Thu, 27 Jul 2017 15:52:57: #2 predicted fragment length is 180 bps INFO @ Thu, 27 Jul 2017 15:52:57: #2 alternative fragment length(s) may be 180 bps INFO @ Thu, 27 Jul 2017 15:52:57: #2.2 Generate R script for model : SRX1929540.05_model.r WARNING @ Thu, 27 Jul 2017 15:52:57: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 27 Jul 2017 15:52:57: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Thu, 27 Jul 2017 15:52:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 27 Jul 2017 15:52:57: #3 Call peaks... INFO @ Thu, 27 Jul 2017 15:52:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 27 Jul 2017 15:53:07: #3 Call peaks for each chromosome... INFO @ Thu, 27 Jul 2017 15:53:07: #3 Call peaks for each chromosome... INFO @ Thu, 27 Jul 2017 15:53:11: #3 Call peaks for each chromosome... INFO @ Thu, 27 Jul 2017 15:53:15: #4 Write output xls file... SRX1929540.20_peaks.xls INFO @ Thu, 27 Jul 2017 15:53:15: #4 Write peak in narrowPeak format file... SRX1929540.20_peaks.narrowPeak INFO @ Thu, 27 Jul 2017 15:53:15: #4 Write summits bed file... SRX1929540.20_summits.bed INFO @ Thu, 27 Jul 2017 15:53:15: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 27 Jul 2017 15:53:16: #4 Write output xls file... SRX1929540.10_peaks.xls INFO @ Thu, 27 Jul 2017 15:53:16: #4 Write peak in narrowPeak format file... SRX1929540.10_peaks.narrowPeak INFO @ Thu, 27 Jul 2017 15:53:16: #4 Write summits bed file... SRX1929540.10_summits.bed INFO @ Thu, 27 Jul 2017 15:53:16: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2243 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 27 Jul 2017 15:53:20: #4 Write output xls file... SRX1929540.05_peaks.xls INFO @ Thu, 27 Jul 2017 15:53:20: #4 Write peak in narrowPeak format file... SRX1929540.05_peaks.narrowPeak INFO @ Thu, 27 Jul 2017 15:53:20: #4 Write summits bed file... SRX1929540.05_summits.bed INFO @ Thu, 27 Jul 2017 15:53:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (7409 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。