Job ID = 9371939 sra ファイルのダウンロード中... Completed: 1165220K bytes transferred in 30 seconds (314589K 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 13485692 spots for /home/okishinya/chipatlas/results/dm3/SRX2548350/SRR5241495.sra Written 13485692 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: 01:36:15 13485692 reads; of these: 13485692 (100.00%) were paired; of these: 4371500 (32.42%) aligned concordantly 0 times 6780505 (50.28%) aligned concordantly exactly 1 time 2333687 (17.30%) aligned concordantly >1 times ---- 4371500 pairs aligned concordantly 0 times; of these: 1254605 (28.70%) aligned discordantly 1 time ---- 3116895 pairs aligned 0 times concordantly or discordantly; of these: 6233790 mates make up the pairs; of these: 5179639 (83.09%) aligned 0 times 409012 (6.56%) aligned exactly 1 time 645139 (10.35%) aligned >1 times 80.80% overall alignment rate Time searching: 01:36:15 Overall time: 01:36:15 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 12 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] 234803 / 10273147 = 0.0229 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 16:47:57: # Command line: callpeak -t SRX2548350.bam -f BAM -g dm -n SRX2548350.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2548350.20 # format = BAM # ChIP-seq file = ['SRX2548350.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 16:47:57: # Command line: callpeak -t SRX2548350.bam -f BAM -g dm -n SRX2548350.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2548350.10 # format = BAM # ChIP-seq file = ['SRX2548350.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 16:47:57: #1 read tag files... INFO @ Fri, 04 Aug 2017 16:47:57: #1 read tag files... INFO @ Fri, 04 Aug 2017 16:47:57: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 16:47:57: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 16:47:57: # Command line: callpeak -t SRX2548350.bam -f BAM -g dm -n SRX2548350.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2548350.05 # format = BAM # ChIP-seq file = ['SRX2548350.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 16:47:57: #1 read tag files... INFO @ Fri, 04 Aug 2017 16:47:57: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 16:48:25: 1000000 INFO @ Fri, 04 Aug 2017 16:48:26: 1000000 INFO @ Fri, 04 Aug 2017 16:48:31: 1000000 INFO @ Fri, 04 Aug 2017 16:48:55: 2000000 INFO @ Fri, 04 Aug 2017 16:48:56: 2000000 INFO @ Fri, 04 Aug 2017 16:49:06: 2000000 INFO @ Fri, 04 Aug 2017 16:49:24: 3000000 INFO @ Fri, 04 Aug 2017 16:49:26: 3000000 INFO @ Fri, 04 Aug 2017 16:49:38: 3000000 INFO @ Fri, 04 Aug 2017 16:49:57: 4000000 INFO @ Fri, 04 Aug 2017 16:49:59: 4000000 INFO @ Fri, 04 Aug 2017 16:50:13: 4000000 INFO @ Fri, 04 Aug 2017 16:50:28: 5000000 INFO @ Fri, 04 Aug 2017 16:50:31: 5000000 INFO @ Fri, 04 Aug 2017 16:50:44: 5000000 INFO @ Fri, 04 Aug 2017 16:51:02: 6000000 INFO @ Fri, 04 Aug 2017 16:51:03: 6000000 INFO @ Fri, 04 Aug 2017 16:51:10: 6000000 INFO @ Fri, 04 Aug 2017 16:51:33: 7000000 INFO @ Fri, 04 Aug 2017 16:51:36: 7000000 INFO @ Fri, 04 Aug 2017 16:51:38: 7000000 INFO @ Fri, 04 Aug 2017 16:52:05: 8000000 INFO @ Fri, 04 Aug 2017 16:52:06: 8000000 INFO @ Fri, 04 Aug 2017 16:52:10: 8000000 INFO @ Fri, 04 Aug 2017 16:52:30: 9000000 INFO @ Fri, 04 Aug 2017 16:52:31: 9000000 INFO @ Fri, 04 Aug 2017 16:52:37: 9000000 INFO @ Fri, 04 Aug 2017 16:52:56: 10000000 INFO @ Fri, 04 Aug 2017 16:53:01: 10000000 INFO @ Fri, 04 Aug 2017 16:53:06: 10000000 INFO @ Fri, 04 Aug 2017 16:53:28: 11000000 INFO @ Fri, 04 Aug 2017 16:53:35: 11000000 INFO @ Fri, 04 Aug 2017 16:53:40: 11000000 INFO @ Fri, 04 Aug 2017 16:53:50: 12000000 INFO @ Fri, 04 Aug 2017 16:54:08: 12000000 INFO @ Fri, 04 Aug 2017 16:54:12: 13000000 