Job ID = 11240721 sra ファイルのダウンロード中... Completed: 644907K bytes transferred in 8 seconds (610100K 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: SINGLE fastq に変換中... Read 31067185 spots for /home/okishinya/chipatlas/results/dm3/SRX3630330/SRR6652852.sra Written 31067185 spots for /home/okishinya/chipatlas/results/dm3/SRX3630330/SRR6652852.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: 00:20:53 31067185 reads; of these: 31067185 (100.00%) were unpaired; of these: 826458 (2.66%) aligned 0 times 10516954 (33.85%) aligned exactly 1 time 19723773 (63.49%) aligned >1 times 97.34% overall alignment rate Time searching: 00:20:53 Overall time: 00:20:53 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_rmdupse_core] 8590262 / 30240727 = 0.2841 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 @ Sun, 07 Oct 2018 20:58:38: # Command line: callpeak -t SRX3630330.bam -f BAM -g dm -n SRX3630330.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3630330.10 # format = BAM # ChIP-seq file = ['SRX3630330.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 @ Sun, 07 Oct 2018 20:58:38: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:58:38: # Command line: callpeak -t SRX3630330.bam -f BAM -g dm -n SRX3630330.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3630330.20 # format = BAM # ChIP-seq file = ['SRX3630330.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 @ Sun, 07 Oct 2018 20:58:38: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:58:38: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:58:38: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:58:38: # Command line: callpeak -t SRX3630330.bam -f BAM -g dm -n SRX3630330.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3630330.05 # format = BAM # ChIP-seq file = ['SRX3630330.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 @ Sun, 07 Oct 2018 20:58:38: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:58:38: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:58:45: 1000000 INFO @ Sun, 07 Oct 2018 20:58:45: 1000000 INFO @ Sun, 07 Oct 2018 20:58:45: 1000000 INFO @ Sun, 07 Oct 2018 20:58:52: 2000000 INFO @ Sun, 07 Oct 2018 20:58:52: 2000000 INFO @ Sun, 07 Oct 2018 20:58:52: 2000000 INFO @ Sun, 07 Oct 2018 20:58:59: 3000000 INFO @ Sun, 07 Oct 2018 20:58:59: 3000000 INFO @ Sun, 07 Oct 2018 20:58:59: 3000000 INFO @ Sun, 07 Oct 2018 20:59:05: 4000000 INFO @ Sun, 07 Oct 2018 20:59:06: 4000000 INFO @ Sun, 07 Oct 2018 20:59:06: 4000000 INFO @ Sun, 07 Oct 2018 20:59:12: 5000000 INFO @ Sun, 07 Oct 2018 20:59:13: 5000000 INFO @ Sun, 07 Oct 2018 20:59:13: 5000000 INFO @ Sun, 07 Oct 2018 20:59:19: 6000000 INFO @ Sun, 07 Oct 2018 20:59:20: 6000000 INFO @ Sun, 07 Oct 2018 20:59:20: 6000000 INFO @ Sun, 07 Oct 2018 20:59:26: 7000000 INFO @ Sun, 07 Oct 2018 20:59:27: 7000000 INFO @ Sun, 07 Oct 2018 20:59:27: 7000000 INFO @ Sun, 07 Oct 2018 20:59:32: 8000000 INFO @ Sun, 07 Oct 2018 20:59:34: 8000000 INFO @ Sun, 07 Oct 2018 20:59:34: 8000000 INFO @ Sun, 07 Oct 2018 20:59:39: 9000000 INFO @ Sun, 07 Oct 2018 20:59:41: 9000000 INFO @ Sun, 07 Oct 2018 20:59:41: 9000000 INFO @ Sun, 07 Oct 2018 20:59:46: 10000000 INFO @ Sun, 07 Oct 2018 20:59:48: 10000000 INFO @ Sun, 07 Oct 2018 20:59:48: 10000000 INFO @ Sun, 07 Oct 2018 20:59:53: 11000000 INFO @ Sun, 07 Oct 2018 20:59:55: 11000000 INFO @ Sun, 07 Oct 2018 20:59:55: 11000000 INFO @ Sun, 07 Oct 2018 20:59:59: 12000000 INFO @ Sun, 07 Oct 2018 21:00:01: 12000000 INFO @ Sun, 07 Oct 2018 21:00:01: 12000000 INFO @ Sun, 07 Oct 2018 21:00:06: 13000000 INFO @ Sun, 07 Oct 2018 21:00:08: 13000000 INFO @ Sun, 07 Oct 2018 21:00:08: 13000000 INFO @ Sun, 07 Oct 2018 21:00:13: 14000000 INFO @ Sun, 07 Oct 2018 21:00:15: 14000000 INFO @ Sun, 07 Oct 2018 21:00:15: 14000000 INFO @ Sun, 07 Oct 2018 21:00:20: 15000000 INFO @ Sun, 07 Oct 2018 21:00:22: 15000000 INFO @ Sun, 07 Oct 2018 21:00:22: 15000000 INFO @ Sun, 07 Oct 2018 21:00:26: 16000000 INFO @ Sun, 07 Oct 2018 21:00:29: 16000000 INFO @ Sun, 07 Oct 2018 21:00:29: 16000000 INFO @ Sun, 07 Oct 2018 21:00:33: 17000000 INFO @ Sun, 07 Oct 2018 21:00:36: 17000000 INFO @ Sun, 07 Oct 2018 21:00:36: 17000000 INFO @ Sun, 07 Oct 2018 21:00:40: 18000000 INFO @ Sun, 07 Oct 2018 21:00:43: 18000000 INFO @ Sun, 07 Oct 2018 21:00:43: 18000000 INFO @ Sun, 07 Oct 2018 21:00:47: 19000000 INFO @ Sun, 07 Oct 2018 21:00:50: 19000000 INFO @ Sun, 07 Oct 2018 21:00:50: 19000000 INFO @ Sun, 07 Oct 2018 21:00:53: 20000000 INFO @ Sun, 07 Oct 2018 21:00:57: 20000000 INFO @ Sun, 07 Oct 2018 21:00:57: 20000000 INFO @ Sun, 07 Oct 2018 21:01:00: 21000000 INFO @ Sun, 07 Oct 2018 21:01:04: 21000000 INFO @ Sun, 07 Oct 2018 21:01:04: 21000000 INFO @ Sun, 07 Oct 2018 21:01:05: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:01:05: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:01:05: #1 total tags in treatment: 21650465 INFO @ Sun, 07 Oct 2018 21:01:05: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:01:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 21:01:05: #1 tags after filtering in treatment: 21650465 INFO @ Sun, 07 Oct 2018 21:01:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:01:05: #1 finished! INFO @ Sun, 07 Oct 2018 21:01:05: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:01:07: #2 number of paired peaks: 925 WARNING @ Sun, 07 Oct 2018 21:01:07: Fewer paired peaks (925) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 925 pairs to build model! INFO @ Sun, 07 Oct 2018 21:01:07: start model_add_line... INFO @ Sun, 07 Oct 2018 21:01:07: start X-correlation... INFO @ Sun, 07 Oct 2018 21:01:07: end of X-cor INFO @ Sun, 07 Oct 2018 21:01:07: #2 finished! INFO @ Sun, 07 Oct 2018 21:01:07: #2 predicted fragment length is 40 bps INFO @ Sun, 07 Oct 2018 21:01:07: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 07 Oct 2018 21:01:07: #2.2 Generate R script for model : SRX3630330.10_model.r WARNING @ Sun, 07 Oct 2018 21:01:07: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:01:07: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 07 Oct 2018 21:01:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 21:01:07: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:01:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:01:08: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:01:08: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:01:08: #1 total tags in treatment: 21650465 INFO @ Sun, 07 Oct 2018 21:01:08: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:01:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 21:01:08: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:01:08: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:01:08: #1 total tags in treatment: 21650465 INFO @ Sun, 07 Oct 2018 21:01:08: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:01:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 21:01:08: #1 tags after filtering in treatment: 21650465 INFO @ Sun, 07 Oct 2018 21:01:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:01:08: #1 finished! INFO @ Sun, 07 Oct 2018 21:01:08: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:01:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:01:09: #1 tags after filtering in treatment: 21650465 INFO @ Sun, 07 Oct 2018 21:01:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:01:09: #1 finished! INFO @ Sun, 07 Oct 2018 21:01:09: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:01:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:01:10: #2 number of paired peaks: 925 WARNING @ Sun, 07 Oct 2018 21:01:10: Fewer paired peaks (925) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 925 pairs to build model! INFO @ Sun, 07 Oct 2018 21:01:10: start model_add_line... INFO @ Sun, 07 Oct 2018 21:01:10: #2 number of paired peaks: 925 WARNING @ Sun, 07 Oct 2018 21:01:10: Fewer paired peaks (925) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 925 pairs to build model! INFO @ Sun, 07 Oct 2018 21:01:10: start model_add_line... INFO @ Sun, 07 Oct 2018 21:01:10: start X-correlation... INFO @ Sun, 07 Oct 2018 21:01:10: end of X-cor INFO @ Sun, 07 Oct 2018 21:01:10: #2 finished! INFO @ Sun, 07 Oct 2018 21:01:10: #2 predicted fragment length is 40 bps INFO @ Sun, 07 Oct 2018 21:01:10: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 07 Oct 2018 21:01:10: #2.2 Generate R script for model : SRX3630330.05_model.r INFO @ Sun, 07 Oct 2018 21:01:10: start X-correlation... WARNING @ Sun, 07 Oct 2018 21:01:10: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:01:10: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 07 Oct 2018 21:01:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 21:01:10: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:01:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:01:10: end of X-cor INFO @ Sun, 07 Oct 2018 21:01:10: #2 finished! INFO @ Sun, 07 Oct 2018 21:01:10: #2 predicted fragment length is 40 bps INFO @ Sun, 07 Oct 2018 21:01:10: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 07 Oct 2018 21:01:10: #2.2 Generate R script for model : SRX3630330.20_model.r WARNING @ Sun, 07 Oct 2018 21:01:11: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:01:11: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 07 Oct 2018 21:01:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 21:01:11: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:01:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:01:48: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:01:53: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:01:54: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:02:11: #4 Write output xls file... SRX3630330.10_peaks.xls INFO @ Sun, 07 Oct 2018 21:02:11: #4 Write peak in narrowPeak format file... SRX3630330.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:02:11: #4 Write summits bed file... SRX3630330.10_summits.bed INFO @ Sun, 07 Oct 2018 21:02:11: Done! pass1 - making usageList (14 chroms): 13 millis pass2 - checking and writing primary data (6274 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 21:02:17: #4 Write output xls file... SRX3630330.05_peaks.xls INFO @ Sun, 07 Oct 2018 21:02:17: #4 Write peak in narrowPeak format file... SRX3630330.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:02:17: #4 Write summits bed file... SRX3630330.05_summits.bed INFO @ Sun, 07 Oct 2018 21:02:18: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (15402 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 21:02:20: #4 Write output xls file... SRX3630330.20_peaks.xls INFO @ Sun, 07 Oct 2018 21:02:20: #4 Write peak in narrowPeak format file... SRX3630330.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:02:20: #4 Write summits bed file... SRX3630330.20_summits.bed INFO @ Sun, 07 Oct 2018 21:02:20: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1846 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。