Job ID = 9371428 sra ファイルのダウンロード中... Completed: 502259K bytes transferred in 9 seconds (447061K 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 3240039 spots for /home/okishinya/chipatlas/results/dm3/SRX1958590/SRR3928904.sra Written 3240039 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: 00:36:59 3240039 reads; of these: 3240039 (100.00%) were paired; of these: 146612 (4.53%) aligned concordantly 0 times 2212395 (68.28%) aligned concordantly exactly 1 time 881032 (27.19%) aligned concordantly >1 times ---- 146612 pairs aligned concordantly 0 times; of these: 11585 (7.90%) aligned discordantly 1 time ---- 135027 pairs aligned 0 times concordantly or discordantly; of these: 270054 mates make up the pairs; of these: 174348 (64.56%) aligned 0 times 47720 (17.67%) aligned exactly 1 time 47986 (17.77%) aligned >1 times 97.31% overall alignment rate Time searching: 00:36:59 Overall time: 00:36:59 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] 48409 / 3086522 = 0.0157 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 14:43:04: # Command line: callpeak -t SRX1958590.bam -f BAM -g dm -n SRX1958590.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1958590.20 # format = BAM # ChIP-seq file = ['SRX1958590.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 14:43:04: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:43:04: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:43:04: # Command line: callpeak -t SRX1958590.bam -f BAM -g dm -n SRX1958590.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1958590.05 # format = BAM # ChIP-seq file = ['SRX1958590.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 14:43:04: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:43:04: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:43:04: # Command line: callpeak -t SRX1958590.bam -f BAM -g dm -n SRX1958590.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1958590.10 # format = BAM # ChIP-seq file = ['SRX1958590.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 14:43:04: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:43:04: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:43:16: 1000000 INFO @ Fri, 04 Aug 2017 14:43:22: 1000000 INFO @ Fri, 04 Aug 2017 14:43:26: 1000000 INFO @ Fri, 04 Aug 2017 14:43:34: 2000000 INFO @ Fri, 04 Aug 2017 14:43:43: 2000000 INFO @ Fri, 04 Aug 2017 14:43:45: 2000000 INFO @ Fri, 04 Aug 2017 14:43:49: 3000000 INFO @ Fri, 04 Aug 2017 14:43:59: 3000000 INFO @ Fri, 04 Aug 2017 14:44:03: 4000000 INFO @ Fri, 04 Aug 2017 14:44:09: 3000000 INFO @ Fri, 04 Aug 2017 14:44:13: 4000000 INFO @ Fri, 04 Aug 2017 14:44:18: 5000000 INFO @ Fri, 04 Aug 2017 14:44:26: 4000000 INFO @ Fri, 04 Aug 2017 14:44:28: 5000000 INFO @ Fri, 04 Aug 2017 14:44:34: 6000000 INFO @ Fri, 04 Aug 2017 14:44:38: #1 tag size is determined as 150 bps INFO @ Fri, 04 Aug 2017 14:44:38: #1 tag size = 150 INFO @ Fri, 04 Aug 2017 14:44:38: #1 total tags in treatment: 3045094 INFO @ Fri, 04 Aug 2017 14:44:38: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:44:38: #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 14:44:38: #1 tags after filtering in treatment: 2908391 INFO @ Fri, 04 Aug 2017 14:44:38: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 04 Aug 2017 14:44:38: #1 finished! INFO @ Fri, 04 Aug 2017 14:44:38: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:44:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:44:38: #2 number of paired peaks: 1185 INFO @ Fri, 04 Aug 2017 14:44:38: start model_add_line... INFO @ Fri, 04 Aug 2017 14:44:38: start X-correlation... INFO @ Fri, 04 Aug 2017 14:44:38: end of X-cor INFO @ Fri, 04 Aug 2017 14:44:38: #2 finished! INFO @ Fri, 04 Aug 2017 14:44:38: #2 predicted fragment length is 223 bps INFO @ Fri, 04 Aug 2017 14:44:38: #2 alternative fragment length(s) may be 223 bps INFO @ Fri, 04 Aug 2017 14:44:38: #2.2 Generate R script for model : SRX1958590.20_model.r WARNING @ Fri, 04 Aug 2017 14:44:38: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:44:38: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Fri, 04 Aug 2017 14:44:38: #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 14:44:38: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:44:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:44:42: 5000000 INFO @ Fri, 04 Aug 2017 14:44:42: 6000000 INFO @ Fri, 04 Aug 2017 