Job ID = 10924607 sra ファイルのダウンロード中... Completed: 504119K bytes transferred in 11 seconds (361214K 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 8561113 spots for /home/okishinya/chipatlas/results/dm3/SRX2396694/SRR5078064.sra Written 8561113 spots for /home/okishinya/chipatlas/results/dm3/SRX2396694/SRR5078064.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: 00:11:26 8561113 reads; of these: 8561113 (100.00%) were paired; of these: 2167182 (25.31%) aligned concordantly 0 times 5764749 (67.34%) aligned concordantly exactly 1 time 629182 (7.35%) aligned concordantly >1 times ---- 2167182 pairs aligned concordantly 0 times; of these: 142036 (6.55%) aligned discordantly 1 time ---- 2025146 pairs aligned 0 times concordantly or discordantly; of these: 4050292 mates make up the pairs; of these: 3738311 (92.30%) aligned 0 times 233030 (5.75%) aligned exactly 1 time 78951 (1.95%) aligned >1 times 78.17% overall alignment rate Time searching: 00:11:26 Overall time: 00:11:26 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] 2437144 / 6533044 = 0.3730 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, 06 Aug 2018 10:41:06: # Command line: callpeak -t SRX2396694.bam -f BAM -g dm -n SRX2396694.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2396694.10 # format = BAM # ChIP-seq file = ['SRX2396694.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, 06 Aug 2018 10:41:06: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:41:06: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:41:06: # Command line: callpeak -t SRX2396694.bam -f BAM -g dm -n SRX2396694.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2396694.20 # format = BAM # ChIP-seq file = ['SRX2396694.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, 06 Aug 2018 10:41:06: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:41:06: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:41:06: # Command line: callpeak -t SRX2396694.bam -f BAM -g dm -n SRX2396694.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2396694.05 # format = BAM # ChIP-seq file = ['SRX2396694.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, 06 Aug 2018 10:41:06: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:41:06: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:41:13: 1000000 INFO @ Mon, 06 Aug 2018 10:41:13: 1000000 INFO @ Mon, 06 Aug 2018 10:41:13: 1000000 INFO @ Mon, 06 Aug 2018 10:41:19: 2000000 INFO @ Mon, 06 Aug 2018 10:41:19: 2000000 INFO @ Mon, 06 Aug 2018 10:41:19: 2000000 INFO @ Mon, 06 Aug 2018 10:41:25: 3000000 INFO @ Mon, 06 Aug 2018 10:41:26: 3000000 INFO @ Mon, 06 Aug 2018 10:41:26: 3000000 INFO @ Mon, 06 Aug 2018 10:41:31: 4000000 INFO @ Mon, 06 Aug 2018 10:41:32: 4000000 INFO @ Mon, 06 Aug 2018 10:41:32: 4000000 INFO @ Mon, 06 Aug 2018 10:41:37: 5000000 INFO @ Mon, 06 Aug 2018 10:41:39: 5000000 INFO @ Mon, 06 Aug 2018 10:41:39: 5000000 INFO @ Mon, 06 Aug 2018 10:41:43: 6000000 INFO @ Mon, 06 Aug 2018 10:41:45: 6000000 INFO @ Mon, 06 Aug 2018 10:41:45: 6000000 INFO @ Mon, 06 Aug 2018 10:41:49: 7000000 INFO @ Mon, 06 Aug 2018 10:41:51: 7000000 INFO @ Mon, 06 Aug 2018 10:41:52: 7000000 INFO @ Mon, 06 Aug 2018 10:41:56: 8000000 INFO @ Mon, 06 Aug 2018 10:41:58: 8000000 INFO @ Mon, 06 Aug 2018 10:41:58: 8000000 INFO @ Mon, 06 Aug 2018 10:41:59: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:41:59: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:41:59: #1 total tags in treatment: 3969154 INFO @ Mon, 06 Aug 2018 10:41:59: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:41:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:41:59: #1 tags after filtering in treatment: 3886784 INFO @ Mon, 06 Aug 2018 10:41:59: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 06 Aug 2018 10:41:59: #1 finished! INFO @ Mon, 06 Aug 2018 10:41:59: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:41:59: #2 number of paired peaks: 830 WARNING @ Mon, 06 Aug 2018 10:41:59: Fewer paired peaks (830) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 830 pairs to build model! INFO @ Mon, 06 Aug 2018 10:41:59: start model_add_line... INFO @ Mon, 06 Aug 2018 10:41:59: start X-correlation... INFO @ Mon, 06 Aug 2018 10:41:59: end of X-cor INFO @ Mon, 06 Aug 2018 10:41:59: #2 finished! INFO @ Mon, 06 Aug 2018 10:41:59: #2 predicted fragment length is 244 bps INFO @ Mon, 06 Aug 2018 10:41:59: #2 alternative fragment length(s) may be 244 bps INFO @ Mon, 06 Aug 2018 10:41:59: #2.2 Generate R script for model : SRX2396694.10_model.r INFO @ Mon, 06 Aug 2018 10:41:59: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:42:02: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:42:02: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:42:02: #1 total tags in treatment: 3969154 INFO @ Mon, 06 Aug 2018 10:42:02: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:42:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:42:02: #1 tags after filtering in treatment: 3886784 INFO @ Mon, 06 Aug 2018 10:42:02: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 06 Aug 2018 10:42:02: #1 finished! INFO @ Mon, 06 Aug 2018 10:42:02: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:42:02: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:42:02: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:42:02: #1 total tags in treatment: 3969154 INFO @ Mon, 06 Aug 2018 10:42:02: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:42:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:42:02: #1 tags after filtering in treatment: 3886784 INFO @ Mon, 06 Aug 2018 10:42:02: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 06 Aug 2018 10:42:02: #1 finished! INFO @ Mon, 06 Aug 2018 10:42:02: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:42:02: #2 number of paired peaks: 830 WARNING @ Mon, 06 Aug 2018 10:42:02: Fewer paired peaks (830) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 830 pairs to build model! INFO @ Mon, 06 Aug 2018 10:42:02: start model_add_line... INFO @ Mon, 06 Aug 2018 10:42:02: start X-correlation... INFO @ Mon, 06 Aug 2018 10:42:02: end of X-cor INFO @ Mon, 06 Aug 2018 10:42:02: #2 finished! INFO @ Mon, 06 Aug 2018 10:42:02: #2 predicted fragment length is 244 bps INFO @ Mon, 06 Aug 2018 10:42:02: #2 alternative fragment length(s) may be 244 bps INFO @ Mon, 06 Aug 2018 10:42:02: #2.2 Generate R script for model : SRX2396694.20_model.r INFO @ Mon, 06 Aug 2018 10:42:02: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:42:02: #2 number of paired peaks: 830 WARNING @ Mon, 06 Aug 2018 10:42:02: Fewer paired peaks (830) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 830 pairs to build model! INFO @ Mon, 06 Aug 2018 10:42:02: start model_add_line... INFO @ Mon, 06 Aug 2018 10:42:02: start X-correlation... INFO @ Mon, 06 Aug 2018 10:42:02: end of X-cor INFO @ Mon, 06 Aug 2018 10:42:02: #2 finished! INFO @ Mon, 06 Aug 2018 10:42:02: #2 predicted fragment length is 244 bps INFO @ Mon, 06 Aug 2018 10:42:02: #2 alternative fragment length(s) may be 244 bps INFO @ Mon, 06 Aug 2018 10:42:02: #2.2 Generate R script for model : SRX2396694.05_model.r INFO @ Mon, 06 Aug 2018 10:42:02: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:42:08: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:42:12: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:42:12: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:42:14: #4 Write output xls file... SRX2396694.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:42:14: #4 Write peak in narrowPeak format file... SRX2396694.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:42:14: #4 Write summits bed file... SRX2396694.10_summits.bed INFO @ Mon, 06 Aug 2018 10:42:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1346 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:42:18: #4 Write output xls file... SRX2396694.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:42:18: #4 Write peak in narrowPeak format file... SRX2396694.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:42:18: #4 Write summits bed file... SRX2396694.05_summits.bed INFO @ Mon, 06 Aug 2018 10:42:18: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3408 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:42:18: #4 Write output xls file... SRX2396694.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:42:18: #4 Write peak in narrowPeak format file... SRX2396694.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:42:18: #4 Write summits bed file... SRX2396694.20_summits.bed INFO @ Mon, 06 Aug 2018 10:42:18: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。