INFO @ Fri, 04 Aug 2017 16:54:15: 12000000 INFO @ Fri, 04 Aug 2017 16:54:36: 14000000 INFO @ Fri, 04 Aug 2017 16:54:42: 13000000 INFO @ Fri, 04 Aug 2017 16:54:51: 13000000 INFO @ Fri, 04 Aug 2017 16:55:03: 15000000 INFO @ Fri, 04 Aug 2017 16:55:16: 14000000 INFO @ Fri, 04 Aug 2017 16:55:28: 14000000 INFO @ Fri, 04 Aug 2017 16:55:34: 16000000 INFO @ Fri, 04 Aug 2017 16:55:51: 15000000 INFO @ Fri, 04 Aug 2017 16:55:54: 15000000 INFO @ Fri, 04 Aug 2017 16:56:05: 17000000 INFO @ Fri, 04 Aug 2017 16:56:16: 16000000 INFO @ Fri, 04 Aug 2017 16:56:28: 16000000 INFO @ Fri, 04 Aug 2017 16:56:38: 18000000 INFO @ Fri, 04 Aug 2017 16:56:44: 17000000 INFO @ Fri, 04 Aug 2017 16:57:00: 17000000 INFO @ Fri, 04 Aug 2017 16:57:09: 19000000 INFO @ Fri, 04 Aug 2017 16:57:16: 18000000 INFO @ Fri, 04 Aug 2017 16:57:32: 18000000 INFO @ Fri, 04 Aug 2017 16:57:39: 19000000 INFO @ Fri, 04 Aug 2017 16:57:40: 20000000 INFO @ Fri, 04 Aug 2017 16:58:04: 19000000 INFO @ Fri, 04 Aug 2017 16:58:06: 20000000 INFO @ Fri, 04 Aug 2017 16:58:12: 21000000 INFO @ Fri, 04 Aug 2017 16:58:22: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 16:58:22: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 16:58:22: #1 total tags in treatment: 8884149 INFO @ Fri, 04 Aug 2017 16:58:22: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 16:58:22: #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 16:58:22: #1 tags after filtering in treatment: 8502740 INFO @ Fri, 04 Aug 2017 16:58:22: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 04 Aug 2017 16:58:22: #1 finished! INFO @ Fri, 04 Aug 2017 16:58:22: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 16:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 16:58:23: #2 number of paired peaks: 325 WARNING @ Fri, 04 Aug 2017 16:58:23: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 04 Aug 2017 16:58:23: start model_add_line... INFO @ Fri, 04 Aug 2017 16:58:23: start X-correlation... INFO @ Fri, 04 Aug 2017 16:58:23: end of X-cor INFO @ Fri, 04 Aug 2017 16:58:23: #2 finished! INFO @ Fri, 04 Aug 2017 16:58:23: #2 predicted fragment length is 172 bps INFO @ Fri, 04 Aug 2017 16:58:23: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 04 Aug 2017 16:58:23: #2.2 Generate R script for model : SRX2548350.10_model.r WARNING @ Fri, 04 Aug 2017 16:58:23: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 16:58:23: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 04 Aug 2017 16:58:23: #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 16:58:23: #3 Call peaks... INFO @ Fri, 04 Aug 2017 16:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 16:58:33: 20000000 INFO @ Fri, 04 Aug 2017 16:58:37: 21000000 INFO @ Fri, 04 Aug 2017 16:58:46: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 16:58:46: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 16:58:46: #1 total tags in treatment: 8884149 INFO @ Fri, 04 Aug 2017 16:58:46: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 16:58:46: #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 16:58:47: #1 tags after filtering in treatment: 8502740 INFO @ Fri, 04 Aug 2017 16:58:47: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 04 Aug 2017 16:58:47: #1 finished! INFO @ Fri, 04 Aug 2017 16:58:47: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 16:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 16:58:48: #2 number of paired peaks: 325 WARNING @ Fri, 04 Aug 2017 16:58:48: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 04 Aug 2017 16:58:48: start model_add_line... INFO @ Fri, 04 Aug 2017 16:58:48: start X-correlation... INFO @ Fri, 04 Aug 2017 16:58:48: end of X-cor INFO @ Fri, 04 Aug 2017 16:58:48: #2 finished! INFO @ Fri, 04 Aug 2017 16:58:48: #2 