Job ID = 9028901 sra ファイルのダウンロード中... Completed: 75301K bytes transferred in 3 seconds (162309K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 22318 0 22318 0 0 2553 0 --:--:-- 0:00:08 --:--:-- 10622 100 48141 0 48141 0 0 5118 0 --:--:-- 0:00:09 --:--:-- 17410 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 3246383 spots for /home/okishinya/chipatlas/results/ce10/SRX982100/SRR1956587.sra Written 3246383 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: 00:00:52 3246383 reads; of these: 3246383 (100.00%) were unpaired; of these: 78210 (2.41%) aligned 0 times 2629487 (81.00%) aligned exactly 1 time 538686 (16.59%) aligned >1 times 97.59% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 282341 / 3168173 = 0.0891 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 12:17:23: # Command line: callpeak -t SRX982100.bam -f BAM -g ce -n SRX982100.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982100.10 # format = BAM # ChIP-seq file = ['SRX982100.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 12:17:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:17:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:17:23: # Command line: callpeak -t SRX982100.bam -f BAM -g ce -n SRX982100.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982100.20 # format = BAM # ChIP-seq file = ['SRX982100.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 12:17:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:17:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:17:23: # Command line: callpeak -t SRX982100.bam -f BAM -g ce -n SRX982100.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982100.05 # format = BAM # ChIP-seq file = ['SRX982100.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 12:17:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:17:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:17:29: 1000000 INFO @ Sat, 03 Jun 2017 12:17:29: 1000000 INFO @ Sat, 03 Jun 2017 12:17:29: 1000000 INFO @ Sat, 03 Jun 2017 12:17:35: 2000000 INFO @ Sat, 03 Jun 2017 12:17:35: 2000000 INFO @ Sat, 03 Jun 2017 12:17:35: 2000000 INFO @ Sat, 03 Jun 2017 12:17:40: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:17:40: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:17:40: #1 total tags in treatment: 2885832 INFO @ Sat, 03 Jun 2017 12:17:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:17:40: #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 12:17:40: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:17:40: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:17:40: #1 total tags in treatment: 2885832 INFO @ Sat, 03 Jun 2017 12:17:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:17:40: #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 12:17:40: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:17:40: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:17:40: #1 total tags in treatment: 2885832 INFO @ Sat, 03 Jun 2017 12:17:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:17:40: #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 12:17:41: #1 tags after filtering in treatment: 2885514 INFO @ Sat, 03 Jun 2017 12:17:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:17:41: #1 finished! INFO @ Sat, 03 Jun 2017 12:17:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:17:41: #1 tags after filtering in treatment: 2885514 INFO @ Sat, 03 Jun 2017 12:17:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:17:41: #1 finished! INFO @ Sat, 03 Jun 2017 12:17:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:17:41: #1 tags after filtering in treatment: 2885514 INFO @ Sat, 03 Jun 2017 12:17:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:17:41: #1 finished! INFO @ Sat, 03 Jun 2017 12:17:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:17:41: #2 number of paired peaks: 405 WARNING @ Sat, 03 Jun 2017 12:17:41: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Sat, 03 Jun 2017 12:17:41: start model_add_line... INFO @ Sat, 03 Jun 2017 12:17:42: #2 number of paired peaks: 405 WARNING @ Sat, 03 Jun 2017 12:17:42: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Sat, 03 Jun 2017 12:17:42: start model_add_line... INFO @ Sat, 03 Jun 2017 12:17:42: #2 number of paired peaks: 405 WARNING @ Sat, 03 Jun 2017 12:17:42: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Sat, 03 Jun 2017 12:17:42: start model_add_line... INFO @ Sat, 03 Jun 2017 12:17:43: start X-correlation... INFO @ Sat, 03 Jun 2017 12:17:43: end of X-cor INFO @ Sat, 03 Jun 2017 12:17:43: #2 finished! INFO @ Sat, 03 Jun 2017 12:17:43: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:17:43: #2 alternative fragment length(s) may be 49,465 bps INFO @ Sat, 03 Jun 2017 12:17:43: #2.2 Generate R script for model : SRX982100.05_model.r WARNING @ Sat, 03 Jun 2017 12:17:43: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:17:43: #2 You may need to consider one of the other alternative d(s): 49,465 WARNING @ Sat, 03 Jun 2017 12:17:43: #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 12:17:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:17:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:17:44: start X-correlation... INFO @ Sat, 03 Jun 2017 12:17:44: end of X-cor INFO @ Sat, 03 Jun 2017 12:17:44: #2 finished! INFO @ Sat, 03 Jun 2017 12:17:44: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:17:44: #2 alternative fragment length(s) may be 49,465 bps INFO @ Sat, 03 Jun 2017 12:17:44: #2.2 Generate R script for model : SRX982100.20_model.r WARNING @ Sat, 03 Jun 2017 12:17:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:17:44: #2 You may need to consider one of the other alternative d(s): 49,465 WARNING @ Sat, 03 Jun 2017 12:17:44: #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 12:17:44: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:17:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:17:44: start X-correlation... INFO @ Sat, 03 Jun 2017 12:17:44: end of X-cor INFO @ Sat, 03 Jun 2017 12:17:44: #2 finished! INFO @ Sat, 03 Jun 2017 12:17:44: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 12:17:44: #2 alternative fragment length(s) may be 49,465 bps INFO @ Sat, 03 Jun 2017 12:17:44: #2.2 Generate R script for model : SRX982100.10_model.r WARNING @ Sat, 03 Jun 2017 12:17:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:17:44: #2 You may need to consider one of the other alternative d(s): 49,465 WARNING @ Sat, 03 Jun 2017 12:17:44: #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 12:17:44: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:17:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:18:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:18:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:18:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:18:13: #4 Write output xls file... SRX982100.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:18:13: #4 Write peak in narrowPeak format file... SRX982100.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:18:13: #4 Write summits bed file... SRX982100.05_summits.bed INFO @ Sat, 03 Jun 2017 12:18:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:18:14: #4 Write output xls file... SRX982100.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:18:14: #4 Write peak in narrowPeak format file... SRX982100.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:18:14: #4 Write summits bed file... SRX982100.20_summits.bed INFO @ Sat, 03 Jun 2017 12:18:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (92 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:18:15: #4 Write output xls file... SRX982100.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:18:15: #4 Write peak in narrowPeak format file... SRX982100.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:18:15: #4 Write summits bed file... SRX982100.10_summits.bed INFO @ Sat, 03 Jun 2017 12:18:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。