Job ID = 9371426 sra ファイルのダウンロード中... Completed: 1570112K bytes transferred in 22 seconds (563299K bits/sec), in 2 files, 3 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 3835702 spots for /home/okishinya/chipatlas/results/dm3/SRX1958585/SRR4011803.sra Written 3835702 spots total Written 6790978 spots for /home/okishinya/chipatlas/results/dm3/SRX1958585/SRR3928899.sra Written 6790978 spots total 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: 01:44:24 10626680 reads; of these: 10626680 (100.00%) were paired; of these: 2839581 (26.72%) aligned concordantly 0 times 5532673 (52.06%) aligned concordantly exactly 1 time 2254426 (21.21%) aligned concordantly >1 times ---- 2839581 pairs aligned concordantly 0 times; of these: 902129 (31.77%) aligned discordantly 1 time ---- 1937452 pairs aligned 0 times concordantly or discordantly; of these: 3874904 mates make up the pairs; of these: 3096197 (79.90%) aligned 0 times 135861 (3.51%) aligned exactly 1 time 642846 (16.59%) aligned >1 times 85.43% overall alignment rate Time searching: 01:44:24 Overall time: 01:44:24 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] 901082 / 8603366 = 0.1047 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 15:54:09: # Command line: callpeak -t SRX1958585.bam -f BAM -g dm -n SRX1958585.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1958585.10 # format = BAM # ChIP-seq file = ['SRX1958585.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 15:54:09: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:54:09: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:54:09: # Command line: callpeak -t SRX1958585.bam -f BAM -g dm -n SRX1958585.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1958585.05 # format = BAM # ChIP-seq file = ['SRX1958585.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 15:54:09: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:54:09: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:54:09: # Command line: callpeak -t SRX1958585.bam -f BAM -g dm -n SRX1958585.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1958585.20 # format = BAM # ChIP-seq file = ['SRX1958585.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 15:54:09: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:54:09: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:54:30: 1000000 INFO @ Fri, 04 Aug 2017 15:54:30: 1000000 INFO @ Fri, 04 Aug 2017 15:54:34: 1000000 INFO @ Fri, 04 Aug 2017 15:54:51: 2000000 INFO @ Fri, 04 Aug 2017 15:54:52: 2000000 INFO @ Fri, 04 Aug 2017 15:54:56: 2000000 INFO @ Fri, 04 Aug 2017 15:55:16: 3000000 INFO @ Fri, 04 Aug 2017 15:55:16: 3000000 INFO @ Fri, 04 Aug 2017 15:55:18: 3000000 INFO @ Fri, 04 Aug 2017 15:55:35: 4000000 INFO @ Fri, 04 Aug 2017 15:55:37: 4000000 INFO @ Fri, 04 Aug 2017 15:55:37: 4000000 INFO @ Fri, 04 Aug 2017 15:55:53: 5000000 INFO @ Fri, 04 Aug 2017 15:55:57: 5000000 INFO @ Fri, 04 Aug 2017 15:55:58: 5000000 INFO @ Fri, 04 Aug 2017 15:56:15: 6000000 INFO @ Fri, 04 Aug 2017 15:56:17: 6000000 INFO @ Fri, 04 Aug 2017 15:56:20: 6000000 INFO @ Fri, 04 Aug 2017 15:56:32: 7000000 INFO @ Fri, 04 Aug 2017 15:56:33: 7000000 INFO @ Fri, 04 Aug 2017 15:56:37: 7000000 INFO @ Fri, 04 Aug 2017 15:56:50: 8000000 INFO @ Fri, 04 Aug 2017 15:56:50: 8000000 INFO @ Fri, 04 Aug 2017 15:56:54: 8000000 INFO @ Fri, 04 Aug 2017 15:57:02: 9000000 INFO @ Fri, 04 Aug 2017 15:57:06: 9000000 INFO @ Fri, 04 Aug 2017 15:57:13: 9000000 INFO @ Fri, 04 Aug 2017 15:57:19: 10000000 INFO @ Fri, 04 Aug 2017 15:57:22: 10000000 INFO @ Fri, 04 Aug 2017 15:57:27: 10000000 INFO @ Fri, 04 Aug 2017 15:57:38: 11000000 INFO @ Fri, 04 Aug 2017 15:57:40: 11000000 INFO @ Fri, 04 Aug 2017 15:57:47: 11000000 INFO @ Fri, 04 Aug 2017 15:57:54: 12000000 INFO @ Fri, 04 Aug 2017 15:57:58: 12000000 INFO @ Fri, 04 Aug 2017 15:57:59: 12000000 INFO @ Fri, 04 Aug 2017 15:58:08: 13000000 INFO @ Fri, 04 Aug 2017 15:58:16: 13000000 INFO @ Fri, 04 Aug 2017 15:58:20: 13000000 INFO @ Fri, 04 Aug 2017 15:58:24: 14000000 INFO @ Fri, 04 Aug 2017 15:58:35: 14000000 INFO @ Fri, 04 Aug 2017 15:58:42: 15000000 INFO @ Fri, 04 Aug 2017 15:58:44: 14000000 INFO @ Fri, 04 Aug 2017 15:58:54: 15000000 INFO @ Fri, 04 Aug 2017 15:59:01: 16000000 INFO @ Fri, 04 Aug 2017 15:59:06: 15000000 INFO @ Fri, 04 Aug 2017 15:59:08: #1 tag size is determined as 151 bps INFO @ Fri, 04 Aug 2017 15:59:08: #1 tag size = 151 INFO @ Fri, 04 Aug 2017 15:59:08: #1 total tags in treatment: 6960551 INFO @ Fri, 04 Aug 2017 15:59:08: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:59:08: #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 15:59:09: #1 tags after filtering in treatment: 6554151 INFO @ Fri, 04 Aug 2017 15:59:09: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 04 Aug 2017 15:59:09: #1 finished! INFO @ Fri, 04 Aug 2017 15:59:09: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:59:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:59:10: #2 number of paired peaks: 1147 INFO @ Fri, 04 