Job ID = 9158164 sra ファイルのダウンロード中... Completed: 1571338K bytes transferred in 16 seconds (797376K 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 12425834 spots for /home/okishinya/chipatlas/results/dm3/SRX1056721/SRR2060655.sra Written 12425834 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: 00:56:43 12425834 reads; of these: 12425834 (100.00%) were paired; of these: 2074260 (16.69%) aligned concordantly 0 times 7013860 (56.45%) aligned concordantly exactly 1 time 3337714 (26.86%) aligned concordantly >1 times ---- 2074260 pairs aligned concordantly 0 times; of these: 66721 (3.22%) aligned discordantly 1 time ---- 2007539 pairs aligned 0 times concordantly or discordantly; of these: 4015078 mates make up the pairs; of these: 3608275 (89.87%) aligned 0 times 239829 (5.97%) aligned exactly 1 time 166974 (4.16%) aligned >1 times 85.48% overall alignment rate Time searching: 00:56:43 Overall time: 00:56:43 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_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] 8157639 / 10390785 = 0.7851 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 @ Tue, 27 Jun 2017 16:35:30: # Command line: callpeak -t SRX1056721.bam -f BAM -g dm -n SRX1056721.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056721.10 # format = BAM # ChIP-seq file = ['SRX1056721.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 @ Tue, 27 Jun 2017 16:35:30: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:35:30: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:35:30: # Command line: callpeak -t SRX1056721.bam -f BAM -g dm -n SRX1056721.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056721.20 # format = BAM # ChIP-seq file = ['SRX1056721.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 @ Tue, 27 Jun 2017 16:35:30: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:35:30: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:35:30: # Command line: callpeak -t SRX1056721.bam -f BAM -g dm -n SRX1056721.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056721.05 # format = BAM # ChIP-seq file = ['SRX1056721.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 @ Tue, 27 Jun 2017 16:35:30: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:35:30: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:35:37: 1000000 INFO @ Tue, 27 Jun 2017 16:35:37: 1000000 INFO @ Tue, 27 Jun 2017 16:35:37: 1000000 INFO @ Tue, 27 Jun 2017 16:35:44: 2000000 INFO @ Tue, 27 Jun 2017 16:35:44: 2000000 INFO @ Tue, 27 Jun 2017 16:35:45: 2000000 INFO @ Tue, 27 Jun 2017 16:35:52: 3000000 INFO @ Tue, 27 Jun 2017 16:35:52: 3000000 INFO @ Tue, 27 Jun 2017 16:35:52: 3000000 INFO @ Tue, 27 Jun 2017 16:35:59: 4000000 INFO @ Tue, 27 Jun 2017 16:35:59: 4000000 INFO @ Tue, 27 Jun 2017 16:36:00: 4000000 INFO @ Tue, 27 Jun 2017 16:36:06: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 16:36:06: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 16:36:06: #1 total tags in treatment: 2243491 INFO @ Tue, 27 Jun 2017 16:36:06: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:36:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 16:36:06: #1 tags after filtering in treatment: 1974503 INFO @ Tue, 27 Jun 2017 16:36:06: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 27 Jun 2017 16:36:06: #1 finished! INFO @ Tue, 27 Jun 2017 16:36:06: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:36:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:36:07: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 16:36:07: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 16:36:07: #1 total tags in treatment: 2243491 INFO @ Tue, 27 Jun 2017 16:36:07: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:36:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 16:36:07: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 16:36:07: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 16:36:07: #1 total tags in treatment: 2243491 INFO @ Tue, 27 Jun 2017 16:36:07: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:36:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 16:36:07: #1 tags after filtering in treatment: 1974503 INFO @ Tue, 27 Jun 2017 16:36:07: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 27 Jun 2017 16:36:07: #1 finished! INFO @ Tue, 27 Jun 2017 