Job ID = 10202000 sra ファイルのダウンロード中... Completed: 1118875K bytes transferred in 82 seconds (110805K 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... Written 12809714 spots for /home/okishinya/chipatlas/results/dm3/SRX2965244/SRR5765702.sra Written 12809714 spots total 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: 00:44:58 12809714 reads; of these: 12809714 (100.00%) were paired; of these: 3971966 (31.01%) aligned concordantly 0 times 6603706 (51.55%) aligned concordantly exactly 1 time 2234042 (17.44%) aligned concordantly >1 times ---- 3971966 pairs aligned concordantly 0 times; of these: 1421590 (35.79%) aligned discordantly 1 time ---- 2550376 pairs aligned 0 times concordantly or discordantly; of these: 5100752 mates make up the pairs; of these: 4056407 (79.53%) aligned 0 times 219138 (4.30%) aligned exactly 1 time 825207 (16.18%) aligned >1 times 84.17% overall alignment rate Time searching: 00:44:58 Overall time: 00:44:58 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 16 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] 702509 / 10153094 = 0.0692 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 @ Mon, 13 Nov 2017 14:05:20: # Command line: callpeak -t SRX2965244.bam -f BAM -g dm -n SRX2965244.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2965244.20 # format = BAM # ChIP-seq file = ['SRX2965244.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 @ Mon, 13 Nov 2017 14:05:20: #1 read tag files... INFO @ Mon, 13 Nov 2017 14:05:20: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 14:05:20: # Command line: callpeak -t SRX2965244.bam -f BAM -g dm -n SRX2965244.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2965244.05 # format = BAM # ChIP-seq file = ['SRX2965244.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 @ Mon, 13 Nov 2017 14:05:20: #1 read tag files... INFO @ Mon, 13 Nov 2017 14:05:20: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 14:05:20: # Command line: callpeak -t SRX2965244.bam -f BAM -g dm -n SRX2965244.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2965244.10 # format = BAM # ChIP-seq file = ['SRX2965244.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 @ Mon, 13 Nov 2017 14:05:20: #1 read tag files... INFO @ Mon, 13 Nov 2017 14:05:20: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 14:05:29: 1000000 INFO @ Mon, 13 Nov 2017 14:05:29: 1000000 INFO @ Mon, 13 Nov 2017 14:05:29: 1000000 INFO @ Mon, 13 Nov 2017 14:05:38: 2000000 INFO @ Mon, 13 Nov 2017 14:05:38: 2000000 INFO @ Mon, 13 Nov 2017 14:05:39: 2000000 INFO @ Mon, 13 Nov 2017 14:05:48: 3000000 INFO @ Mon, 13 Nov 2017 14:05:48: 3000000 INFO @ Mon, 13 Nov 2017 14:05:49: 3000000 INFO @ Mon, 13 Nov 2017 14:05:57: 4000000 INFO @ Mon, 13 Nov 2017 14:05:57: 4000000 INFO @ Mon, 13 Nov 2017 14:05:59: 4000000 INFO @ Mon, 13 Nov 2017 14:06:06: 5000000 INFO @ Mon, 13 Nov 2017 14:06:06: 5000000 INFO @ Mon, 13 Nov 2017 14:06:08: 5000000 INFO @ Mon, 13 Nov 2017 14:06:15: 6000000 INFO @ Mon, 13 Nov 2017 14:06:15: 6000000 INFO @ Mon, 13 Nov 2017 14:06:18: 6000000 INFO @ Mon, 13 Nov 2017 14:06:24: 7000000 INFO @ Mon, 13 Nov 2017 14:06:24: 7000000 INFO @ Mon, 13 Nov 2017 14:06:28: 7000000 INFO @ Mon, 13 Nov 2017 14:06:33: 8000000 INFO @ Mon, 13 Nov 2017 14:06:33: 8000000 INFO @ Mon, 13 Nov 2017 14:06:38: 8000000 INFO @ Mon, 13 Nov 2017 14:06:43: 9000000 INFO @ Mon, 13 Nov 2017 14:06:43: 9000000 INFO @ Mon, 13 Nov 2017 14:06:47: 9000000 INFO @ Mon, 13 Nov 2017 14:06:52: 10000000 INFO @ Mon, 13 Nov 2017 14:06:52: 10000000 INFO @ Mon, 13 Nov 2017 14:06:57: 10000000 INFO @ Mon, 13 Nov 2017 