Job ID = 9028920 sra ファイルのダウンロード中... Completed: 220891K bytes transferred in 5 seconds (346816K 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 22318 0 22318 0 0 2753 0 --:--:-- 0:00:08 --:--:-- 14343 100 44726 0 44726 0 0 5005 0 --:--:-- 0:00:08 --:--:-- 18753 100 54917 0 54917 0 0 6033 0 --:--:-- 0:00:09 --:--:-- 21519 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 9510751 spots for /home/okishinya/chipatlas/results/ce10/SRX982109/SRR1956599.sra Written 9510751 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: 00:01:58 9510751 reads; of these: 9510751 (100.00%) were unpaired; of these: 3883041 (40.83%) aligned 0 times 4763191 (50.08%) aligned exactly 1 time 864519 (9.09%) aligned >1 times 59.17% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 304752 / 5627710 = 0.0542 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 12:26:06: # Command line: callpeak -t SRX982109.bam -f BAM -g ce -n SRX982109.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982109.10 # format = BAM # ChIP-seq file = ['SRX982109.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 12:26:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:26:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:26:06: # Command line: callpeak -t SRX982109.bam -f BAM -g ce -n SRX982109.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982109.20 # format = BAM # ChIP-seq file = ['SRX982109.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 12:26:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:26:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:26:06: # Command line: callpeak -t SRX982109.bam -f BAM -g ce -n SRX982109.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982109.05 # format = BAM # ChIP-seq file = ['SRX982109.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 12:26:06: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:26:06: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:26:13: 1000000 INFO @ Sat, 03 Jun 2017 12:26:13: 1000000 INFO @ Sat, 03 Jun 2017 12:26:13: 1000000 INFO @ Sat, 03 Jun 2017 12:26:21: 2000000 INFO @ Sat, 03 Jun 2017 12:26:21: 2000000 INFO @ Sat, 03 Jun 2017 12:26:21: 2000000 INFO @ Sat, 03 Jun 2017 12:26:29: 3000000 INFO @ Sat, 03 Jun 2017 12:26:29: 3000000 INFO @ Sat, 03 Jun 2017 12:26:29: 3000000 INFO @ Sat, 03 Jun 2017 12:26:36: 4000000 INFO @ Sat, 03 Jun 2017 12:26:36: 4000000 INFO @ Sat, 03 Jun 2017 12:26:36: 4000000 INFO @ Sat, 03 Jun 2017 12:26:42: 5000000 INFO @ Sat, 03 Jun 2017 12:26:43: 5000000 INFO @ Sat, 03 Jun 2017 12:26:43: 5000000 INFO @ Sat, 03 Jun 2017 12:26:44: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:26:44: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:26:44: #1 total tags in treatment: 5322958 INFO @ Sat, 03 Jun 2017 12:26:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:26:44: #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 12:26:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:26:45: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:26:45: #1 total tags in treatment: 5322958 INFO @ Sat, 03 Jun 2017 12:26:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:26:45: #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 12:26:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:26:45: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:26:45: #1 total tags in treatment: 5322958 INFO @ Sat, 03 Jun 2017 12:26:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:26:45: #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 12:26:45: #1 tags after filtering in treatment: 5322452 INFO @ Sat, 03 Jun 2017 12:26:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:26:45: #1 finished! INFO @ Sat, 03 Jun 2017 12:26:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:26:46: #1 tags after filtering in treatment: 5322452 INFO @ Sat, 03 Jun 2017 12:26:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:26:46: #1 finished! INFO @ Sat, 03 Jun 2017 12:26:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:26:46: #1 tags after filtering in treatment: 5322452 INFO @ Sat, 03 Jun 2017 12:26:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:26:46: #1 finished! INFO @ Sat, 03 Jun 2017 12:26:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:26:46: #2 number of paired peaks: 327 WARNING @ Sat, 03 Jun 2017 12:26:46: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Sat, 03 Jun 2017 12:26:46: start model_add_line... INFO @ Sat, 03 Jun 2017 12:26:47: #2 number of paired peaks: 327 WARNING @ Sat, 03 Jun 2017 12:26:47: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Sat, 03 Jun 2017 12:26:47: start model_add_line... INFO @ Sat, 03 Jun 2017 12:26:47: #2 number of paired peaks: 327 WARNING @ Sat, 03 Jun 2017 12:26:47: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Sat, 03 Jun 2017 12:26:47: start model_add_line... INFO @ Sat, 03 Jun 2017 12:26:49: start X-correlation... INFO @ Sat, 03 Jun 2017 12:26:49: end of X-cor INFO @ Sat, 03 Jun 2017 12:26:49: #2 finished! INFO @ Sat, 03 Jun 2017 12:26:49: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:26:49: #2 alternative fragment length(s) may be 4,51,496,563,576 bps INFO @ Sat, 03 Jun 2017 12:26:49: #2.2 Generate R script for model : SRX982109.20_model.r WARNING @ Sat, 03 Jun 2017 12:26:49: #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 12:26:49: #2 You may need to consider one of the other alternative d(s): 4,51,496,563,576 WARNING @ Sat, 03 Jun 2017 12:26:49: #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 12:26:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:26:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:26:50: start X-correlation... INFO @ Sat, 03 Jun 2017 12:26:50: end of X-cor INFO @ Sat, 03 Jun 2017 12:26:50: #2 finished! INFO @ Sat, 03 Jun 2017 12:26:50: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:26:50: #2 alternative fragment length(s) may be 4,51,496,563,576 bps INFO @ Sat, 03 Jun 2017 12:26:50: #2.2 Generate R script for model : SRX982109.10_model.r WARNING @ Sat, 03 Jun 2017 12:26:50: #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 12:26:50: #2 You may need to consider one of the other alternative d(s): 4,51,496,563,576 WARNING @ Sat, 03 Jun 2017 12:26:50: #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 12:26:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:26:50: start X-correlation... INFO @ Sat, 03 Jun 2017 12:26:50: end of X-cor INFO @ Sat, 03 Jun 2017 12:26:50: #2 finished! INFO @ Sat, 03 Jun 2017 12:26:50: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 12:26:50: #2 alternative fragment length(s) may be 4,51,496,563,576 bps INFO @ Sat, 03 Jun 2017 12:26:50: #2.2 Generate R script for model : SRX982109.05_model.r WARNING @ Sat, 03 Jun 2017 12:26:50: #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 12:26:50: #2 You may need to consider one of the other alternative d(s): 4,51,496,563,576 WARNING @ Sat, 03 Jun 2017 12:26:50: #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 12:26:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:27:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:27:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:27:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:27:40: #4 Write output xls file... SRX982109.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:40: #4 Write peak in narrowPeak format file... SRX982109.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:40: #4 Write summits bed file... SRX982109.10_summits.bed INFO @ Sat, 03 Jun 2017 12:27:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (266 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:27:41: #4 Write output xls file... SRX982109.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:41: #4 Write peak in narrowPeak format file... SRX982109.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:41: #4 Write summits bed file... SRX982109.20_summits.bed INFO @ Sat, 03 Jun 2017 12:27:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (106 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:27:44: #4 Write output xls file... SRX982109.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:44: #4 Write peak in narrowPeak format file... SRX982109.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:44: #4 Write summits bed file... SRX982109.05_summits.bed INFO @ Sat, 03 Jun 2017 12:27:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (444 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。