Aug 2017 15:59:10: start model_add_line... INFO @ Fri, 04 Aug 2017 15:59:10: start X-correlation... INFO @ Fri, 04 Aug 2017 15:59:10: end of X-cor INFO @ Fri, 04 Aug 2017 15:59:10: #2 finished! INFO @ Fri, 04 Aug 2017 15:59:10: #2 predicted fragment length is 188 bps INFO @ Fri, 04 Aug 2017 15:59:10: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 04 Aug 2017 15:59:10: #2.2 Generate R script for model : SRX1958585.05_model.r WARNING @ Fri, 04 Aug 2017 15:59:10: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:59:10: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Fri, 04 Aug 2017 15:59:10: #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 15:59:10: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:59:15: 16000000 INFO @ Fri, 04 Aug 2017 15:59:20: 16000000 INFO @ Fri, 04 Aug 2017 15:59:22: #1 tag size is determined as 151 bps INFO @ Fri, 04 Aug 2017 15:59:22: #1 tag size = 151 INFO @ Fri, 04 Aug 2017 15:59:22: #1 total tags in treatment: 6960551 INFO @ Fri, 04 Aug 2017 15:59:22: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:59:22: #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 15:59:23: #1 tags after filtering in treatment: 6554151 INFO @ Fri, 04 Aug 2017 15:59:23: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 04 Aug 2017 15:59:23: #1 finished! INFO @ Fri, 04 Aug 2017 15:59:23: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:59:23: #2 number of paired peaks: 1147 INFO @ Fri, 04 Aug 2017 15:59:23: start model_add_line... INFO @ Fri, 04 Aug 2017 15:59:24: start X-correlation... INFO @ Fri, 04 Aug 2017 15:59:24: end of X-cor INFO @ Fri, 04 Aug 2017 15:59:24: #2 finished! INFO @ Fri, 04 Aug 2017 15:59:24: #2 predicted fragment length is 188 bps INFO @ Fri, 04 Aug 2017 15:59:24: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 04 Aug 2017 15:59:24: #2.2 Generate R script for model : SRX1958585.10_model.r WARNING @ Fri, 04 Aug 2017 15:59:24: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:59:24: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Fri, 04 Aug 2017 15:59:24: #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 15:59:24: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:59:24: #1 tag size is determined as 151 bps INFO @ Fri, 04 Aug 2017 15:59:24: #1 tag size = 151 INFO @ Fri, 04 Aug 2017 15:59:24: #1 total tags in treatment: 6960551 INFO @ Fri, 04 Aug 2017 15:59:24: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:59:24: #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 15:59:25: #1 tags after filtering in treatment: 6554151 INFO @ Fri, 04 Aug 2017 15:59:25: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 04 Aug 2017 15:59:25: #1 finished! INFO @ Fri, 04 Aug 2017 15:59:25: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:59:25: #2 number of paired peaks: 1147 INFO @ Fri, 04 Aug 2017 15:59:25: start model_add_line... INFO @ Fri, 04 Aug 2017 15:59:26: start X-correlation... INFO @ Fri, 04 Aug 2017 15:59:26: end of X-cor INFO @ Fri, 04 Aug 2017 15:59:26: #2 finished! INFO @ Fri, 04 Aug 2017 15:59:26: #2 predicted fragment length is 188 bps INFO @ Fri, 04 Aug 2017 15:59:26: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 04 Aug 2017 15:59:26: #2.2 Generate R script for model : SRX1958585.20_model.r WARNING @ Fri, 04 Aug 2017 15:59:26: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:59:26: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Fri, 04 Aug 2017 15:59:26: #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 15:59:26: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:59:33: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:59:47: #4 Write output xls file... SRX1958585.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:59:47: #4 Write peak in narrowPeak format file... SRX1958585.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:59:47: #4 Write summits bed file... SRX1958585.05_summits.bed INFO @ Fri, 04 Aug 2017 15:59:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2352 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:59:48: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:59:50: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 16:00:02: #4 Write output xls file... SRX1958585.20_peaks.xls INFO @ Fri, 04 Aug 2017 16:00:02: #4 Write peak in narrowPeak format file... SRX1958585.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 16:00:02: #4 Write summits bed file... SRX1958585.20_summits.bed INFO @ Fri, 04 Aug 2017 16:00:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (823 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 16:00:03: #4 Write output xls file... SRX1958585.10_peaks.xls INFO @ Fri, 04 Aug 2017 16:00:03: #4 Write peak in narrowPeak format file... SRX1958585.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 16:00:03: #4 Write summits bed file... SRX1958585.10_summits.bed INFO @ Fri, 04 Aug 2017 16:00:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (1458 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。