Job ID = 9029777 sra ファイルのダウンロード中... Completed: 377149K bytes transferred in 6 seconds (477018K 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 --:--:-- 0 100 14324 0 14324 0 0 1879 0 --:--:-- 0:00:07 --:--:-- 13694 100 49196 0 49196 0 0 5821 0 --:--:-- 0:00:08 --:--:-- 26223 100 51067 0 51067 0 0 6042 0 --:--:-- 0:00:08 --:--:-- 27206 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 16887197 spots for /home/okishinya/chipatlas/results/dm3/SRX2055959/SRR4069191.sra Written 16887197 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: 00:08:01 16887197 reads; of these: 16887197 (100.00%) were unpaired; of these: 677508 (4.01%) aligned 0 times 10512007 (62.25%) aligned exactly 1 time 5697682 (33.74%) aligned >1 times 95.99% overall alignment rate Time searching: 00:08:01 Overall time: 00:08:01 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] 1666300 / 16209689 = 0.1028 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 15:22:36: # Command line: callpeak -t SRX2055959.bam -f BAM -g dm -n SRX2055959.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055959.10 # format = BAM # ChIP-seq file = ['SRX2055959.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 15:22:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:22:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:22:36: # Command line: callpeak -t SRX2055959.bam -f BAM -g dm -n SRX2055959.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055959.20 # format = BAM # ChIP-seq file = ['SRX2055959.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 15:22:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:22:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:22:36: # Command line: callpeak -t SRX2055959.bam -f BAM -g dm -n SRX2055959.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055959.05 # format = BAM # ChIP-seq file = ['SRX2055959.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 15:22:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:22:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:22:42: 1000000 INFO @ Sat, 03 Jun 2017 15:22:42: 1000000 INFO @ Sat, 03 Jun 2017 15:22:42: 1000000 INFO @ Sat, 03 Jun 2017 15:22:48: 2000000 INFO @ Sat, 03 Jun 2017 15:22:48: 2000000 INFO @ Sat, 03 Jun 2017 15:22:48: 2000000 INFO @ Sat, 03 Jun 2017 15:22:53: 3000000 INFO @ Sat, 03 Jun 2017 15:22:54: 3000000 INFO @ Sat, 03 Jun 2017 15:22:54: 3000000 INFO @ Sat, 03 Jun 2017 15:22:59: 4000000 INFO @ Sat, 03 Jun 2017 15:22:59: 4000000 INFO @ Sat, 03 Jun 2017 15:23:00: 4000000 INFO @ Sat, 03 Jun 2017 15:23:05: 5000000 INFO @ Sat, 03 Jun 2017 15:23:05: 5000000 INFO @ Sat, 03 Jun 2017 15:23:06: 5000000 INFO @ Sat, 03 Jun 2017 15:23:11: 6000000 INFO @ Sat, 03 Jun 2017 15:23:11: 6000000 INFO @ Sat, 03 Jun 2017 15:23:11: 6000000 INFO @ Sat, 03 Jun 2017 15:23:16: 7000000 INFO @ Sat, 03 Jun 2017 15:23:17: 7000000 INFO @ Sat, 03 Jun 2017 15:23:17: 7000000 INFO @ Sat, 03 Jun 2017 15:23:22: 8000000 INFO @ Sat, 03 Jun 2017 15:23:23: 8000000 INFO @ Sat, 03 Jun 2017 15:23:23: 8000000 INFO @ Sat, 03 Jun 2017 15:23:27: 9000000 INFO @ Sat, 03 Jun 2017 15:23:28: 9000000 INFO @ Sat, 03 Jun 2017 15:23:29: 9000000 INFO @ Sat, 03 Jun 2017 15:23:33: 10000000 INFO @ Sat, 03 Jun 2017 15:23:34: 10000000 INFO @ Sat, 03 Jun 2017 15:23:35: 10000000 INFO @ Sat, 03 Jun 2017 15:23:38: 11000000 INFO @ Sat, 03 Jun 2017 15:23:40: 11000000 INFO @ Sat, 03 Jun 2017 15:23:41: 11000000 INFO @ Sat, 03 Jun 2017 15:23:44: 12000000 INFO @ Sat, 03 Jun 2017 15:23:46: 12000000 INFO @ Sat, 03 Jun 2017 15:23:47: 12000000 INFO @ Sat, 03 Jun 2017 15:23:49: 13000000 INFO @ Sat, 03 Jun 2017 15:23:52: 13000000 INFO @ Sat, 03 Jun 2017 15:23:53: 13000000 INFO @ Sat, 03 Jun 2017 15:23:55: 14000000 INFO @ Sat, 03 Jun 2017 15:23:58: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:23:58: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:23:58: #1 total tags in treatment: 14543389 INFO @ Sat, 03 Jun 2017 15:23:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:23:58: #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 15:23:58: 14000000 INFO @ Sat, 03 Jun 2017 15:23:59: 14000000 INFO @ Sat, 03 Jun 2017 15:24:00: #1 tags after filtering in treatment: 14541460 INFO @ Sat, 03 Jun 2017 15:24:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:24:00: #1 finished! INFO @ Sat, 03 Jun 2017 15:24:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:24:01: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:24:01: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:24:01: #1 total tags in treatment: 14543389 INFO @ Sat, 03 Jun 2017 15:24:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:24:01: #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 15:24:03: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:24:03: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:24:03: #1 total tags in