Job ID = 9028875 sra ファイルのダウンロード中... Completed: 636579K bytes transferred in 8 seconds (644317K 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 18662 0 18662 0 0 2306 0 --:--:-- 0:00:08 --:--:-- 12433 100 47622 0 47622 0 0 5241 0 --:--:-- 0:00:09 --:--:-- 19079 100 50109 0 50109 0 0 5515 0 --:--:-- 0:00:09 --:--:-- 20067 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 14068260 spots for /home/okishinya/chipatlas/results/ce10/SRX982089/SRR1956576.sra Written 14068260 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: 00:05:46 14068260 reads; of these: 14068260 (100.00%) were unpaired; of these: 937704 (6.67%) aligned 0 times 10974772 (78.01%) aligned exactly 1 time 2155784 (15.32%) aligned >1 times 93.33% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2318482 / 13130556 = 0.1766 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 12:18:38: # Command line: callpeak -t SRX982089.bam -f BAM -g ce -n SRX982089.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982089.05 # format = BAM # ChIP-seq file = ['SRX982089.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:18:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:18:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:18:38: # Command line: callpeak -t SRX982089.bam -f BAM -g ce -n SRX982089.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982089.10 # format = BAM # ChIP-seq file = ['SRX982089.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:18:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:18:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:18:38: # Command line: callpeak -t SRX982089.bam -f BAM -g ce -n SRX982089.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982089.20 # format = BAM # ChIP-seq file = ['SRX982089.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:18:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:18:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:18:45: 1000000 INFO @ Sat, 03 Jun 2017 12:18:46: 1000000 INFO @ Sat, 03 Jun 2017 12:18:46: 1000000 INFO @ Sat, 03 Jun 2017 12:18:52: 2000000 INFO @ Sat, 03 Jun 2017 12:18:53: 2000000 INFO @ Sat, 03 Jun 2017 12:18:53: 2000000 INFO @ Sat, 03 Jun 2017 12:18:59: 3000000 INFO @ Sat, 03 Jun 2017 12:19:01: 3000000 INFO @ Sat, 03 Jun 2017 12:19:01: 3000000 INFO @ Sat, 03 Jun 2017 12:19:06: 4000000 INFO @ Sat, 03 Jun 2017 12:19:08: 4000000 INFO @ Sat, 03 Jun 2017 12:19:09: 4000000 INFO @ Sat, 03 Jun 2017 12:19:12: 5000000 INFO @ Sat, 03 Jun 2017 12:19:16: 5000000 INFO @ Sat, 03 Jun 2017 12:19:16: 5000000 INFO @ Sat, 03 Jun 2017 12:19:19: 6000000 INFO @ Sat, 03 Jun 2017 12:19:24: 6000000 INFO @ Sat, 03 Jun 2017 12:19:24: 6000000 INFO @ Sat, 03 Jun 2017 12:19:26: 7000000 INFO @ Sat, 03 Jun 2017 12:19:32: 7000000 INFO @ Sat, 03 Jun 2017 12:19:32: 7000000 INFO @ Sat, 03 Jun 2017 12:19:33: 8000000 INFO @ Sat, 03 Jun 2017 12:19:39: 8000000 INFO @ Sat, 03 Jun 2017 12:19:40: 9000000 INFO @ Sat, 03 Jun 2017 12:19:40: 8000000 INFO @ Sat, 03 Jun 2017 12:19:47: 10000000 INFO @ Sat, 03 Jun 2017 12:19:47: 9000000 INFO @ Sat, 03 Jun 2017 12:19:48: 9000000 INFO @ Sat, 03 Jun 2017 12:19:52: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 12:19:52: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 12:19:52: #1 total tags in treatment: 10812074 INFO @ Sat, 03 Jun 2017 12:19:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:19:52: #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 12:19:55: #1 tags after filtering in treatment: 10809430 INFO @ Sat, 03 Jun 2017 12:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:19:55: #1 finished! INFO @ Sat, 03 Jun 2017 12:19:55: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:19:55: 10000000 INFO @ Sat, 03 Jun 2017 12:19:56: 10000000 INFO @ Sat, 03 Jun 2017 12:19:57: #2 number of paired peaks: 336 WARNING @ Sat, 03 Jun 2017 12:19:57: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Sat, 03 Jun 2017 12:19:57: start model_add_line... INFO @ Sat, 03 Jun 2017 12:20:01: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 12:20:01: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 12:20:01: #1 total tags in treatment: 10812074 INFO @ Sat, 03 Jun 2017 12:20:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:20:01: #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 12:20:02: start X-correlation... INFO @ Sat, 03 Jun 2017 12:20:02: end of X-cor INFO @ Sat, 03 Jun 2017 12:20:02: #2 finished! INFO @ Sat, 03 Jun 2017 12:20:02: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Jun 2017 