Job ID = 10609598 sra ファイルのダウンロード中... Completed: 463513K bytes transferred in 37 seconds (100131K 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 15792541 spots for /home/okishinya/chipatlas/results/dm3/SRX3011247/SRR5834724.sra Written 15792541 spots for /home/okishinya/chipatlas/results/dm3/SRX3011247/SRR5834724.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: 00:07:01 15792541 reads; of these: 15792541 (100.00%) were unpaired; of these: 846329 (5.36%) aligned 0 times 11651589 (73.78%) aligned exactly 1 time 3294623 (20.86%) aligned >1 times 94.64% overall alignment rate Time searching: 00:07:01 Overall time: 00:07:02 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] 3316408 / 14946212 = 0.2219 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, 07 May 2018 12:54:17: # Command line: callpeak -t SRX3011247.bam -f BAM -g dm -n SRX3011247.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011247.05 # format = BAM # ChIP-seq file = ['SRX3011247.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, 07 May 2018 12:54:17: #1 read tag files... INFO @ Mon, 07 May 2018 12:54:17: #1 read treatment tags... INFO @ Mon, 07 May 2018 12:54:17: # Command line: callpeak -t SRX3011247.bam -f BAM -g dm -n SRX3011247.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011247.10 # format = BAM # ChIP-seq file = ['SRX3011247.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, 07 May 2018 12:54:17: #1 read tag files... INFO @ Mon, 07 May 2018 12:54:17: #1 read treatment tags... INFO @ Mon, 07 May 2018 12:54:17: # Command line: callpeak -t SRX3011247.bam -f BAM -g dm -n SRX3011247.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011247.20 # format = BAM # ChIP-seq file = ['SRX3011247.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, 07 May 2018 12:54:17: #1 read tag files... INFO @ Mon, 07 May 2018 12:54:17: #1 read treatment tags... INFO @ Mon, 07 May 2018 12:54:25: 1000000 INFO @ Mon, 07 May 2018 12:54:25: 1000000 INFO @ Mon, 07 May 2018 12:54:25: 1000000 INFO @ Mon, 07 May 2018 12:54:32: 2000000 INFO @ Mon, 07 May 2018 12:54:32: 2000000 INFO @ Mon, 07 May 2018 12:54:33: 2000000 INFO @ Mon, 07 May 2018 12:54:39: 3000000 INFO @ Mon, 07 May 2018 12:54:40: 3000000 INFO @ Mon, 07 May 2018 12:54:40: 3000000 INFO @ Mon, 07 May 2018 12:54:47: 4000000 INFO @ Mon, 07 May 2018 12:54:48: 4000000 INFO @ Mon, 07 May 2018 12:54:48: 4000000 INFO @ Mon, 07 May 2018 12:54:54: 5000000 INFO @ Mon, 07 May 2018 12:54:56: 5000000 INFO @ Mon, 07 May 2018 12:54:57: 5000000 INFO @ Mon, 07 May 2018 12:55:01: 6000000 INFO @ Mon, 07 May 2018 12:55:03: 6000000 INFO @ Mon, 07 May 2018 12:55:05: 6000000 INFO @ Mon, 07 May 2018 12:55:08: 7000000 INFO @ Mon, 07 May 2018 12:55:11: 7000000 INFO @ Mon, 07 May 2018 12:55:12: 7000000 INFO @ Mon, 07 May 2018 12:55:15: 8000000 INFO @ Mon, 07 May 2018 12:55:19: 8000000 INFO @ Mon, 07 May 2018 12:55:21: 8000000 INFO @ Mon, 07 May 2018 12:55:22: 9000000 INFO @ Mon, 07 May 2018 12:55:27: 9000000 INFO @ Mon, 07 May 2018 12:55:29: 9000000 INFO @ Mon, 07 May 2018 12:55:30: 10000000 INFO @ Mon, 07 May 2018 12:55:35: 10000000 INFO @ Mon, 07 May 2018 12:55:37: 11000000 INFO @ Mon, 07 May 2018 12:55:37: 10000000 INFO @ Mon, 07 May 2018 12:55:41: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 12:55:41: #1 tag size = 80 INFO @ Mon, 07 May 2018 12:55:41: #1 total tags in treatment: 11629804 INFO @ Mon, 07 May 2018 12:55:41: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 12:55:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 12:55:42: #1 tags after filtering in treatment: 11629804 INFO @ Mon, 07 May 2018 12:55:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 12:55:42: #1 finished! INFO @ Mon, 07 May 2018 12:55:42: #2 Build Peak Model... INFO @ Mon, 07 May 2018 12:55:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 12:55:43: #2 number of paired peaks: 967 WARNING @ Mon, 07 May 2018 12:55:43: Fewer paired peaks (967) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 967 pairs to build model! INFO @ Mon, 07 May 2018 12:55:43: start model_add_line... INFO @ Mon, 07 May 2018 12:55:43: 11000000 INFO @ Mon, 07 May 2018 12:55:43: start X-correlation... INFO @ Mon, 07 May 2018 12:55:43: end of X-cor INFO @ Mon, 07 May 2018 12:55:43: #2 finished! INFO @ Mon, 07 May 2018 12:55:43: #2 predicted fragment length is 150 bps INFO @ Mon, 07 May 2018 12:55:43: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 07 May 2018 12:55:43: #2.2 Generate R script for model : SRX3011247.20_model.r WARNING @ Mon, 07 May 2018 12:55:43: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 12:55:43: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Mon, 07 May 2018 12:55:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 