Job ID = 9028849 sra ファイルのダウンロード中... Completed: 404546K bytes transferred in 6 seconds (498953K 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 1906 0 --:--:-- 0:00:07 --:--:-- 15205 100 38318 0 38318 0 0 4593 0 --:--:-- 0:00:08 --:--:-- 21636 100 51731 0 51731 0 0 6079 0 --:--:-- 0:00:08 --:--:-- 26692 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 11868925 spots for /home/okishinya/chipatlas/results/ce10/SRX982076/SRR1956556.sra Written 11868925 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: 00:03:44 11868925 reads; of these: 11868925 (100.00%) were unpaired; of these: 130217 (1.10%) aligned 0 times 9535754 (80.34%) aligned exactly 1 time 2202954 (18.56%) aligned >1 times 98.90% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 1069641 / 11738708 = 0.0911 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 12:08:49: # Command line: callpeak -t SRX982076.bam -f BAM -g ce -n SRX982076.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982076.20 # format = BAM # ChIP-seq file = ['SRX982076.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 12:08:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:49: # Command line: callpeak -t SRX982076.bam -f BAM -g ce -n SRX982076.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982076.05 # format = BAM # ChIP-seq file = ['SRX982076.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 12:08:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:49: # Command line: callpeak -t SRX982076.bam -f BAM -g ce -n SRX982076.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982076.10 # format = BAM # ChIP-seq file = ['SRX982076.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 12:08:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:56: 1000000 INFO @ Sat, 03 Jun 2017 12:08:56: 1000000 INFO @ Sat, 03 Jun 2017 12:08:56: 1000000 INFO @ Sat, 03 Jun 2017 12:09:03: 2000000 INFO @ Sat, 03 Jun 2017 12:09:04: 2000000 INFO @ Sat, 03 Jun 2017 12:09:04: 2000000 INFO @ Sat, 03 Jun 2017 12:09:11: 3000000 INFO @ Sat, 03 Jun 2017 12:09:12: 3000000 INFO @ Sat, 03 Jun 2017 12:09:12: 3000000 INFO @ Sat, 03 Jun 2017 12:09:18: 4000000 INFO @ Sat, 03 Jun 2017 12:09:20: 4000000 INFO @ Sat, 03 Jun 2017 12:09:21: 4000000 INFO @ Sat, 03 Jun 2017 12:09:26: 5000000 INFO @ Sat, 03 Jun 2017 12:09:28: 5000000 INFO @ Sat, 03 Jun 2017 12:09:29: 5000000 INFO @ Sat, 03 Jun 2017 12:09:33: 6000000 INFO @ Sat, 03 Jun 2017 12:09:36: 6000000 INFO @ Sat, 03 Jun 2017 12:09:37: 6000000 INFO @ Sat, 03 Jun 2017 12:09:41: 7000000 INFO @ Sat, 03 Jun 2017 12:09:44: 7000000 INFO @ Sat, 03 Jun 2017 12:09:45: 7000000 INFO @ Sat, 03 Jun 2017 12:09:48: 8000000 INFO @ Sat, 03 Jun 2017 12:09:52: 8000000 INFO @ Sat, 03 Jun 2017 12:09:52: 8000000 INFO @ Sat, 03 Jun 2017 12:09:56: 9000000 INFO @ Sat, 03 Jun 2017 12:10:00: 9000000 INFO @ Sat, 03 Jun 2017 12:10:00: 9000000 INFO @ Sat, 03 Jun 2017 12:10:03: 10000000 INFO @ Sat, 03 Jun 2017 12:10:08: 10000000 INFO @ Sat, 03 Jun 2017 12:10:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:10:09: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:10:09: #1 total tags in treatment: 10669067 INFO @ Sat, 03 Jun 2017 12:10:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:10:09: #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 12:10:09: 10000000 INFO @ Sat, 03 Jun 2017 12:10:11: #1 tags after filtering in treatment: 10667883 INFO @ Sat, 03 Jun 2017 12:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:10:11: #1 finished! INFO @ Sat, 03 Jun 2017 12:10:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:10:13: #2 number of paired peaks: 343 WARNING @ Sat, 03 Jun 2017 12:10:13: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Sat, 03 Jun 2017 12:10:13: start model_add_line... INFO @ Sat, 03 Jun 2017 12:10:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:10:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:10:14: #1 total tags in treatment: 10669067 INFO @ Sat, 03 Jun 2017 12:10:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:10:14: #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 12:10:15: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:10:15: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:10:15: #1 total tags in treatment: 10669067 INFO @ Sat, 03 Jun 2017 12:10:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:10:15: #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 12:10:16: #1 tags after filtering in treatment: 10667883 INFO @ Sat, 03 Jun 2017 12:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:10:16: #1 finished! INFO @ Sat, 03 Jun 2017 12:10:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:10:18: start X-correlation... INFO @ Sat, 03 Jun 2017 12:10:18: end of X-cor INFO @ Sat, 03 Jun 2017 12:10:18: #2 finished! INFO @ Sat, 03 Jun 2017 12:10:18: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 12:10:18: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sat, 03 Jun 2017 12:10:18: #2.2 Generate R script for model : SRX982076.20_model.r WARNING @ Sat, 03 Jun 2017 12:10:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:10:18: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sat, 03 Jun 2017 12:10:18: #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 12:10:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:10:18: #1 tags after filtering in treatment: 10667883 INFO @ Sat, 03 Jun 2017 12:10:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:10:18: #1 finished! INFO @ Sat, 03 Jun 2017 12:10:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:10:18: #2 number of paired peaks: 343 WARNING @ Sat, 03 Jun 2017 12:10:18: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Sat, 03 Jun 2017 12:10:18: start model_add_line... INFO @ Sat, 03 Jun 2017 12:10:19: #2 number of paired peaks: 343 WARNING @ Sat, 03 Jun 2017 12:10:19: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Sat, 03 Jun 2017 12:10:19: start model_add_line... INFO @ Sat, 03 Jun 2017 12:10:23: start X-correlation... INFO @ Sat, 03 Jun 2017 12:10:23: end of X-cor INFO @ Sat, 03 Jun 2017 12:10:23: #2 finished! INFO @ Sat, 03 Jun 2017 12:10:23: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 12:10:23: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sat, 03 Jun 2017 12:10:23: #2.2 Generate R script for model : SRX982076.05_model.r WARNING @ Sat, 03 Jun 2017 12:10:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:10:23: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sat, 03 Jun 2017 12:10:23: #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 12:10:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:10:24: start X-correlation... INFO @ Sat, 03 Jun 2017 12:10:24: end of X-cor INFO @ Sat, 03 Jun 2017 12:10:24: #2 finished! INFO @ Sat, 03 Jun 2017 12:10:24: #2 predicted fragment length is 48 bps INFO @ Sat, 03 Jun 2017 12:10:24: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sat, 03 Jun 2017 12:10:24: #2.2 Generate R script for model : SRX982076.10_model.r WARNING @ Sat, 03 Jun 2017 12:10:24: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:10:24: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sat, 03 Jun 2017 12:10:24: #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 12:10:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:11:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:11:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:11:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:11:52: #4 Write output xls file... SRX982076.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:11:52: #4 Write peak in narrowPeak format file... SRX982076.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:11:52: #4 Write summits bed file... SRX982076.20_summits.bed INFO @ Sat, 03 Jun 2017 12:11:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:11:57: #4 Write output xls file... SRX982076.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:11:57: #4 Write peak in narrowPeak format file... SRX982076.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:11:57: #4 Write summits bed file... SRX982076.05_summits.bed INFO @ Sat, 03 Jun 2017 12:11:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (763 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:12:05: #4 Write output xls file... SRX982076.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:12:05: #4 Write peak in narrowPeak format file... SRX982076.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:12:05: #4 Write summits bed file... SRX982076.10_summits.bed INFO @ Sat, 03 Jun 2017 12:12:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (378 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。