Job ID = 9028897 sra ファイルのダウンロード中... Completed: 205493K bytes transferred in 4 seconds (347108K 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 --:--:-- 0:00:06 --:--:-- 0 100 22318 0 22318 0 0 2903 0 --:--:-- 0:00:07 --:--:-- 17740 100 45479 0 45479 0 0 5340 0 --:--:-- 0:00:08 --:--:-- 21781 100 47350 0 47350 0 0 5559 0 --:--:-- 0:00:08 --:--:-- 22677 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 6722011 spots for /home/okishinya/chipatlas/results/ce10/SRX982098/SRR1956585.sra Written 6722011 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: 00:02:01 6722011 reads; of these: 6722011 (100.00%) were unpaired; of these: 301547 (4.49%) aligned 0 times 5375872 (79.97%) aligned exactly 1 time 1044592 (15.54%) aligned >1 times 95.51% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 326861 / 6420464 = 0.0509 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 12:18:22: # Command line: callpeak -t SRX982098.bam -f BAM -g ce -n SRX982098.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982098.05 # format = BAM # ChIP-seq file = ['SRX982098.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 12:18:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:18:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:18:22: # Command line: callpeak -t SRX982098.bam -f BAM -g ce -n SRX982098.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982098.20 # format = BAM # ChIP-seq file = ['SRX982098.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 12:18:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:18:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:18:22: # Command line: callpeak -t SRX982098.bam -f BAM -g ce -n SRX982098.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982098.10 # format = BAM # ChIP-seq file = ['SRX982098.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 12:18:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:18:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:18:30: 1000000 INFO @ Sat, 03 Jun 2017 12:18:31: 1000000 INFO @ Sat, 03 Jun 2017 12:18:31: 1000000 INFO @ Sat, 03 Jun 2017 12:18:38: 2000000 INFO @ Sat, 03 Jun 2017 12:18:39: 2000000 INFO @ Sat, 03 Jun 2017 12:18:39: 2000000 INFO @ Sat, 03 Jun 2017 12:18:46: 3000000 INFO @ Sat, 03 Jun 2017 12:18:46: 3000000 INFO @ Sat, 03 Jun 2017 12:18:48: 3000000 INFO @ Sat, 03 Jun 2017 12:18:53: 4000000 INFO @ Sat, 03 Jun 2017 12:18:53: 4000000 INFO @ Sat, 03 Jun 2017 12:18:55: 4000000 INFO @ Sat, 03 Jun 2017 12:19:00: 5000000 INFO @ Sat, 03 Jun 2017 12:19:00: 5000000 INFO @ Sat, 03 Jun 2017 12:19:02: 5000000 INFO @ Sat, 03 Jun 2017 12:19:06: 6000000 INFO @ Sat, 03 Jun 2017 12:19:07: 6000000 INFO @ Sat, 03 Jun 2017 12:19:07: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:19:07: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:19:07: #1 total tags in treatment: 6093603 INFO @ Sat, 03 Jun 2017 12:19:07: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:19:07: #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 12:19:08: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:19:08: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:19:08: #1 total tags in treatment: 6093603 INFO @ Sat, 03 Jun 2017 12:19:08: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:19:08: #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 12:19:08: #1 tags after filtering in treatment: 6093120 INFO @ Sat, 03 Jun 2017 12:19:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:19:08: #1 finished! INFO @ Sat, 03 Jun 2017 12:19:08: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:19:09: 6000000 INFO @ Sat, 03 Jun 2017 12:19:09: #1 tags after filtering in treatment: 6093120 INFO @ Sat, 03 Jun 2017 12:19:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:19:09: #1 finished! INFO @ Sat, 03 Jun 2017 12:19:09: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:19:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:19:09: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:19:09: #1 total tags in treatment: 6093603 INFO @ Sat, 03 Jun 2017 12:19:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:19:09: #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 12:19:09: #2 number of paired peaks: 351 WARNING @ Sat, 03 Jun 2017 12:19:09: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Sat, 03 Jun 2017 12:19:09: start model_add_line... INFO @ Sat, 03 Jun 2017 12:19:10: #2 number of paired peaks: 351 WARNING @ Sat, 03 Jun 2017 12:19:10: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Sat, 03 Jun 2017 12:19:10: start model_add_line... INFO @ Sat, 03 Jun 2017 12:19:11: #1 tags after filtering in treatment: 6093120 INFO @ Sat, 03 Jun 2017 12:19:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:19:11: #1 finished! INFO @ Sat, 03 Jun 2017 12:19:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:19:12: #2 number of paired peaks: 351 WARNING @ Sat, 03 Jun 2017 12:19:12: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Sat, 03 Jun 2017 12:19:12: start model_add_line... INFO @ Sat, 03 Jun 2017 12:19:13: start X-correlation... INFO @ Sat, 03 Jun 2017 12:19:13: end of X-cor INFO @ Sat, 03 Jun 2017 12:19:13: #2 finished! INFO @ Sat, 03 Jun 2017 12:19:13: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:19:13: #2 alternative fragment length(s) may be 4,51,557 bps INFO @ Sat, 03 Jun 2017 12:19:13: #2.2 Generate R script for model : SRX982098.20_model.r WARNING @ Sat, 03 Jun 2017 12:19:13: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:19:13: #2 You may need to consider one of the other alternative d(s): 4,51,557 WARNING @ Sat, 03 Jun 2017 12:19:13: #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 12:19:13: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:19:13: start X-correlation... INFO @ Sat, 03 Jun 2017 12:19:13: end of X-cor INFO @ Sat, 03 Jun 2017 12:19:13: #2 finished! INFO @ Sat, 03 Jun 2017 12:19:13: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:19:13: #2 alternative fragment length(s) may be 4,51,557 bps INFO @ Sat, 03 Jun 2017 12:19:13: #2.2 Generate R script for model : SRX982098.10_model.r WARNING @ Sat, 03 Jun 2017 12:19:13: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:19:13: #2 You may need to consider one of the other alternative d(s): 4,51,557 WARNING @ Sat, 03 Jun 2017 12:19:13: #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 12:19:13: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:19:15: start X-correlation... INFO @ Sat, 03 Jun 2017 12:19:15: end of X-cor INFO @ Sat, 03 Jun 2017 12:19:15: #2 finished! INFO @ Sat, 03 Jun 2017 12:19:15: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:19:15: #2 alternative fragment length(s) may be 4,51,557 bps INFO @ Sat, 03 Jun 2017 12:19:15: #2.2 Generate R script for model : SRX982098.05_model.r WARNING @ Sat, 03 Jun 2017 12:19:15: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:19:15: #2 You may need to consider one of the other alternative d(s): 4,51,557 WARNING @ Sat, 03 Jun 2017 12:19:15: #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 12:19:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:19:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:19:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:19:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:19:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:20:13: #4 Write output xls file... SRX982098.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:20:13: #4 Write peak in narrowPeak format file... SRX982098.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:20:13: #4 Write summits bed file... SRX982098.20_summits.bed INFO @ Sat, 03 Jun 2017 12:20:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:20:14: #4 Write output xls file... SRX982098.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:20:14: #4 Write peak in narrowPeak format file... SRX982098.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:20:14: #4 Write summits bed file... SRX982098.10_summits.bed INFO @ Sat, 03 Jun 2017 12:20:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (298 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:20:16: #4 Write output xls file... SRX982098.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:20:16: #4 Write peak in narrowPeak format file... SRX982098.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:20:16: #4 Write summits bed file... SRX982098.05_summits.bed INFO @ Sat, 03 Jun 2017 12:20:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (464 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。