12:55:43: #3 Call peaks... INFO @ Mon, 07 May 2018 12:55:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 12:55:45: 11000000 INFO @ Mon, 07 May 2018 12:55:48: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 12:55:48: #1 tag size = 80 INFO @ Mon, 07 May 2018 12:55:48: #1 total tags in treatment: 11629804 INFO @ Mon, 07 May 2018 12:55:48: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 12:55:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 12:55:48: #1 tags after filtering in treatment: 11629804 INFO @ Mon, 07 May 2018 12:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 12:55:48: #1 finished! INFO @ Mon, 07 May 2018 12:55:48: #2 Build Peak Model... INFO @ Mon, 07 May 2018 12:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 12:55:49: #2 number of paired peaks: 967 WARNING @ Mon, 07 May 2018 12:55:49: Fewer paired peaks (967) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 967 pairs to build model! INFO @ Mon, 07 May 2018 12:55:49: start model_add_line... INFO @ Mon, 07 May 2018 12:55:49: start X-correlation... INFO @ Mon, 07 May 2018 12:55:49: end of X-cor INFO @ Mon, 07 May 2018 12:55:49: #2 finished! INFO @ Mon, 07 May 2018 12:55:49: #2 predicted fragment length is 150 bps INFO @ Mon, 07 May 2018 12:55:49: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 07 May 2018 12:55:49: #2.2 Generate R script for model : SRX3011247.10_model.r WARNING @ Mon, 07 May 2018 12:55:49: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 12:55:49: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Mon, 07 May 2018 12:55:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 12:55:49: #3 Call peaks... INFO @ Mon, 07 May 2018 12:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 12:55:50: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 12:55:50: #1 tag size = 80 INFO @ Mon, 07 May 2018 12:55:50: #1 total tags in treatment: 11629804 INFO @ Mon, 07 May 2018 12:55:50: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 12:55:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 12:55:50: #1 tags after filtering in treatment: 11629804 INFO @ Mon, 07 May 2018 12:55:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 12:55:50: #1 finished! INFO @ Mon, 07 May 2018 12:55:50: #2 Build Peak Model... INFO @ Mon, 07 May 2018 12:55:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 12:55:51: #2 number of paired peaks: 967 WARNING @ Mon, 07 May 2018 12:55:51: Fewer paired peaks (967) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 967 pairs to build model! INFO @ Mon, 07 May 2018 12:55:51: start model_add_line... INFO @ Mon, 07 May 2018 12:55:51: start X-correlation... INFO @ Mon, 07 May 2018 12:55:51: end of X-cor INFO @ Mon, 07 May 2018 12:55:51: #2 finished! INFO @ Mon, 07 May 2018 12:55:51: #2 predicted fragment length is 150 bps INFO @ Mon, 07 May 2018 12:55:51: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 07 May 2018 12:55:51: #2.2 Generate R script for model : SRX3011247.05_model.r WARNING @ Mon, 07 May 2018 12:55:51: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 12:55:51: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Mon, 07 May 2018 12:55:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 12:55:51: #3 Call peaks... INFO @ Mon, 07 May 2018 12:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 12:56:13: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 12:56:17: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 12:56:20: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 12:56:28: #4 Write output xls file... SRX3011247.20_peaks.xls INFO @ Mon, 07 May 2018 12:56:28: #4 Write peak in narrowPeak format file... SRX3011247.20_peaks.narrowPeak INFO @ Mon, 07 May 2018 12:56:28: #4 Write summits bed file... SRX3011247.20_summits.bed INFO @ Mon, 07 May 2018 12:56:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1736 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 12:56:33: #4 Write output xls file... SRX3011247.10_peaks.xls INFO @ Mon, 07 May 2018 12:56:33: #4 Write peak in narrowPeak format file... SRX3011247.10_peaks.narrowPeak INFO @ Mon, 07 May 2018 12:56:33: #4 Write summits bed file... SRX3011247.10_summits.bed INFO @ Mon, 07 May 2018 12:56:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3746 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 12:56:38: #4 Write output xls file... SRX3011247.05_peaks.xls INFO @ Mon, 07 May 2018 12:56:38: #4 Write peak in narrowPeak format file... SRX3011247.05_peaks.narrowPeak INFO @ Mon, 07 May 2018 12:56:39: #4 Write summits bed file... SRX3011247.05_summits.bed INFO @ Mon, 07 May 2018 12:56:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6887 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。