treatment: 14543389 INFO @ Sat, 03 Jun 2017 15:24:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:24:03: #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 15:24:03: #2 number of paired peaks: 981 WARNING @ Sat, 03 Jun 2017 15:24:03: Fewer paired peaks (981) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 981 pairs to build model! INFO @ Sat, 03 Jun 2017 15:24:03: start model_add_line... INFO @ Sat, 03 Jun 2017 15:24:04: #1 tags after filtering in treatment: 14541460 INFO @ Sat, 03 Jun 2017 15:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:24:04: #1 finished! INFO @ Sat, 03 Jun 2017 15:24:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:24:06: #1 tags after filtering in treatment: 14541460 INFO @ Sat, 03 Jun 2017 15:24:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:24:06: #1 finished! INFO @ Sat, 03 Jun 2017 15:24:06: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:24:07: #2 number of paired peaks: 981 WARNING @ Sat, 03 Jun 2017 15:24:07: Fewer paired peaks (981) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 981 pairs to build model! INFO @ Sat, 03 Jun 2017 15:24:07: start model_add_line... INFO @ Sat, 03 Jun 2017 15:24:09: #2 number of paired peaks: 981 WARNING @ Sat, 03 Jun 2017 15:24:09: Fewer paired peaks (981) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 981 pairs to build model! INFO @ Sat, 03 Jun 2017 15:24:09: start model_add_line... INFO @ Sat, 03 Jun 2017 15:24:12: start X-correlation... INFO @ Sat, 03 Jun 2017 15:24:12: end of X-cor INFO @ Sat, 03 Jun 2017 15:24:12: #2 finished! INFO @ Sat, 03 Jun 2017 15:24:12: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 15:24:12: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 15:24:12: #2.2 Generate R script for model : SRX2055959.20_model.r WARNING @ Sat, 03 Jun 2017 15:24:12: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:24:12: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 15:24:12: #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 15:24:12: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:24:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:24:16: start X-correlation... INFO @ Sat, 03 Jun 2017 15:24:16: end of X-cor INFO @ Sat, 03 Jun 2017 15:24:16: #2 finished! INFO @ Sat, 03 Jun 2017 15:24:16: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 15:24:16: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 15:24:16: #2.2 Generate R script for model : SRX2055959.10_model.r WARNING @ Sat, 03 Jun 2017 15:24:16: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:24:16: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 15:24:16: #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 15:24:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:24:18: start X-correlation... INFO @ Sat, 03 Jun 2017 15:24:18: end of X-cor INFO @ Sat, 03 Jun 2017 15:24:18: #2 finished! INFO @ Sat, 03 Jun 2017 15:24:18: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 15:24:18: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 15:24:18: #2.2 Generate R script for model : SRX2055959.05_model.r WARNING @ Sat, 03 Jun 2017 15:24:18: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:24:18: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 15:24:18: #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 15:24:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:24:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:25:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:25:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:25:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:26:30: #4 Write output xls file... SRX2055959.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:26:30: #4 Write output xls file... SRX2055959.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:26:30: #4 Write peak in narrowPeak format file... SRX2055959.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:26:30: #4 Write peak in narrowPeak format file... SRX2055959.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:26:30: #4 Write summits bed file... SRX2055959.20_summits.bed INFO @ Sat, 03 Jun 2017 15:26:30: Done! INFO @ Sat, 03 Jun 2017 15:26:30: #4 Write summits bed file... SRX2055959.05_summits.bed INFO @ Sat, 03 Jun 2017 15:26:30: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1220 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3320 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:26:36: #4 Write output xls file... SRX2055959.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:26:36: #4 Write peak in narrowPeak format file... SRX2055959.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:26:36: #4 Write summits bed file... SRX2055959.10_summits.bed INFO @ Sat, 03 Jun 2017 15:26:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2362 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。