12:20:02: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sat, 03 Jun 2017 12:20:02: #2.2 Generate R script for model : SRX982089.10_model.r WARNING @ Sat, 03 Jun 2017 12:20:02: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:20:02: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sat, 03 Jun 2017 12:20:02: #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 12:20:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:20:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:20:02: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 12:20:02: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 12:20:02: #1 total tags in treatment: 10812074 INFO @ Sat, 03 Jun 2017 12:20:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:20:02: #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 12:20:03: #1 tags after filtering in treatment: 10809430 INFO @ Sat, 03 Jun 2017 12:20:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:20:03: #1 finished! INFO @ Sat, 03 Jun 2017 12:20:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:20:04: #1 tags after filtering in treatment: 10809430 INFO @ Sat, 03 Jun 2017 12:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:20:04: #1 finished! INFO @ Sat, 03 Jun 2017 12:20:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:20:05: #2 number of paired peaks: 336 WARNING @ Sat, 03 Jun 2017 12:20:05: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Sat, 03 Jun 2017 12:20:05: start model_add_line... INFO @ Sat, 03 Jun 2017 12:20:06: #2 number of paired peaks: 336 WARNING @ Sat, 03 Jun 2017 12:20:06: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Sat, 03 Jun 2017 12:20:06: start model_add_line... INFO @ Sat, 03 Jun 2017 12:20:09: start X-correlation... INFO @ Sat, 03 Jun 2017 12:20:09: end of X-cor INFO @ Sat, 03 Jun 2017 12:20:10: #2 finished! INFO @ Sat, 03 Jun 2017 12:20:10: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Jun 2017 12:20:10: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sat, 03 Jun 2017 12:20:10: #2.2 Generate R script for model : SRX982089.20_model.r WARNING @ Sat, 03 Jun 2017 12:20:10: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:20:10: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sat, 03 Jun 2017 12:20:10: #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 12:20:10: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:20:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:20:11: start X-correlation... INFO @ Sat, 03 Jun 2017 12:20:11: end of X-cor INFO @ Sat, 03 Jun 2017 12:20:11: #2 finished! INFO @ Sat, 03 Jun 2017 12:20:11: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Jun 2017 12:20:11: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sat, 03 Jun 2017 12:20:11: #2.2 Generate R script for model : SRX982089.05_model.r WARNING @ Sat, 03 Jun 2017 12:20:11: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:20:11: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sat, 03 Jun 2017 12:20:11: #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 12:20:11: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:20:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:20:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:21:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:21:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:21:38: #4 Write output xls file... SRX982089.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:21:38: #4 Write peak in narrowPeak format file... SRX982089.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:21:38: #4 Write summits bed file... SRX982089.10_summits.bed INFO @ Sat, 03 Jun 2017 12:21:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (392 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:21:50: #4 Write output xls file... SRX982089.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:21:50: #4 Write peak in narrowPeak format file... SRX982089.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:21:50: #4 Write summits bed file... SRX982089.20_summits.bed INFO @ Sat, 03 Jun 2017 12:21:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (224 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:21:52: #4 Write output xls file... SRX982089.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:21:52: #4 Write peak in narrowPeak format file... SRX982089.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:21:52: #4 Write summits bed file... SRX982089.05_summits.bed INFO @ Sat, 03 Jun 2017 12:21:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (560 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。