Job ID = 11171253 sra ファイルのダウンロード中... Completed: 1440867K bytes transferred in 77 seconds (152055K 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 27794263 spots for /home/okishinya/chipatlas/results/dm3/SRX2659844/SRR5364417.sra Written 27794263 spots for /home/okishinya/chipatlas/results/dm3/SRX2659844/SRR5364417.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: 00:54:00 27794263 reads; of these: 27794263 (100.00%) were paired; of these: 11282678 (40.59%) aligned concordantly 0 times 13947467 (50.18%) aligned concordantly exactly 1 time 2564118 (9.23%) aligned concordantly >1 times ---- 11282678 pairs aligned concordantly 0 times; of these: 1074655 (9.52%) aligned discordantly 1 time ---- 10208023 pairs aligned 0 times concordantly or discordantly; of these: 20416046 mates make up the pairs; of these: 18485152 (90.54%) aligned 0 times 1153167 (5.65%) aligned exactly 1 time 777727 (3.81%) aligned >1 times 66.75% overall alignment rate Time searching: 00:54:00 Overall time: 00:54:00 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] 885387 / 17310743 = 0.0511 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 @ Sat, 08 Sep 2018 14:26:21: # Command line: callpeak -t SRX2659844.bam -f BAM -g dm -n SRX2659844.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2659844.10 # format = BAM # ChIP-seq file = ['SRX2659844.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 @ Sat, 08 Sep 2018 14:26:21: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:26:21: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:26:21: # Command line: callpeak -t SRX2659844.bam -f BAM -g dm -n SRX2659844.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2659844.05 # format = BAM # ChIP-seq file = ['SRX2659844.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 @ Sat, 08 Sep 2018 14:26:21: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:26:21: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:26:21: # Command line: callpeak -t SRX2659844.bam -f BAM -g dm -n SRX2659844.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2659844.20 # format = BAM # ChIP-seq file = ['SRX2659844.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 @ Sat, 08 Sep 2018 14:26:21: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:26:21: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:26:29: 1000000 INFO @ Sat, 08 Sep 2018 14:26:29: 1000000 INFO @ Sat, 08 Sep 2018 14:26:29: 1000000 INFO @ Sat, 08 Sep 2018 14:26:38: 2000000 INFO @ Sat, 08 Sep 2018 14:26:38: 2000000 INFO @ Sat, 08 Sep 2018 14:26:38: 2000000 INFO @ Sat, 08 Sep 2018 14:26:47: 3000000 INFO @ Sat, 08 Sep 2018 14:26:47: 3000000 INFO @ Sat, 08 Sep 2018 14:26:47: 3000000 INFO @ Sat, 08 Sep 2018 14:26:56: 4000000 INFO @ Sat, 08 Sep 2018 14:26:56: 4000000 INFO @ Sat, 08 Sep 2018 14:26:56: 4000000 INFO @ Sat, 08 Sep 2018 14:27:05: 5000000 INFO @ Sat, 08 Sep 2018 14:27:06: 5000000 INFO @ Sat, 08 Sep 2018 14:27:06: 5000000 INFO @ Sat, 08 Sep 2018 14:27:15: 6000000 INFO @ Sat, 08 Sep 2018 14:27:15: 6000000 INFO @ Sat, 08 Sep 2018 14:27:15: 6000000 INFO @ Sat, 08 Sep 2018 14:27:24: 7000000 INFO @ Sat, 08 Sep 2018 14:27:24: 7000000 INFO @ Sat, 08 Sep 2018 14:27:24: 7000000 INFO @ Sat, 08 Sep 2018 14:27:33: 8000000 INFO @ Sat, 08 Sep 2018 14:27:33: 8000000 INFO @ Sat, 08 Sep 2018 14:27:33: 8000000 INFO @ Sat, 08 Sep 2018 14:27:42: 9000000 INFO @ Sat, 08 Sep 2018 14:27:42: 9000000 INFO @ Sat, 08 Sep 2018 14:27:42: 9000000 INFO @ Sat, 08 Sep 2018 14:27:51: 10000000 INFO @ Sat, 08 Sep 2018 14:27:51: 10000000 INFO @ Sat, 08 Sep 2018 14:27:51: 10000000 INFO @ Sat, 08 Sep 2018 14:28:00: 11000000 INFO @ Sat, 08 Sep 2018 14:28:00: 11000000 INFO @ Sat, 08 Sep 2018 14:28:00: 11000000 INFO @ Sat, 08 Sep 2018 14:28:09: 12000000 INFO @ Sat, 08 Sep 2018 14:28:09: 12000000 INFO @ Sat, 08 Sep 2018 14:28:09: 12000000 INFO @ Sat, 08 Sep 2018 14:28:18: 13000000 INFO @ Sat, 08 Sep 2018 14:28:18: 13000000 INFO @ Sat, 08 Sep 2018 14:28:18: 13000000 INFO @ Sat, 08 Sep 2018 14:28:27: 14000000 INFO @ Sat, 08 Sep 2018 14:28:27: 14000000 INFO @ Sat, 08 Sep 2018 14:28:27: 14000000 INFO @ Sat, 08 Sep 2018 14:28:36: 15000000 INFO @ Sat, 08 Sep 2018 14:28:36: 15000000 INFO @ Sat, 08 Sep 2018 