14:44:45: #1 tag size is determined as 150 bps INFO @ Fri, 04 Aug 2017 14:44:45: #1 tag size = 150 INFO @ Fri, 04 Aug 2017 14:44:45: #1 total tags in treatment: 3045094 INFO @ Fri, 04 Aug 2017 14:44:45: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:44:45: #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 14:44:45: #1 tags after filtering in treatment: 2908391 INFO @ Fri, 04 Aug 2017 14:44:45: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 04 Aug 2017 14:44:45: #1 finished! INFO @ Fri, 04 Aug 2017 14:44:45: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:44:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:44:46: #2 number of paired peaks: 1185 INFO @ Fri, 04 Aug 2017 14:44:46: start model_add_line... INFO @ Fri, 04 Aug 2017 14:44:46: start X-correlation... INFO @ Fri, 04 Aug 2017 14:44:46: end of X-cor INFO @ Fri, 04 Aug 2017 14:44:46: #2 finished! INFO @ Fri, 04 Aug 2017 14:44:46: #2 predicted fragment length is 223 bps INFO @ Fri, 04 Aug 2017 14:44:46: #2 alternative fragment length(s) may be 223 bps INFO @ Fri, 04 Aug 2017 14:44:46: #2.2 Generate R script for model : SRX1958590.10_model.r WARNING @ Fri, 04 Aug 2017 14:44:46: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:44:46: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Fri, 04 Aug 2017 14:44:46: #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 14:44:46: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:44:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:44:48: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:44:54: #4 Write output xls file... SRX1958590.20_peaks.xls INFO @ Fri, 04 Aug 2017 14:44:54: #4 Write peak in narrowPeak format file... SRX1958590.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:44:54: #4 Write summits bed file... SRX1958590.20_summits.bed INFO @ Fri, 04 Aug 2017 14:44:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (516 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:44:56: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:44:57: 6000000 INFO @ Fri, 04 Aug 2017 14:45:00: #1 tag size is determined as 150 bps INFO @ Fri, 04 Aug 2017 14:45:00: #1 tag size = 150 INFO @ Fri, 04 Aug 2017 14:45:00: #1 total tags in treatment: 3045094 INFO @ Fri, 04 Aug 2017 14:45:00: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:45:00: #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 14:45:00: #1 tags after filtering in treatment: 2908391 INFO @ Fri, 04 Aug 2017 14:45:00: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 04 Aug 2017 14:45:00: #1 finished! INFO @ Fri, 04 Aug 2017 14:45:00: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:45:00: #2 number of paired peaks: 1185 INFO @ Fri, 04 Aug 2017 14:45:00: start model_add_line... INFO @ Fri, 04 Aug 2017 14:45:00: start X-correlation... INFO @ Fri, 04 Aug 2017 14:45:00: end of X-cor INFO @ Fri, 04 Aug 2017 14:45:00: #2 finished! INFO @ Fri, 04 Aug 2017 14:45:00: #2 predicted fragment length is 223 bps INFO @ Fri, 04 Aug 2017 14:45:00: #2 alternative fragment length(s) may be 223 bps INFO @ Fri, 04 Aug 2017 14:45:00: #2.2 Generate R script for model : SRX1958590.05_model.r WARNING @ Fri, 04 Aug 2017 14:45:00: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:45:00: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Fri, 04 Aug 2017 14:45:00: #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 14:45:00: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:45:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:45:02: #4 Write output xls file... SRX1958590.10_peaks.xls INFO @ Fri, 04 Aug 2017 14:45:02: #4 Write peak in narrowPeak format file... SRX1958590.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:45:02: #4 Write summits bed file... SRX1958590.10_summits.bed INFO @ Fri, 04 Aug 2017 14:45:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (880 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:45:10: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:45:15: #4 Write output xls file... SRX1958590.05_peaks.xls INFO @ Fri, 04 Aug 2017 14:45:16: #4 Write peak in narrowPeak format file... SRX1958590.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:45:16: #4 Write summits bed file... SRX1958590.05_summits.bed INFO @ Fri, 04 Aug 2017 14:45:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1492 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。