Job ID = 10609079 sra ファイルのダウンロード中... Completed: 177780K bytes transferred in 8 seconds (162839K 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 3421866 spots for /home/okishinya/chipatlas/results/dm3/SRX2200904/SRR4309627.sra Written 3421866 spots for /home/okishinya/chipatlas/results/dm3/SRX2200904/SRR4309627.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: 00:09:30 3421866 reads; of these: 3421866 (100.00%) were paired; of these: 1386425 (40.52%) aligned concordantly 0 times 1363425 (39.84%) aligned concordantly exactly 1 time 672016 (19.64%) aligned concordantly >1 times ---- 1386425 pairs aligned concordantly 0 times; of these: 36559 (2.64%) aligned discordantly 1 time ---- 1349866 pairs aligned 0 times concordantly or discordantly; of these: 2699732 mates make up the pairs; of these: 2545411 (94.28%) aligned 0 times 78485 (2.91%) aligned exactly 1 time 75836 (2.81%) aligned >1 times 62.81% overall alignment rate Time searching: 00:09:30 Overall time: 00:09:30 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] 34343 / 2006004 = 0.0171 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 07:15:21: # Command line: callpeak -t SRX2200904.bam -f BAM -g dm -n SRX2200904.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2200904.20 # format = BAM # ChIP-seq file = ['SRX2200904.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 07:15:21: #1 read tag files... INFO @ Fri, 04 May 2018 07:15:21: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:21: # Command line: callpeak -t SRX2200904.bam -f BAM -g dm -n SRX2200904.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2200904.05 # format = BAM # ChIP-seq file = ['SRX2200904.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 07:15:21: #1 read tag files... INFO @ Fri, 04 May 2018 07:15:21: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:21: # Command line: callpeak -t SRX2200904.bam -f BAM -g dm -n SRX2200904.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2200904.10 # format = BAM # ChIP-seq file = ['SRX2200904.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 07:15:21: #1 read tag files... INFO @ Fri, 04 May 2018 07:15:21: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:27: 1000000 INFO @ Fri, 04 May 2018 07:15:27: 1000000 INFO @ Fri, 04 May 2018 07:15:27: 1000000 INFO @ Fri, 04 May 2018 07:15:34: 2000000 INFO @ Fri, 04 May 2018 07:15:34: 2000000 INFO @ Fri, 04 May 2018 07:15:34: 2000000 INFO @ Fri, 04 May 2018 07:15:41: 3000000 INFO @ Fri, 04 May 2018 07:15:41: 3000000 INFO @ Fri, 04 May 2018 07:15:42: 3000000 INFO @ Fri, 04 May 2018 07:15:48: 4000000 INFO @ Fri, 04 May 2018 07:15:48: 4000000 INFO @ Fri, 04 May 2018 07:15:49: 4000000 INFO @ Fri, 04 May 2018 07:15:49: #1 tag size is determined as 82 bps INFO @ Fri, 04 May 2018 07:15:49: #1 tag size = 82 INFO @ Fri, 04 May 2018 07:15:49: #1 total tags in treatment: 2001126 INFO @ Fri, 04 May 2018 07:15:49: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:49: #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 07:15:49: #1 tag size is determined as 82 bps INFO @ Fri, 04 May 2018 07:15:49: #1 tag size = 82 INFO @ Fri, 04 May 2018 07:15:49: #1 total tags in treatment: 2001126 INFO @ Fri, 04 May 2018 07:15:49: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:49: #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 07:15:49: #1 tags after filtering in treatment: 1936514 INFO @ Fri, 04 May 2018 07:15:49: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 04 May 2018 07:15:49: #1 finished! INFO @ Fri, 04 May 2018 07:15:49: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:49: #1 tags after filtering in treatment: 1936514 INFO @ Fri, 04 May 2018 07:15:49: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 04 May 2018 07:15:49: #1 finished! INFO @ Fri, 04 May 2018 07:15:49: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:50: #2 number of paired peaks: 1426 INFO @ Fri, 04 May 2018 07:15:50: start model_add_line... INFO @ Fri, 04 May 2018 07:15:50: start X-correlation... INFO @ Fri, 04 May 2018 07:15:50: end of X-cor INFO @ Fri, 04 May 2018 07:15:50: #2 finished! INFO @ Fri, 04 May 2018 07:15:50: #2 predicted fragment length is 150 bps INFO @ Fri, 04 May 2018 07:15:50: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 04 May 2018 07:15:50: #2.2 Generate R script for model : SRX2200904.10_model.r WARNING @ Fri, 04 May 2018 07:15:50: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:15:50: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 04 May 2018 07:15:50: #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 07:15:50: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:50: #2 number of paired peaks: 1426 INFO @ Fri, 04 May 2018 07:15:50: start model_add_line... INFO @ Fri, 04 May 2018 07:15:50: start X-correlation... INFO @ Fri, 04 May 2018 07:15:50: end of X-cor INFO @ Fri, 04 May 2018 07:15:50: #2 finished! INFO @ Fri, 04 May 2018 07:15:50: #2 predicted fragment length is 150 bps INFO @ Fri, 04 May 2018 07:15:50: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 04 May 2018 07:15:50: #2.2 Generate R script for model : SRX2200904.20_model.r WARNING @ Fri, 04 May 2018 07:15:50: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:15:50: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 04 May 2018 07:15:50: #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 07:15:50: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:50: #1 tag size is determined as 82 bps INFO @ Fri, 04 May 2018 07:15:50: #1 tag size = 82 INFO @ Fri, 04 May 2018 07:15:50: #1 total tags in treatment: 2001126 INFO @ Fri, 04 May 2018 07:15:50: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:50: #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 07:15:51: #1 tags after filtering in treatment: 1936514 INFO @ Fri, 04 May 2018 07:15:51: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 04 May 2018 07:15:51: #1 finished! INFO @ Fri, 04 May 2018 07:15:51: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:51: #2 number of paired peaks: 1426 INFO @ Fri, 04 May 2018 07:15:51: start model_add_line... INFO @ Fri, 04 May 2018 07:15:51: start X-correlation... INFO @ Fri, 04 May 2018 07:15:51: end of X-cor INFO @ Fri, 04 May 2018 07:15:51: #2 finished! INFO @ Fri, 04 May 2018 07:15:51: #2 predicted fragment length is 150 bps INFO @ Fri, 04 May 2018 07:15:51: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 04 May 2018 07:15:51: #2.2 Generate R script for model : SRX2200904.05_model.r WARNING @ Fri, 04 May 2018 07:15:51: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:15:51: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 04 May 2018 07:15:51: #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 07:15:51: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:54: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:55: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:56: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:57: #4 Write output xls file... SRX2200904.10_peaks.xls INFO @ Fri, 04 May 2018 07:15:57: #4 Write peak in narrowPeak format file... SRX2200904.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:57: #4 Write summits bed file... SRX2200904.10_summits.bed INFO @ Fri, 04 May 2018 07:15:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:15:58: #4 Write output xls file... SRX2200904.20_peaks.xls INFO @ Fri, 04 May 2018 07:15:58: #4 Write peak in narrowPeak format file... SRX2200904.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:58: #4 Write summits bed file... SRX2200904.20_summits.bed INFO @ Fri, 04 May 2018 07:15:58: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:15:59: #4 Write output xls file... SRX2200904.05_peaks.xls INFO @ Fri, 04 May 2018 07:15:59: #4 Write peak in narrowPeak format file... SRX2200904.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:59: #4 Write summits bed file... SRX2200904.05_summits.bed INFO @ Fri, 04 May 2018 07:15:59: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1043 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。