Job ID = 9025524 sra ファイルのダウンロード中... Completed: 150041K bytes transferred in 4 seconds (278185K 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 1943 0 --:--:-- 0:00:07 --:--:-- 14812 100 45239 0 45239 0 0 5516 0 --:--:-- 0:00:08 --:--:-- 25174 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 6497093 spots for /home/okishinya/chipatlas/results/ce10/SRX1388773/SRR2832489.sra Written 6497093 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: 00:02:05 6497093 reads; of these: 6497093 (100.00%) were unpaired; of these: 177029 (2.72%) aligned 0 times 4761169 (73.28%) aligned exactly 1 time 1558895 (23.99%) aligned >1 times 97.28% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 540096 / 6320064 = 0.0855 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 04:17:44: # Command line: callpeak -t SRX1388773.bam -f BAM -g ce -n SRX1388773.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388773.20 # format = BAM # ChIP-seq file = ['SRX1388773.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 04:17:44: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:17:44: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:17:44: # Command line: callpeak -t SRX1388773.bam -f BAM -g ce -n SRX1388773.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388773.10 # format = BAM # ChIP-seq file = ['SRX1388773.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 04:17:44: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:17:44: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:17:44: # Command line: callpeak -t SRX1388773.bam -f BAM -g ce -n SRX1388773.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388773.05 # format = BAM # ChIP-seq file = ['SRX1388773.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 04:17:44: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:17:44: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:17:50: 1000000 INFO @ Sat, 03 Jun 2017 04:17:50: 1000000 INFO @ Sat, 03 Jun 2017 04:17:50: 1000000 INFO @ Sat, 03 Jun 2017 04:17:55: 2000000 INFO @ Sat, 03 Jun 2017 04:17:55: 2000000 INFO @ Sat, 03 Jun 2017 04:17:55: 2000000 INFO @ Sat, 03 Jun 2017 04:18:01: 3000000 INFO @ Sat, 03 Jun 2017 04:18:01: 3000000 INFO @ Sat, 03 Jun 2017 04:18:01: 3000000 INFO @ Sat, 03 Jun 2017 04:18:07: 4000000 INFO @ Sat, 03 Jun 2017 04:18:07: 4000000 INFO @ Sat, 03 Jun 2017 04:18:07: 4000000 INFO @ Sat, 03 Jun 2017 04:18:12: 5000000 INFO @ Sat, 03 Jun 2017 04:18:12: 5000000 INFO @ Sat, 03 Jun 2017 04:18:13: 5000000 INFO @ Sat, 03 Jun 2017 04:18:16: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:18:16: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:18:16: #1 total tags in treatment: 5779968 INFO @ Sat, 03 Jun 2017 04:18:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:18:16: #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 04:18:17: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:18:17: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:18:17: #1 total tags in treatment: 5779968 INFO @ Sat, 03 Jun 2017 04:18:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:18:17: #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 04:18:17: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:18:17: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:18:17: #1 total tags in treatment: 5779968 INFO @ Sat, 03 Jun 2017 04:18:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:18:17: #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 04:18:17: #1 tags after filtering in treatment: 5779030 INFO @ Sat, 03 Jun 2017 04:18:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:18:17: #1 finished! INFO @ Sat, 03 Jun 2017 04:18:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:18:18: #1 tags after filtering in treatment: 5779030 INFO @ Sat, 03 Jun 2017 04:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:18:18: #1 finished! INFO @ Sat, 03 Jun 2017 04:18:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:18:18: #1 tags after filtering in treatment: 5779030 INFO @ Sat, 03 Jun 2017 04:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:18:18: #1 finished! INFO @ Sat, 03 Jun 2017 04:18:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:18:19: #2 number of paired peaks: 879 WARNING @ Sat, 03 Jun 2017 04:18:19: Fewer paired peaks (879) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 879 pairs to build model! INFO @ Sat, 03 Jun 2017 04:18:19: start model_add_line... INFO @ Sat, 03 Jun 2017 04:18:19: #2 number of paired peaks: 879 WARNING @ Sat, 03 Jun 2017 04:18:19: Fewer paired peaks (879) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 879 pairs to build model! INFO @ Sat, 03 Jun 2017 04:18:19: start model_add_line... INFO @ Sat, 03 Jun 2017 04:18:20: #2 number of paired peaks: 879 WARNING @ Sat, 03 Jun 2017 04:18:20: Fewer paired peaks (879) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 879 pairs to build model! INFO @ Sat, 03 Jun 2017 04:18:20: start model_add_line... INFO @ Sat, 03 Jun 2017 04:18:25: start X-correlation... INFO @ Sat, 03 Jun 2017 04:18:25: end of X-cor INFO @ Sat, 03 Jun 2017 04:18:25: #2 finished! INFO @ Sat, 03 Jun 2017 04:18:25: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 04:18:25: #2 alternative fragment length(s) may be 4,55,576,590 bps INFO @ Sat, 03 Jun 2017 04:18:25: #2.2 Generate R script for model : SRX1388773.05_model.r WARNING @ Sat, 03 Jun 2017 04:18:25: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:18:25: #2 You may need to consider one of the other alternative d(s): 4,55,576,590 WARNING @ Sat, 03 Jun 2017 04:18:25: #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 04:18:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:18:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:18:26: start X-correlation... INFO @ Sat, 03 Jun 2017 04:18:26: end of X-cor INFO @ Sat, 03 Jun 2017 04:18:26: #2 finished! INFO @ Sat, 03 Jun 2017 04:18:26: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 04:18:26: #2 alternative fragment length(s) may be 4,55,576,590 bps INFO @ Sat, 03 Jun 2017 04:18:26: #2.2 Generate R script for model : SRX1388773.20_model.r WARNING @ Sat, 03 Jun 2017 04:18:26: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:18:26: #2 You may need to consider one of the other alternative d(s): 4,55,576,590 WARNING @ Sat, 03 Jun 2017 04:18:26: #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 04:18:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:18:26: start X-correlation... INFO @ Sat, 03 Jun 2017 04:18:26: end of X-cor INFO @ Sat, 03 Jun 2017 04:18:26: #2 finished! INFO @ Sat, 03 Jun 2017 04:18:26: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 04:18:26: #2 alternative fragment length(s) may be 4,55,576,590 bps INFO @ Sat, 03 Jun 2017 04:18:26: #2.2 Generate R script for model : SRX1388773.10_model.r WARNING @ Sat, 03 Jun 2017 04:18:26: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:18:26: #2 You may need to consider one of the other alternative d(s): 4,55,576,590 WARNING @ Sat, 03 Jun 2017 04:18:26: #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 04:18:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:18:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:18:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:18:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:19:21: #4 Write output xls file... SRX1388773.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:19:21: #4 Write peak in narrowPeak format file... SRX1388773.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:19:21: #4 Write summits bed file... SRX1388773.10_summits.bed INFO @ Sat, 03 Jun 2017 04:19:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (374 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:19:21: #4 Write output xls file... SRX1388773.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:19:21: #4 Write peak in narrowPeak format file... SRX1388773.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:19:21: #4 Write summits bed file... SRX1388773.05_summits.bed INFO @ Sat, 03 Jun 2017 04:19:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (600 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:19:22: #4 Write output xls file... SRX1388773.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:19:22: #4 Write peak in narrowPeak format file... SRX1388773.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:19:22: #4 Write summits bed file... SRX1388773.20_summits.bed INFO @ Sat, 03 Jun 2017 04:19:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (161 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。