Job ID = 9028823 sra ファイルのダウンロード中... Completed: 554191K bytes transferred in 7 seconds (587084K 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 7663 0 7663 0 0 1083 0 --:--:-- 0:00:07 --:--:-- 11386 100 28797 0 28797 0 0 3570 0 --:--:-- 0:00:08 --:--:-- 17254 100 53413 0 53413 0 0 6003 0 --:--:-- 0:00:08 --:--:-- 21373 100 118k 0 118k 0 0 12447 0 --:--:-- 0:00:09 --:--:-- 36379 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 12423035 spots for /home/okishinya/chipatlas/results/ce10/SRX982063/SRR1956539.sra Written 12423035 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: 00:04:24 12423035 reads; of these: 12423035 (100.00%) were unpaired; of these: 1968825 (15.85%) aligned 0 times 8872167 (71.42%) aligned exactly 1 time 1582043 (12.73%) aligned >1 times 84.15% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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] 1626557 / 10454210 = 0.1556 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 12:01:36: # Command line: callpeak -t SRX982063.bam -f BAM -g ce -n SRX982063.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982063.05 # format = BAM # ChIP-seq file = ['SRX982063.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 12:01:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:01:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:01:36: # Command line: callpeak -t SRX982063.bam -f BAM -g ce -n SRX982063.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982063.20 # format = BAM # ChIP-seq file = ['SRX982063.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 12:01:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:01:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:01:36: # Command line: callpeak -t SRX982063.bam -f BAM -g ce -n SRX982063.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982063.10 # format = BAM # ChIP-seq file = ['SRX982063.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 12:01:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:01:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:01:41: 1000000 INFO @ Sat, 03 Jun 2017 12:01:42: 1000000 INFO @ Sat, 03 Jun 2017 12:01:42: 1000000 INFO @ Sat, 03 Jun 2017 12:01:47: 2000000 INFO @ Sat, 03 Jun 2017 12:01:48: 2000000 INFO @ Sat, 03 Jun 2017 12:01:48: 2000000 INFO @ Sat, 03 Jun 2017 12:01:53: 3000000 INFO @ Sat, 03 Jun 2017 12:01:53: 3000000 INFO @ Sat, 03 Jun 2017 12:01:55: 3000000 INFO @ Sat, 03 Jun 2017 12:01:59: 4000000 INFO @ Sat, 03 Jun 2017 12:01:59: 4000000 INFO @ Sat, 03 Jun 2017 12:02:02: 4000000 INFO @ Sat, 03 Jun 2017 12:02:05: 5000000 INFO @ Sat, 03 Jun 2017 12:02:06: 5000000 INFO @ Sat, 03 Jun 2017 12:02:09: 5000000 INFO @ Sat, 03 Jun 2017 12:02:11: 6000000 INFO @ Sat, 03 Jun 2017 12:02:13: 6000000 INFO @ Sat, 03 Jun 2017 12:02:16: 6000000 INFO @ Sat, 03 Jun 2017 12:02:17: 7000000 INFO @ Sat, 03 Jun 2017 12:02:19: 7000000 INFO @ Sat, 03 Jun 2017 12:02:23: 8000000 INFO @ Sat, 03 Jun 2017 12:02:24: 7000000 INFO @ Sat, 03 Jun 2017 12:02:26: 8000000 INFO @ Sat, 03 Jun 2017 12:02:28: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 12:02:28: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 12:02:28: #1 total tags in treatment: 8827653 INFO @ Sat, 03 Jun 2017 12:02:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:02:28: #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 12:02:29: #1 tags after filtering in treatment: 8824146 INFO @ Sat, 03 Jun 2017 12:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:02:29: #1 finished! INFO @ Sat, 03 Jun 2017 12:02:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:02:31: #2 number of paired peaks: 772 WARNING @ Sat, 03 Jun 2017 12:02:31: Fewer paired peaks (772) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 772 pairs to build model! INFO @ Sat, 03 Jun 2017 12:02:31: start model_add_line... INFO @ Sat, 03 Jun 2017 12:02:31: 8000000 INFO @ Sat, 03 Jun 2017 12:02:32: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 12:02:32: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 12:02:32: #1 total tags in treatment: 8827653 INFO @ Sat, 03 Jun 2017 12:02:32: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:02:32: #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 12:02:34: #1 tags after filtering in treatment: 8824146 INFO @ Sat, 03 Jun 2017 12:02:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:02:34: #1 finished! INFO @ Sat, 03 Jun 2017 12:02:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:02:35: #2 number of paired peaks: 772 WARNING @ Sat, 03 Jun 2017 