Job ID = 10609077 sra ファイルのダウンロード中... Completed: 149330K bytes transferred in 10 seconds (118458K 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: PAIRED fastq に変換中... Read 2740360 spots for /home/okishinya/chipatlas/results/dm3/SRX2200902/SRR4309625.sra Written 2740360 spots for /home/okishinya/chipatlas/results/dm3/SRX2200902/SRR4309625.sra 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:45 2740360 reads; of these: 2740360 (100.00%) were paired; of these: 1245385 (45.45%) aligned concordantly 0 times 1010490 (36.87%) aligned concordantly exactly 1 time 484485 (17.68%) aligned concordantly >1 times ---- 1245385 pairs aligned concordantly 0 times; of these: 16528 (1.33%) aligned discordantly 1 time ---- 1228857 pairs aligned 0 times concordantly or discordantly; of these: 2457714 mates make up the pairs; of these: 2388634 (97.19%) aligned 0 times 33537 (1.36%) aligned exactly 1 time 35543 (1.45%) aligned >1 times 56.42% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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_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] 28370 / 1455619 = 0.0195 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 May 2018 07:11:40: # Command line: callpeak -t SRX2200902.bam -f BAM -g dm -n SRX2200902.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2200902.05 # format = BAM # ChIP-seq file = ['SRX2200902.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 May 2018 07:11:40: # Command line: callpeak -t SRX2200902.bam -f BAM -g dm -n SRX2200902.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2200902.10 # format = BAM # ChIP-seq file = ['SRX2200902.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 May 2018 07:11:40: # Command line: callpeak -t SRX2200902.bam -f BAM -g dm -n SRX2200902.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2200902.20 # format = BAM # ChIP-seq file = ['SRX2200902.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 May 2018 07:11:40: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:40: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:40: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:40: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:40: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:40: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:47: 1000000 INFO @ Fri, 04 May 2018 07:11:47: 1000000 INFO @ Fri, 04 May 2018 07:11:47: 1000000 INFO @ Fri, 04 May 2018 07:11:54: 2000000 INFO @ Fri, 04 May 2018 07:11:54: 2000000 INFO @ Fri, 04 May 2018 07:11:54: 2000000 INFO @ Fri, 04 May 2018 07:12:01: 3000000 INFO @ Fri, 04 May 2018 07:12:01: #1 tag size is determined as 82 bps INFO @ Fri, 04 May 2018 07:12:01: #1 tag size = 82 INFO @ Fri, 04 May 2018 07:12:01: #1 total tags in treatment: 1466636 INFO @ Fri, 04 May 2018 07:12:01: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:12:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:12:01: #1 tags after filtering in treatment: 1423216 INFO @ Fri, 04 May 2018 07:12:01: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 04 May 2018 07:12:01: #1 finished! INFO @ Fri, 04 May 2018 07:12:01: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:12:01: #2 number of paired peaks: 1366 INFO @ Fri, 04 May 2018 07:12:01: start model_add_line... INFO @ Fri, 04 May 2018 07:12:01: start X-correlation... INFO @ Fri, 04 May 2018 07:12:01: 3000000 INFO @ Fri, 04 May 2018 07:12:01: end of X-cor INFO @ Fri, 04 May 2018 07:12:01: #2 finished! INFO @ Fri, 04 May 2018 07:12:01: #2 predicted fragment length is 145 bps INFO @ Fri, 04 May 2018 07:12:01: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 04 May 2018 07:12:01: #2.2 Generate R script for model : SRX2200902.05_model.r WARNING @ Fri, 04 May 2018 07:12:01: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:12:01: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 04 May 2018 07:12:01: #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 May 2018 07:12:01: #3 Call peaks... INFO @ Fri, 04 May 2018 07:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:12:02: #1 tag size is determined as 82 bps INFO @ Fri, 04 May 2018 07:12:02: #1 tag size = 82 INFO @ Fri, 04 May 2018 07:12:02: #1 total tags in treatment: 1466636 INFO @ Fri, 04 May 2018 07:12:02: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:12:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:12:02: #1 tags after filtering in treatment: 1423216 INFO @ Fri, 04 May 2018 07:12:02: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 04 May 2018 07:12:02: #1 finished! INFO @ Fri, 04 May 2018 07:12:02: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:12:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:12:02: #2 number of paired peaks: 1366 INFO @ Fri, 04 May 2018 07:12:02: start model_add_line... INFO @ Fri, 04 May 2018 07:12:02: start X-correlation... INFO @ Fri, 04 May 2018 07:12:02: end of X-cor INFO @ Fri, 04 May 2018 07:12:02: #2 finished! INFO @ Fri, 04 May 2018 07:12:02: #2 predicted fragment length is 145 bps INFO @ Fri, 04 May 2018 07:12:02: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 04 May 2018 07:12:02: #2.2 Generate R script for model : SRX2200902.10_model.r WARNING @ Fri, 04 May 2018 07:12:02: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:12:02: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 04 May 2018 07:12:02: #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 May 2018 07:12:02: #3 Call peaks... INFO @ Fri, 04 May 2018 07:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:12:02: 3000000 INFO @ Fri, 04 May 2018 07:12:02: #1 tag size is determined as 82 bps INFO @ Fri, 04 May 2018 07:12:02: #1 tag size = 82 INFO @ Fri, 04 May 2018 07:12:02: #1 total tags in treatment: 1466636 INFO @ Fri, 04 May 2018 07:12:02: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:12:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:12:02: #1 tags after filtering in treatment: 1423216 INFO @ Fri, 04 May 2018 07:12:02: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 04 May 2018 07:12:02: #1 finished! INFO @ Fri, 04 May 2018 07:12:02: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:12:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:12:02: #2 number of paired peaks: 1366 INFO @ Fri, 04 May 2018 07:12:02: start model_add_line... INFO @ Fri, 04 May 2018 07:12:02: start X-correlation... INFO @ Fri, 04 May 2018 07:12:02: end of X-cor INFO @ Fri, 04 May 2018 07:12:02: #2 finished! INFO @ Fri, 04 May 2018 07:12:02: #2 predicted fragment length is 145 bps INFO @ Fri, 04 May 2018 07:12:02: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 04 May 2018 07:12:02: #2.2 Generate R script for model : SRX2200902.20_model.r WARNING @ Fri, 04 May 2018 07:12:02: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:12:02: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 04 May 2018 07:12:02: #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 May 2018 07:12:02: #3 Call peaks... INFO @ Fri, 04 May 2018 07:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:12:05: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:12:06: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:12:06: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:12:07: #4 Write output xls file... SRX2200902.05_peaks.xls INFO @ Fri, 04 May 2018 07:12:07: #4 Write peak in narrowPeak format file... SRX2200902.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:12:07: #4 Write summits bed file... SRX2200902.05_summits.bed INFO @ Fri, 04 May 2018 07:12:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (836 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:12:08: #4 Write output xls file... SRX2200902.10_peaks.xls INFO @ Fri, 04 May 2018 07:12:08: #4 Write peak in narrowPeak format file... SRX2200902.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:12:08: #4 Write summits bed file... SRX2200902.10_summits.bed INFO @ Fri, 04 May 2018 07:12:08: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (528 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:12:08: #4 Write output xls file... SRX2200902.20_peaks.xls INFO @ Fri, 04 May 2018 07:12:08: #4 Write peak in narrowPeak format file... SRX2200902.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:12:08: #4 Write summits bed file... SRX2200902.20_summits.bed INFO @ Fri, 04 May 2018 07:12:08: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。