Job ID = 9028886 sra ファイルのダウンロード中... Completed: 410462K bytes transferred in 6 seconds (512397K 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 1955 0 --:--:-- 0:00:07 --:--:-- 15157 100 53042 0 53042 0 0 6503 0 --:--:-- 0:00:08 --:--:-- 29899 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 12160308 spots for /home/okishinya/chipatlas/results/ce10/SRX982093/SRR1956580.sra Written 12160308 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: 00:04:32 12160308 reads; of these: 12160308 (100.00%) were unpaired; of these: 769013 (6.32%) aligned 0 times 8274139 (68.04%) aligned exactly 1 time 3117156 (25.63%) aligned >1 times 93.68% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 2231529 / 11391295 = 0.1959 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 12:19:11: # Command line: callpeak -t SRX982093.bam -f BAM -g ce -n SRX982093.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982093.10 # format = BAM # ChIP-seq file = ['SRX982093.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 12:19:11: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:19:11: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:19:11: # Command line: callpeak -t SRX982093.bam -f BAM -g ce -n SRX982093.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982093.20 # format = BAM # ChIP-seq file = ['SRX982093.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 12:19:11: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:19:11: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:19:11: # Command line: callpeak -t SRX982093.bam -f BAM -g ce -n SRX982093.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982093.05 # format = BAM # ChIP-seq file = ['SRX982093.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 12:19:11: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:19:11: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:19:17: 1000000 INFO @ Sat, 03 Jun 2017 12:19:17: 1000000 INFO @ Sat, 03 Jun 2017 12:19:17: 1000000 INFO @ Sat, 03 Jun 2017 12:19:23: 2000000 INFO @ Sat, 03 Jun 2017 12:19:24: 2000000 INFO @ Sat, 03 Jun 2017 12:19:24: 2000000 INFO @ Sat, 03 Jun 2017 12:19:28: 3000000 INFO @ Sat, 03 Jun 2017 12:19:30: 3000000 INFO @ Sat, 03 Jun 2017 12:19:31: 3000000 INFO @ Sat, 03 Jun 2017 12:19:33: 4000000 INFO @ Sat, 03 Jun 2017 12:19:37: 4000000 INFO @ Sat, 03 Jun 2017 12:19:38: 4000000 INFO @ Sat, 03 Jun 2017 12:19:39: 5000000 INFO @ Sat, 03 Jun 2017 12:19:43: 5000000 INFO @ Sat, 03 Jun 2017 12:19:44: 6000000 INFO @ Sat, 03 Jun 2017 12:19:45: 5000000 INFO @ Sat, 03 Jun 2017 12:19:50: 7000000 INFO @ Sat, 03 Jun 2017 12:19:50: 6000000 INFO @ Sat, 03 Jun 2017 12:19:53: 6000000 INFO @ Sat, 03 Jun 2017 12:19:55: 8000000 INFO @ Sat, 03 Jun 2017 12:19:56: 7000000 INFO @ Sat, 03 Jun 2017 12:19:59: 7000000 INFO @ Sat, 03 Jun 2017 12:20:01: 9000000 INFO @ Sat, 03 Jun 2017 12:20:02: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:20:02: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:20:02: #1 total tags in treatment: 9159766 INFO @ Sat, 03 Jun 2017 12:20:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:20:02: #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 12:20:03: 8000000 INFO @ Sat, 03 Jun 2017 12:20:03: #1 tags after filtering in treatment: 9156551 INFO @ Sat, 03 Jun 2017 12:20:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:20:03: #1 finished! INFO @ Sat, 03 Jun 2017 12:20:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:20:05: #2 number of paired peaks: 706 WARNING @ Sat, 03 Jun 2017 12:20:05: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 03 Jun 2017 12:20:05: start model_add_line... INFO @ Sat, 03 Jun 2017 12:20:06: 8000000 INFO @ Sat, 03 Jun 2017 12:20:09: 9000000 INFO @ Sat, 03 Jun 2017 12:20:10: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:20:10: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:20:10: #1 total tags in treatment: 9159766 INFO @ Sat, 03 Jun 2017 12:20:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:20:10: #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 12:20:12: #1 tags after filtering in treatment: 9156551 INFO @ Sat, 03 Jun 2017 12:20:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:20:12: #1 finished! INFO @ Sat, 03 Jun 2017 12:20:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:20:13: 9000000 INFO @ Sat, 03 Jun 2017 12:20:14: #2 number of paired peaks: 706 WARNING @ Sat, 03 Jun 2017 12:20:14: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 03 Jun 2017 12:20:14: start model_add_line... INFO @ Sat, 03 Jun 2017 12:20:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:20:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:20:14: #1 total tags in treatment: 9159766 INFO @ Sat, 03 Jun 2017 12:20:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:20:14: #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 12:20:14: start X-correlation... INFO @ Sat, 03 Jun 2017 12:20:14: end of X-cor INFO @ Sat, 03 Jun 2017 12:20:14: #2 finished! INFO @ Sat, 03 Jun 2017 12:20:14: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Jun 2017 12:20:14: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sat, 03 Jun 2017 12:20:14: #2.2 Generate R script for model : SRX982093.05_model.r WARNING @ Sat, 03 Jun 2017 12:20:14: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:20:14: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sat, 03 Jun 2017 12:20:14: #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 12:20:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:20:15: #1 tags after filtering in treatment: 9156551 INFO @ Sat, 03 Jun 2017 12:20:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:20:15: #1 finished! INFO @ Sat, 03 Jun 2017 12:20:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:20:17: #2 number of paired peaks: 706 WARNING @ Sat, 03 Jun 2017 12:20:17: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 03 Jun 2017 12:20:17: start model_add_line... INFO @ Sat, 03 Jun 2017 12:20:22: start X-correlation... INFO @ Sat, 03 Jun 2017 12:20:22: end of X-cor INFO @ Sat, 03 Jun 2017 12:20:22: #2 finished! INFO @ Sat, 03 Jun 2017 12:20:22: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Jun 2017 12:20:22: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sat, 03 Jun 2017 12:20:22: #2.2 Generate R script for model : SRX982093.20_model.r WARNING @ Sat, 03 Jun 2017 12:20:23: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:20:23: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sat, 03 Jun 2017 12:20:23: #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 12:20:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:20:26: start X-correlation... INFO @ Sat, 03 Jun 2017 12:20:26: end of X-cor INFO @ Sat, 03 Jun 2017 12:20:26: #2 finished! INFO @ Sat, 03 Jun 2017 12:20:26: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Jun 2017 12:20:26: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sat, 03 Jun 2017 12:20:26: #2.2 Generate R script for model : SRX982093.10_model.r WARNING @ Sat, 03 Jun 2017 12:20:26: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:20:26: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sat, 03 Jun 2017 12:20:26: #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 12:20:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:20:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:21:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:21:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:21:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:21:40: #4 Write output xls file... SRX982093.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:21:40: #4 Write peak in narrowPeak format file... SRX982093.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:21:40: #4 Write summits bed file... SRX982093.05_summits.bed INFO @ Sat, 03 Jun 2017 12:21:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1089 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:21:44: #4 Write output xls file... SRX982093.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:21:44: #4 Write peak in narrowPeak format file... SRX982093.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:21:44: #4 Write summits bed file... SRX982093.20_summits.bed INFO @ Sat, 03 Jun 2017 12:21:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (284 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:21:56: #4 Write output xls file... SRX982093.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:21:56: #4 Write peak in narrowPeak format file... SRX982093.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:21:56: #4 Write summits bed file... SRX982093.10_summits.bed INFO @ Sat, 03 Jun 2017 12:21:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (624 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。