14:07:01: 11000000 INFO @ Mon, 13 Nov 2017 14:07:01: 11000000 INFO @ Mon, 13 Nov 2017 14:07:07: 11000000 INFO @ Mon, 13 Nov 2017 14:07:10: 12000000 INFO @ Mon, 13 Nov 2017 14:07:10: 12000000 INFO @ Mon, 13 Nov 2017 14:07:16: 12000000 INFO @ Mon, 13 Nov 2017 14:07:19: 13000000 INFO @ Mon, 13 Nov 2017 14:07:19: 13000000 INFO @ Mon, 13 Nov 2017 14:07:26: 13000000 INFO @ Mon, 13 Nov 2017 14:07:28: 14000000 INFO @ Mon, 13 Nov 2017 14:07:28: 14000000 INFO @ Mon, 13 Nov 2017 14:07:35: 14000000 INFO @ Mon, 13 Nov 2017 14:07:37: 15000000 INFO @ Mon, 13 Nov 2017 14:07:37: 15000000 INFO @ Mon, 13 Nov 2017 14:07:45: 15000000 INFO @ Mon, 13 Nov 2017 14:07:46: 16000000 INFO @ Mon, 13 Nov 2017 14:07:46: 16000000 INFO @ Mon, 13 Nov 2017 14:07:54: 16000000 INFO @ Mon, 13 Nov 2017 14:07:55: 17000000 INFO @ Mon, 13 Nov 2017 14:07:55: 17000000 INFO @ Mon, 13 Nov 2017 14:08:04: 17000000 INFO @ Mon, 13 Nov 2017 14:08:05: 18000000 INFO @ Mon, 13 Nov 2017 14:08:05: 18000000 INFO @ Mon, 13 Nov 2017 14:08:13: 18000000 INFO @ Mon, 13 Nov 2017 14:08:14: 19000000 INFO @ Mon, 13 Nov 2017 14:08:14: 19000000 INFO @ Mon, 13 Nov 2017 14:08:23: 20000000 INFO @ Mon, 13 Nov 2017 14:08:24: 19000000 INFO @ Mon, 13 Nov 2017 14:08:24: 20000000 INFO @ Mon, 13 Nov 2017 14:08:24: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 14:08:24: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 14:08:24: #1 total tags in treatment: 8180453 INFO @ Mon, 13 Nov 2017 14:08:24: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 14:08:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 14:08:24: #1 tags after filtering in treatment: 7811079 INFO @ Mon, 13 Nov 2017 14:08:24: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 13 Nov 2017 14:08:24: #1 finished! INFO @ Mon, 13 Nov 2017 14:08:24: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 14:08:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 14:08:25: #2 number of paired peaks: 1172 INFO @ Mon, 13 Nov 2017 14:08:25: start model_add_line... INFO @ Mon, 13 Nov 2017 14:08:25: start X-correlation... INFO @ Mon, 13 Nov 2017 14:08:25: end of X-cor INFO @ Mon, 13 Nov 2017 14:08:25: #2 finished! INFO @ Mon, 13 Nov 2017 14:08:25: #2 predicted fragment length is 175 bps INFO @ Mon, 13 Nov 2017 14:08:25: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 13 Nov 2017 14:08:25: #2.2 Generate R script for model : SRX2965244.20_model.r WARNING @ Mon, 13 Nov 2017 14:08:25: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 14:08:25: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Mon, 13 Nov 2017 14:08:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 14:08:25: #3 Call peaks... INFO @ Mon, 13 Nov 2017 14:08:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 14:08:26: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 14:08:26: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 14:08:26: #1 total tags in treatment: 8180453 INFO @ Mon, 13 Nov 2017 14:08:26: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 14:08:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 14:08:26: #1 tags after filtering in treatment: 7811079 INFO @ Mon, 13 Nov 2017 14:08:26: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 13 Nov 2017 14:08:26: #1 finished! INFO @ Mon, 13 Nov 2017 14:08:26: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 14:08:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 14:08:27: #2 number of paired peaks: 1172 INFO @ Mon, 13 Nov 2017 14:08:27: start model_add_line... INFO @ Mon, 13 Nov 2017 14:08:27: start X-correlation... INFO @ Mon, 13 Nov 2017 14:08:27: end of X-cor INFO @ Mon, 