Job ID = 11171316 sra ファイルのダウンロード中... Completed: 599787K bytes transferred in 44 seconds (109240K 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 13379438 spots for /home/okishinya/chipatlas/results/dm3/SRX3511947/SRR6418932.sra Written 13379438 spots for /home/okishinya/chipatlas/results/dm3/SRX3511947/SRR6418932.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: 00:06:21 13379438 reads; of these: 13379438 (100.00%) were unpaired; of these: 2322542 (17.36%) aligned 0 times 9232400 (69.00%) aligned exactly 1 time 1824496 (13.64%) aligned >1 times 82.64% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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_rmdupse_core] 716057 / 11056896 = 0.0648 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 13:53:22: # Command line: callpeak -t SRX3511947.bam -f BAM -g dm -n SRX3511947.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3511947.10 # format = BAM # ChIP-seq file = ['SRX3511947.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 13:53:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:53:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:53:22: # Command line: callpeak -t SRX3511947.bam -f BAM -g dm -n SRX3511947.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3511947.05 # format = BAM # ChIP-seq file = ['SRX3511947.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 13:53:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:53:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:53:22: # Command line: callpeak -t SRX3511947.bam -f BAM -g dm -n SRX3511947.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3511947.20 # format = BAM # ChIP-seq file = ['SRX3511947.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 13:53:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:53:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:53:30: 1000000 INFO @ Sat, 08 Sep 2018 13:53:30: 1000000 INFO @ Sat, 08 Sep 2018 13:53:30: 1000000 INFO @ Sat, 08 Sep 2018 13:53:38: 2000000 INFO @ Sat, 08 Sep 2018 13:53:38: 2000000 INFO @ Sat, 08 Sep 2018 13:53:38: 2000000 INFO @ Sat, 08 Sep 2018 13:53:45: 3000000 INFO @ Sat, 08 Sep 2018 13:53:45: 3000000 INFO @ Sat, 08 Sep 2018 13:53:46: 3000000 INFO @ Sat, 08 Sep 2018 13:53:53: 4000000 INFO @ Sat, 08 Sep 2018 13:53:53: 4000000 INFO @ Sat, 08 Sep 2018 13:53:53: 4000000 INFO @ Sat, 08 Sep 2018 13:54:01: 5000000 INFO @ Sat, 08 Sep 2018 13:54:01: 5000000 INFO @ Sat, 08 Sep 2018 13:54:01: 5000000 INFO @ Sat, 08 Sep 2018 13:54:08: 6000000 INFO @ Sat, 08 Sep 2018 13:54:08: 6000000 INFO @ Sat, 08 Sep 2018 13:54:09: 6000000 INFO @ Sat, 08 Sep 2018 13:54:16: 7000000 INFO @ Sat, 08 Sep 2018 13:54:16: 7000000 INFO @ Sat, 08 Sep 2018 13:54:17: 7000000 INFO @ Sat, 08 Sep 2018 13:54:24: 8000000 INFO @ Sat, 08 Sep 2018 13:54:24: 8000000 INFO @ Sat, 08 Sep 2018 13:54:24: 8000000 INFO @ Sat, 08 Sep 2018 13:54:31: 9000000 INFO @ Sat, 08 Sep 2018 13:54:31: 9000000 INFO @ Sat, 08 Sep 2018 13:54:32: 9000000 INFO @ Sat, 08 Sep 2018 13:54:39: 10000000 INFO @ Sat, 08 Sep 2018 13:54:39: 10000000 INFO @ Sat, 08 Sep 2018 13:54:40: 10000000 INFO @ Sat, 08 Sep 2018 13:54:41: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:54:41: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:54:41: #1 total tags in treatment: 10340839 INFO @ Sat, 08 Sep 2018 13:54:41: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:41: #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 13:54:42: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:54:42: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:54:42: #1 total tags in treatment: 10340839 INFO @ Sat, 08 Sep 2018 13:54:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:42: #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 13:54:42: #1 tags after filtering in treatment: 10340839 INFO @ Sat, 08 Sep 2018 13:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:42: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:42: #1 tags after filtering in treatment: 10340839 INFO @ Sat, 08 Sep 2018 13:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:42: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:42: #2 number of paired peaks: 100 WARNING @ Sat, 08 Sep 2018 13:54:42: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:42: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:43: #2 number of paired peaks: 100 WARNING @ Sat, 08 Sep 2018 13:54:43: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:43: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:43: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:43: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:43: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:43: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:43: #2 predicted fragment length is 91 bps INFO @ Sat, 08 Sep 2018 13:54:43: #2 alternative fragment length(s) may be 91,210,270,482,503 bps INFO @ Sat, 08 Sep 2018 13:54:43: #2.2 Generate R script for model : SRX3511947.10_model.r INFO @ Sat, 08 Sep 2018 13:54:43: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:43: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:43: #2 predicted fragment length is 91 bps INFO @ Sat, 08 Sep 2018 13:54:43: #2 alternative fragment length(s) may be 91,210,270,482,503 bps INFO @ Sat, 08 Sep 2018 13:54:43: #2.2 Generate R script for model : SRX3511947.05_model.r WARNING @ Sat, 08 Sep 2018 13:54:43: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:43: #2 You may need to consider one of the other alternative d(s): 91,210,270,482,503 WARNING @ Sat, 08 Sep 2018 13:54:43: #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 13:54:43: #3 Call peaks... WARNING @ Sat, 08 Sep 2018 13:54:43: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:43: #2 You may need to consider one of the other alternative d(s): 91,210,270,482,503 WARNING @ Sat, 08 Sep 2018 13:54:43: #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 13:54:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:54:43: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:54:43: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:54:43: #1 total tags in treatment: 10340839 INFO @ Sat, 08 Sep 2018 13:54:43: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:43: #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 13:54:43: #1 tags after filtering in treatment: 10340839 INFO @ Sat, 08 Sep 2018 13:54:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:43: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:43: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:44: #2 number of paired peaks: 100 WARNING @ Sat, 08 Sep 2018 13:54:44: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:44: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:44: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:44: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:44: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:44: #2 predicted fragment length is 91 bps INFO @ Sat, 08 Sep 2018 13:54:44: #2 alternative fragment length(s) may be 91,210,270,482,503 bps INFO @ Sat, 08 Sep 2018 13:54:44: #2.2 Generate R script for model : SRX3511947.20_model.r WARNING @ Sat, 08 Sep 2018 13:54:44: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:44: #2 You may need to consider one of the other alternative d(s): 91,210,270,482,503 WARNING @ Sat, 08 Sep 2018 13:54:44: #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 13:54:44: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:55:05: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:55:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:55:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:55:17: #4 Write output xls file... SRX3511947.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:55:17: #4 Write peak in narrowPeak format file... SRX3511947.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:55:17: #4 Write summits bed file... SRX3511947.05_summits.bed INFO @ Sat, 08 Sep 2018 13:55:17: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (281 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:55:18: #4 Write output xls file... SRX3511947.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:55:18: #4 Write peak in narrowPeak format file... SRX3511947.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:55:18: #4 Write summits bed file... SRX3511947.10_summits.bed INFO @ Sat, 08 Sep 2018 13:55:18: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (137 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:55:19: #4 Write output xls file... SRX3511947.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:55:19: #4 Write peak in narrowPeak format file... SRX3511947.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:55:19: #4 Write summits bed file... SRX3511947.20_summits.bed INFO @ Sat, 08 Sep 2018 13:55:19: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (60 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。