14:28:36: 15000000 INFO @ Sat, 08 Sep 2018 14:28:45: 16000000 INFO @ Sat, 08 Sep 2018 14:28:45: 16000000 INFO @ Sat, 08 Sep 2018 14:28:45: 16000000 INFO @ Sat, 08 Sep 2018 14:28:54: 17000000 INFO @ Sat, 08 Sep 2018 14:28:54: 17000000 INFO @ Sat, 08 Sep 2018 14:28:54: 17000000 INFO @ Sat, 08 Sep 2018 14:29:03: 18000000 INFO @ Sat, 08 Sep 2018 14:29:03: 18000000 INFO @ Sat, 08 Sep 2018 14:29:03: 18000000 INFO @ Sat, 08 Sep 2018 14:29:12: 19000000 INFO @ Sat, 08 Sep 2018 14:29:12: 19000000 INFO @ Sat, 08 Sep 2018 14:29:12: 19000000 INFO @ Sat, 08 Sep 2018 14:29:21: 20000000 INFO @ Sat, 08 Sep 2018 14:29:21: 20000000 INFO @ Sat, 08 Sep 2018 14:29:21: 20000000 INFO @ Sat, 08 Sep 2018 14:29:31: 21000000 INFO @ Sat, 08 Sep 2018 14:29:31: 21000000 INFO @ Sat, 08 Sep 2018 14:29:31: 21000000 INFO @ Sat, 08 Sep 2018 14:29:40: 22000000 INFO @ Sat, 08 Sep 2018 14:29:40: 22000000 INFO @ Sat, 08 Sep 2018 14:29:40: 22000000 INFO @ Sat, 08 Sep 2018 14:29:49: 23000000 INFO @ Sat, 08 Sep 2018 14:29:49: 23000000 INFO @ Sat, 08 Sep 2018 14:29:49: 23000000 INFO @ Sat, 08 Sep 2018 14:29:58: 24000000 INFO @ Sat, 08 Sep 2018 14:29:58: 24000000 INFO @ Sat, 08 Sep 2018 14:29:58: 24000000 INFO @ Sat, 08 Sep 2018 14:30:07: 25000000 INFO @ Sat, 08 Sep 2018 14:30:07: 25000000 INFO @ Sat, 08 Sep 2018 14:30:07: 25000000 INFO @ Sat, 08 Sep 2018 14:30:16: 26000000 INFO @ Sat, 08 Sep 2018 14:30:16: 26000000 INFO @ Sat, 08 Sep 2018 14:30:16: 26000000 INFO @ Sat, 08 Sep 2018 14:30:25: 27000000 INFO @ Sat, 08 Sep 2018 14:30:25: 27000000 INFO @ Sat, 08 Sep 2018 14:30:25: 27000000 INFO @ Sat, 08 Sep 2018 14:30:34: 28000000 INFO @ Sat, 08 Sep 2018 14:30:34: 28000000 INFO @ Sat, 08 Sep 2018 14:30:34: 28000000 INFO @ Sat, 08 Sep 2018 14:30:43: 29000000 INFO @ Sat, 08 Sep 2018 14:30:43: 29000000 INFO @ Sat, 08 Sep 2018 14:30:43: 29000000 INFO @ Sat, 08 Sep 2018 14:30:52: 30000000 INFO @ Sat, 08 Sep 2018 14:30:52: 30000000 INFO @ Sat, 08 Sep 2018 14:30:52: 30000000 INFO @ Sat, 08 Sep 2018 14:31:01: 31000000 INFO @ Sat, 08 Sep 2018 14:31:01: 31000000 INFO @ Sat, 08 Sep 2018 14:31:01: 31000000 INFO @ Sat, 08 Sep 2018 14:31:10: 32000000 INFO @ Sat, 08 Sep 2018 14:31:10: 32000000 INFO @ Sat, 08 Sep 2018 14:31:10: 32000000 INFO @ Sat, 08 Sep 2018 14:31:19: 33000000 INFO @ Sat, 08 Sep 2018 14:31:19: 33000000 INFO @ Sat, 08 Sep 2018 14:31:19: 33000000 INFO @ Sat, 08 Sep 2018 14:31:28: 34000000 INFO @ Sat, 08 Sep 2018 14:31:28: 34000000 INFO @ Sat, 08 Sep 2018 14:31:28: 34000000 INFO @ Sat, 08 Sep 2018 14:31:37: 35000000 INFO @ Sat, 08 Sep 2018 14:31:37: 35000000 INFO @ Sat, 08 Sep 2018 14:31:37: 35000000 INFO @ Sat, 08 Sep 2018 14:31:40: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 14:31:40: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 14:31:40: #1 total tags in treatment: 15685515 INFO @ Sat, 08 Sep 2018 14:31:40: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:31:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:31:40: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 14:31:40: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 14:31:40: #1 total tags in treatment: 15685515 INFO @ Sat, 08 Sep 2018 14:31:40: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:31:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:31:40: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 14:31:40: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 14:31:40: #1 total tags in treatment: 15685515 INFO @ Sat, 08 Sep 2018 14:31:40: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:31:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 14:31:40: #1 tags after filtering in treatment: 13649031 INFO @ Sat, 08 Sep 2018 14:31:40: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 08 Sep 2018 14:31:40: #1 finished! INFO @ Sat, 08 Sep 2018 14:31:40: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:31:40: #1 tags after filtering in treatment: 13649031 INFO @ Sat, 08 Sep 2018 14:31:40: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 08 Sep 2018 14:31:40: #1 finished! INFO @ Sat, 08 Sep 2018 14:31:40: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:31:40: #1 tags after filtering in treatment: 13649031 INFO @ Sat, 08 Sep 2018 