13 Nov 2017 14:08:27: #2 finished! INFO @ Mon, 13 Nov 2017 14:08:27: #2 predicted fragment length is 175 bps INFO @ Mon, 13 Nov 2017 14:08:27: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 13 Nov 2017 14:08:27: #2.2 Generate R script for model : SRX2965244.05_model.r WARNING @ Mon, 13 Nov 2017 14:08:27: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 14:08:27: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Mon, 13 Nov 2017 14:08:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 14:08:27: #3 Call peaks... INFO @ Mon, 13 Nov 2017 14:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 14:08:33: 20000000 INFO @ Mon, 13 Nov 2017 14:08:35: #1 tag size is determined as 126 bps INFO @ Mon, 13 Nov 2017 14:08:35: #1 tag size = 126 INFO @ Mon, 13 Nov 2017 14:08:35: #1 total tags in treatment: 8180453 INFO @ Mon, 13 Nov 2017 14:08:35: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 14:08:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 14:08:35: #1 tags after filtering in treatment: 7811079 INFO @ Mon, 13 Nov 2017 14:08:35: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 13 Nov 2017 14:08:35: #1 finished! INFO @ Mon, 13 Nov 2017 14:08:35: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 14:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 14:08:36: #2 number of paired peaks: 1172 INFO @ Mon, 13 Nov 2017 14:08:36: start model_add_line... INFO @ Mon, 13 Nov 2017 14:08:36: start X-correlation... INFO @ Mon, 13 Nov 2017 14:08:36: end of X-cor INFO @ Mon, 13 Nov 2017 14:08:36: #2 finished! INFO @ Mon, 13 Nov 2017 14:08:36: #2 predicted fragment length is 175 bps INFO @ Mon, 13 Nov 2017 14:08:36: #2 alternative fragment length(s) may be 175 bps INFO @ Mon, 13 Nov 2017 14:08:36: #2.2 Generate R script for model : SRX2965244.10_model.r WARNING @ Mon, 13 Nov 2017 14:08:36: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 14:08:36: #2 You may need to consider one of the other alternative d(s): 175 WARNING @ Mon, 13 Nov 2017 14:08:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 14:08:36: #3 Call peaks... INFO @ Mon, 13 Nov 2017 14:08:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 14:08:45: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 14:08:48: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 14:08:55: #4 Write output xls file... SRX2965244.20_peaks.xls INFO @ Mon, 13 Nov 2017 14:08:55: #4 Write peak in narrowPeak format file... SRX2965244.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 14:08:55: #4 Write summits bed file... SRX2965244.20_summits.bed INFO @ Mon, 13 Nov 2017 14:08:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (933 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 14:08:56: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 14:08:59: #4 Write output xls file... SRX2965244.05_peaks.xls INFO @ Mon, 13 Nov 2017 14:08:59: #4 Write peak in narrowPeak format file... SRX2965244.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 14:08:59: #4 Write summits bed file... SRX2965244.05_summits.bed INFO @ Mon, 13 Nov 2017 14:08:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2603 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 14:09:06: #4 Write output xls file... SRX2965244.10_peaks.xls INFO @ Mon, 13 Nov 2017 14:09:06: #4 Write peak in narrowPeak format file... SRX2965244.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 14:09:06: #4 Write summits bed file... SRX2965244.10_summits.bed INFO @ Mon, 13 Nov 2017 14:09:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1634 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。