12:02:35: Fewer paired peaks (772) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 772 pairs to build model! INFO @ Sat, 03 Jun 2017 12:02:35: start model_add_line... INFO @ Sat, 03 Jun 2017 12:02:36: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 12:02:36: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 12:02:36: #1 total tags in treatment: 8827653 INFO @ Sat, 03 Jun 2017 12:02:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:02:36: #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 12:02:38: #1 tags after filtering in treatment: 8824146 INFO @ Sat, 03 Jun 2017 12:02:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:02:38: #1 finished! INFO @ Sat, 03 Jun 2017 12:02:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:02:39: start X-correlation... INFO @ Sat, 03 Jun 2017 12:02:39: end of X-cor INFO @ Sat, 03 Jun 2017 12:02:39: #2 finished! INFO @ Sat, 03 Jun 2017 12:02:39: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Jun 2017 12:02:39: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 03 Jun 2017 12:02:39: #2.2 Generate R script for model : SRX982063.10_model.r WARNING @ Sat, 03 Jun 2017 12:02:39: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:02:39: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 03 Jun 2017 12:02:39: #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 12:02:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:02:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:02:40: #2 number of paired peaks: 772 WARNING @ Sat, 03 Jun 2017 12:02:40: Fewer paired peaks (772) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 772 pairs to build model! INFO @ Sat, 03 Jun 2017 12:02:40: start model_add_line... INFO @ Sat, 03 Jun 2017 12:02:43: start X-correlation... INFO @ Sat, 03 Jun 2017 12:02:43: end of X-cor INFO @ Sat, 03 Jun 2017 12:02:43: #2 finished! INFO @ Sat, 03 Jun 2017 12:02:43: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Jun 2017 12:02:43: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 03 Jun 2017 12:02:43: #2.2 Generate R script for model : SRX982063.20_model.r WARNING @ Sat, 03 Jun 2017 12:02:43: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:02:43: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 03 Jun 2017 12:02:43: #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 12:02:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:02:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:02:48: start X-correlation... INFO @ Sat, 03 Jun 2017 12:02:48: end of X-cor INFO @ Sat, 03 Jun 2017 12:02:48: #2 finished! INFO @ Sat, 03 Jun 2017 12:02:48: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Jun 2017 12:02:48: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 03 Jun 2017 12:02:48: #2.2 Generate R script for model : SRX982063.05_model.r WARNING @ Sat, 03 Jun 2017 12:02:48: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:02:48: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 03 Jun 2017 12:02:48: #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 12:02:48: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:03:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:03:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:03:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:04:05: #4 Write output xls file... SRX982063.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:04:05: #4 Write peak in narrowPeak format file... SRX982063.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:04:05: #4 Write summits bed file... SRX982063.10_summits.bed INFO @ Sat, 03 Jun 2017 12:04:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1292 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:04:10: #4 Write output xls file... SRX982063.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:04:10: #4 Write peak in narrowPeak format file... SRX982063.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:04:10: #4 Write summits bed file... SRX982063.20_summits.bed INFO @ Sat, 03 Jun 2017 12:04:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (827 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:04:14: #4 Write output xls file... SRX982063.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:04:14: #4 Write peak in narrowPeak format file... SRX982063.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:04:14: #4 Write summits bed file... SRX982063.05_summits.bed INFO @ Sat, 03 Jun 2017 12:04:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2023 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。