Job ID = 9029885 sra ファイルのダウンロード中... Completed: 1061985K bytes transferred in 11 seconds (780668K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 12695 0 12695 0 0 1596 0 --:--:-- 0:00:07 --:--:-- 8070 100 30786 0 30786 0 0 3572 0 --:--:-- 0:00:08 --:--:-- 13762 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... Written 22367998 spots for /home/okishinya/chipatlas/results/dm3/SRX2541747/SRR5234221.sra Written 22367998 spots total 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: 00:06:34 22367998 reads; of these: 22367998 (100.00%) were unpaired; of these: 10507910 (46.98%) aligned 0 times 8019921 (35.85%) aligned exactly 1 time 3840167 (17.17%) aligned >1 times 53.02% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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] 1468347 / 11860088 = 0.1238 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, 03 Jun 2017 15:46:46: # Command line: callpeak -t SRX2541747.bam -f BAM -g dm -n SRX2541747.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2541747.05 # format = BAM # ChIP-seq file = ['SRX2541747.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 INFO @ Sat, 03 Jun 2017 15:46:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:46:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:46:46: # Command line: callpeak -t SRX2541747.bam -f BAM -g dm -n SRX2541747.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2541747.10 # format = BAM # ChIP-seq file = ['SRX2541747.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 INFO @ Sat, 03 Jun 2017 15:46:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:46:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:46:46: # Command line: callpeak -t SRX2541747.bam -f BAM -g dm -n SRX2541747.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2541747.20 # format = BAM # ChIP-seq file = ['SRX2541747.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 INFO @ Sat, 03 Jun 2017 15:46:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:46:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:46:51: 1000000 INFO @ Sat, 03 Jun 2017 15:46:52: 1000000 INFO @ Sat, 03 Jun 2017 15:46:52: 1000000 INFO @ Sat, 03 Jun 2017 15:46:57: 2000000 INFO @ Sat, 03 Jun 2017 15:46:57: 2000000 INFO @ Sat, 03 Jun 2017 15:46:58: 2000000 INFO @ Sat, 03 Jun 2017 15:47:03: 3000000 INFO @ Sat, 03 Jun 2017 15:47:03: 3000000 INFO @ Sat, 03 Jun 2017 15:47:04: 3000000 INFO @ Sat, 03 Jun 2017 15:47:09: 4000000 INFO @ Sat, 03 Jun 2017 15:47:09: 4000000 INFO @ Sat, 03 Jun 2017 15:47:10: 4000000 INFO @ Sat, 03 Jun 2017 15:47:15: 5000000 INFO @ Sat, 03 Jun 2017 15:47:15: 5000000 INFO @ Sat, 03 Jun 2017 15:47:16: 5000000 INFO @ Sat, 03 Jun 2017 15:47:21: 6000000 INFO @ Sat, 03 Jun 2017 15:47:21: 6000000 INFO @ Sat, 03 Jun 2017 15:47:22: 6000000 INFO @ Sat, 03 Jun 2017 15:47:26: 7000000 INFO @ Sat, 03 Jun 2017 15:47:27: 7000000 INFO @ Sat, 03 Jun 2017 15:47:28: 7000000 INFO @ Sat, 03 Jun 2017 15:47:33: 8000000 INFO @ Sat, 03 Jun 2017 15:47:35: 8000000 INFO @ Sat, 03 Jun 2017 15:47:35: 8000000 INFO @ Sat, 03 Jun 2017 15:47:39: 9000000 INFO @ Sat, 03 Jun 2017 15:47:41: 9000000 INFO @ Sat, 03 Jun 2017 15:47:42: 9000000 INFO @ Sat, 03 Jun 2017 15:47:45: 10000000 INFO @ Sat, 03 Jun 2017 15:47:48: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:47:48: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:47:48: #1 total tags in treatment: 10391741 INFO @ Sat, 03 Jun 2017 15:47:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:47:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:47:48: 10000000 INFO @ Sat, 03 Jun 2017 15:47:48: 10000000 INFO @ Sat, 03 Jun 2017 15:47:50: #1 tags after filtering in treatment: 10388716 INFO @ Sat, 03 Jun 2017 15:47:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:47:50: #1 finished! INFO @ Sat, 03 Jun 2017 15:47:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:47:50: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:47:50: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:47:50: #1 total tags in treatment: 10391741 INFO @ Sat, 03 Jun 2017 15:47:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:47:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:47:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:47:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:47:51: #1 total tags in treatment: 10391741 INFO @ Sat, 03 Jun 2017 15:47:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:47:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:47:52: #2 number of paired peaks: 277 WARNING @ Sat, 03 Jun 2017 15:47:52: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 