predicted fragment length is 172 bps INFO @ Fri, 04 Aug 2017 16:58:48: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 04 Aug 2017 16:58:48: #2.2 Generate R script for model : SRX2548350.05_model.r WARNING @ Fri, 04 Aug 2017 16:58:48: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 16:58:48: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 04 Aug 2017 16:58:48: #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 16:58:48: #3 Call peaks... INFO @ Fri, 04 Aug 2017 16:58:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 16:58:55: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 16:59:05: 21000000 INFO @ Fri, 04 Aug 2017 16:59:11: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 16:59:11: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 16:59:11: #1 total tags in treatment: 8884149 INFO @ Fri, 04 Aug 2017 16:59:11: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 16:59:11: #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 16:59:11: #1 tags after filtering in treatment: 8502740 INFO @ Fri, 04 Aug 2017 16:59:11: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 04 Aug 2017 16:59:11: #1 finished! INFO @ Fri, 04 Aug 2017 16:59:11: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 16:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 16:59:12: #2 number of paired peaks: 325 WARNING @ Fri, 04 Aug 2017 16:59:12: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 04 Aug 2017 16:59:12: start model_add_line... INFO @ Fri, 04 Aug 2017 16:59:12: start X-correlation... INFO @ Fri, 04 Aug 2017 16:59:12: end of X-cor INFO @ Fri, 04 Aug 2017 16:59:12: #2 finished! INFO @ Fri, 04 Aug 2017 16:59:12: #2 predicted fragment length is 172 bps INFO @ Fri, 04 Aug 2017 16:59:12: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 04 Aug 2017 16:59:12: #2.2 Generate R script for model : SRX2548350.20_model.r WARNING @ Fri, 04 Aug 2017 16:59:12: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 16:59:12: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Fri, 04 Aug 2017 16:59:12: #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 16:59:12: #3 Call peaks... INFO @ Fri, 04 Aug 2017 16:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 16:59:13: #4 Write output xls file... SRX2548350.10_peaks.xls INFO @ Fri, 04 Aug 2017 16:59:13: #4 Write peak in narrowPeak format file... SRX2548350.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 16:59:13: #4 Write summits bed file... SRX2548350.10_summits.bed INFO @ Fri, 04 Aug 2017 16:59:13: Done! pass1 - making usageList (13 chroms): 10 millis pass2 - checking and writing primary data (1179 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 16:59:16: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 16:59:35: #4 Write output xls file... SRX2548350.05_peaks.xls INFO @ Fri, 04 Aug 2017 16:59:35: #4 Write peak in narrowPeak format file... SRX2548350.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 16:59:35: #4 Write summits bed file... SRX2548350.05_summits.bed INFO @ Fri, 04 Aug 2017 16:59:35: Done! pass1 - making usageList (14 chroms): 10 millis pass2 - checking and writing primary data (1786 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 16:59:44: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 17:00:01: #4 Write output xls file... SRX2548350.20_peaks.xls INFO @ Fri, 04 Aug 2017 17:00:01: #4 Write peak in narrowPeak format file... SRX2548350.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 17:00:01: #4 Write summits bed file... SRX2548350.20_summits.bed INFO @ Fri, 04 Aug 2017 17:00:01: Done! pass1 - making usageList (11 chroms): 4 millis pass2 - checking and writing primary data (666 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。