14:31:40: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 08 Sep 2018 14:31:40: #1 finished! INFO @ Sat, 08 Sep 2018 14:31:40: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:31:41: #2 number of paired peaks: 1928 INFO @ Sat, 08 Sep 2018 14:31:41: start model_add_line... INFO @ Sat, 08 Sep 2018 14:31:41: #2 number of paired peaks: 1928 INFO @ Sat, 08 Sep 2018 14:31:41: start model_add_line... INFO @ Sat, 08 Sep 2018 14:31:41: #2 number of paired peaks: 1928 INFO @ Sat, 08 Sep 2018 14:31:41: start model_add_line... INFO @ Sat, 08 Sep 2018 14:31:42: start X-correlation... INFO @ Sat, 08 Sep 2018 14:31:42: end of X-cor INFO @ Sat, 08 Sep 2018 14:31:42: #2 finished! INFO @ Sat, 08 Sep 2018 14:31:42: #2 predicted fragment length is 75 bps INFO @ Sat, 08 Sep 2018 14:31:42: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 08 Sep 2018 14:31:42: #2.2 Generate R script for model : SRX2659844.05_model.r INFO @ Sat, 08 Sep 2018 14:31:42: start X-correlation... INFO @ Sat, 08 Sep 2018 14:31:42: end of X-cor INFO @ Sat, 08 Sep 2018 14:31:42: #2 finished! INFO @ Sat, 08 Sep 2018 14:31:42: #2 predicted fragment length is 75 bps INFO @ Sat, 08 Sep 2018 14:31:42: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 08 Sep 2018 14:31:42: #2.2 Generate R script for model : SRX2659844.10_model.r WARNING @ Sat, 08 Sep 2018 14:31:42: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:31:42: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 08 Sep 2018 14:31:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:31:42: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:31:42: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 08 Sep 2018 14:31:42: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:31:42: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 08 Sep 2018 14:31:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:31:42: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:31:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:31:42: start X-correlation... INFO @ Sat, 08 Sep 2018 14:31:42: end of X-cor INFO @ Sat, 08 Sep 2018 14:31:42: #2 finished! INFO @ Sat, 08 Sep 2018 14:31:42: #2 predicted fragment length is 75 bps INFO @ Sat, 08 Sep 2018 14:31:42: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 08 Sep 2018 14:31:42: #2.2 Generate R script for model : SRX2659844.20_model.r WARNING @ Sat, 08 Sep 2018 14:31:42: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:31:42: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 08 Sep 2018 14:31:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 14:31:42: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:31:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:32:12: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:32:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:32:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:32:32: #4 Write output xls file... SRX2659844.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:32:32: #4 Write output xls file... SRX2659844.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:32:32: #4 Write peak in narrowPeak format file... SRX2659844.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:32:32: #4 Write peak in narrowPeak format file... SRX2659844.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:32:32: #4 Write summits bed file... SRX2659844.20_summits.bed INFO @ Sat, 08 Sep 2018 14:32:32: Done! INFO @ Sat, 08 Sep 2018 14:32:32: #4 Write summits bed file... SRX2659844.05_summits.bed INFO @ Sat, 08 Sep 2018 14:32:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5005 records, 4 fields): 8 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 7 millis pass2 - checking and writing primary data (14808 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:32:34: #4 Write output xls file... SRX2659844.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:32:34: #4 Write peak in narrowPeak format file... SRX2659844.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:32:34: #4 Write summits bed file... SRX2659844.10_summits.bed INFO @ Sat, 08 Sep 2018 14:32:35: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9859 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。