03 Jun 2017 15:47:52: start model_add_line... INFO @ Sat, 03 Jun 2017 15:47:52: #1 tags after filtering in treatment: 10388716 INFO @ Sat, 03 Jun 2017 15:47:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:47:52: #1 finished! INFO @ Sat, 03 Jun 2017 15:47:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:47:53: #1 tags after filtering in treatment: 10388716 INFO @ Sat, 03 Jun 2017 15:47:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:47:53: #1 finished! INFO @ Sat, 03 Jun 2017 15:47:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:47:54: #2 number of paired peaks: 277 WARNING @ Sat, 03 Jun 2017 15:47:54: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 03 Jun 2017 15:47:54: start model_add_line... INFO @ Sat, 03 Jun 2017 15:47:54: #2 number of paired peaks: 277 WARNING @ Sat, 03 Jun 2017 15:47:54: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 03 Jun 2017 15:47:54: start model_add_line... INFO @ Sat, 03 Jun 2017 15:47:55: start X-correlation... INFO @ Sat, 03 Jun 2017 15:47:55: end of X-cor INFO @ Sat, 03 Jun 2017 15:47:55: #2 finished! INFO @ Sat, 03 Jun 2017 15:47:55: #2 predicted fragment length is 69 bps INFO @ Sat, 03 Jun 2017 15:47:55: #2 alternative fragment length(s) may be 69 bps INFO @ Sat, 03 Jun 2017 15:47:55: #2.2 Generate R script for model : SRX2541747.20_model.r WARNING @ Sat, 03 Jun 2017 15:47:55: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:47:55: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sat, 03 Jun 2017 15:47:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 15:47:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:47:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:47:57: start X-correlation... INFO @ Sat, 03 Jun 2017 15:47:57: end of X-cor INFO @ Sat, 03 Jun 2017 15:47:57: #2 finished! INFO @ Sat, 03 Jun 2017 15:47:57: #2 predicted fragment length is 69 bps INFO @ Sat, 03 Jun 2017 15:47:57: #2 alternative fragment length(s) may be 69 bps INFO @ Sat, 03 Jun 2017 15:47:57: #2.2 Generate R script for model : SRX2541747.10_model.r WARNING @ Sat, 03 Jun 2017 15:47:57: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:47:57: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sat, 03 Jun 2017 15:47:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 15:47:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:47:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:47:57: start X-correlation... INFO @ Sat, 03 Jun 2017 15:47:57: end of X-cor INFO @ Sat, 03 Jun 2017 15:47:57: #2 finished! INFO @ Sat, 03 Jun 2017 15:47:57: #2 predicted fragment length is 69 bps INFO @ Sat, 03 Jun 2017 15:47:57: #2 alternative fragment length(s) may be 69 bps INFO @ Sat, 03 Jun 2017 15:47:57: #2.2 Generate R script for model : SRX2541747.05_model.r WARNING @ Sat, 03 Jun 2017 15:47:57: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:47:57: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sat, 03 Jun 2017 15:47:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 15:47:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:47:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:48:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:48:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:48:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:49:34: #4 Write output xls file... SRX2541747.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:49:34: #4 Write peak in narrowPeak format file... SRX2541747.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:49:34: #4 Write summits bed file... SRX2541747.20_summits.bed INFO @ Sat, 03 Jun 2017 15:49:34: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (893 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:49:40: #4 Write output xls file... SRX2541747.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:49:40: #4 Write peak in narrowPeak format file... SRX2541747.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:49:40: #4 Write summits bed file... SRX2541747.10_summits.bed INFO @ Sat, 03 Jun 2017 15:49:41: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1575 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:49:42: #4 Write output xls file... SRX2541747.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:49:42: #4 Write peak in narrowPeak format file... SRX2541747.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:49:42: #4 Write summits bed file... SRX2541747.05_summits.bed INFO @ Sat, 03 Jun 2017 15:49:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2684 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。