16:36:07: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:36:07: #1 tags after filtering in treatment: 1974503 INFO @ Tue, 27 Jun 2017 16:36:07: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 27 Jun 2017 16:36:07: #1 finished! INFO @ Tue, 27 Jun 2017 16:36:07: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:36:07: #2 number of paired peaks: 5599 INFO @ Tue, 27 Jun 2017 16:36:07: start model_add_line... INFO @ Tue, 27 Jun 2017 16:36:07: start X-correlation... INFO @ Tue, 27 Jun 2017 16:36:07: end of X-cor INFO @ Tue, 27 Jun 2017 16:36:07: #2 finished! INFO @ Tue, 27 Jun 2017 16:36:07: #2 predicted fragment length is 171 bps INFO @ Tue, 27 Jun 2017 16:36:07: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 27 Jun 2017 16:36:07: #2.2 Generate R script for model : SRX1056721.20_model.r WARNING @ Tue, 27 Jun 2017 16:36:07: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:36:07: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Tue, 27 Jun 2017 16:36:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 16:36:07: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:36:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:36:07: #2 number of paired peaks: 5599 INFO @ Tue, 27 Jun 2017 16:36:07: start model_add_line... INFO @ Tue, 27 Jun 2017 16:36:07: #2 number of paired peaks: 5599 INFO @ Tue, 27 Jun 2017 16:36:07: start model_add_line... INFO @ Tue, 27 Jun 2017 16:36:07: start X-correlation... INFO @ Tue, 27 Jun 2017 16:36:07: end of X-cor INFO @ Tue, 27 Jun 2017 16:36:07: #2 finished! INFO @ Tue, 27 Jun 2017 16:36:07: #2 predicted fragment length is 171 bps INFO @ Tue, 27 Jun 2017 16:36:07: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 27 Jun 2017 16:36:07: #2.2 Generate R script for model : SRX1056721.05_model.r INFO @ Tue, 27 Jun 2017 16:36:07: start X-correlation... INFO @ Tue, 27 Jun 2017 16:36:07: end of X-cor INFO @ Tue, 27 Jun 2017 16:36:07: #2 finished! INFO @ Tue, 27 Jun 2017 16:36:07: #2 predicted fragment length is 171 bps WARNING @ Tue, 27 Jun 2017 16:36:07: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Tue, 27 Jun 2017 16:36:07: #2 alternative fragment length(s) may be 171 bps WARNING @ Tue, 27 Jun 2017 16:36:07: #2 You may need to consider one of the other alternative d(s): 171 INFO @ Tue, 27 Jun 2017 16:36:07: #2.2 Generate R script for model : SRX1056721.10_model.r WARNING @ Tue, 27 Jun 2017 16:36:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 16:36:07: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:36:07: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 27 Jun 2017 16:36:07: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:36:07: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Tue, 27 Jun 2017 16:36:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 16:36:07: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:36:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:36:12: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:36:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:36:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:36:15: #4 Write output xls file... SRX1056721.20_peaks.xls INFO @ Tue, 27 Jun 2017 16:36:15: #4 Write peak in narrowPeak format file... SRX1056721.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:36:15: #4 Write summits bed file... SRX1056721.20_summits.bed INFO @ Tue, 27 Jun 2017 16:36:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (901 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:36:16: #4 Write output xls file... SRX1056721.10_peaks.xls INFO @ Tue, 27 Jun 2017 16:36:16: #4 Write peak in narrowPeak format file... SRX1056721.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:36:16: #4 Write summits bed file... SRX1056721.10_summits.bed INFO @ Tue, 27 Jun 2017 16:36:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2447 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:36:16: #4 Write output xls file... SRX1056721.05_peaks.xls INFO @ Tue, 27 Jun 2017 16:36:16: #4 Write peak in narrowPeak format file... SRX1056721.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:36:16: #4 Write summits bed file... SRX1056721.05_summits.bed INFO @ Tue, 27 Jun 2017 16:36:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4756 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。