Job ID = 9028817 sra ファイルのダウンロード中... Completed: 844025K bytes transferred in 10 seconds (637662K 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 --:--:-- 0:00:06 --:--:-- 0 100 22317 0 22317 0 0 2878 0 --:--:-- 0:00:07 --:--:-- 19189 100 74445 0 74445 0 0 8508 0 --:--:-- 0:00:08 --:--:-- 34481 100 106k 0 106k 0 0 11747 0 --:--:-- 0:00:09 --:--:-- 40886 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 18405815 spots for /home/okishinya/chipatlas/results/ce10/SRX982060/SRR1956536.sra Written 18405815 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: 00:06:37 18405815 reads; of these: 18405815 (100.00%) were unpaired; of these: 4540046 (24.67%) aligned 0 times 11616294 (63.11%) aligned exactly 1 time 2249475 (12.22%) aligned >1 times 75.33% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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] 3679435 / 13865769 = 0.2654 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 12:04:09: # Command line: callpeak -t SRX982060.bam -f BAM -g ce -n SRX982060.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982060.10 # format = BAM # ChIP-seq file = ['SRX982060.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 12:04:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:04:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:04:09: # Command line: callpeak -t SRX982060.bam -f BAM -g ce -n SRX982060.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982060.05 # format = BAM # ChIP-seq file = ['SRX982060.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 12:04:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:04:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:04:09: # Command line: callpeak -t SRX982060.bam -f BAM -g ce -n SRX982060.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982060.20 # format = BAM # ChIP-seq file = ['SRX982060.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 12:04:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:04:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:04:17: 1000000 INFO @ Sat, 03 Jun 2017 12:04:18: 1000000 INFO @ Sat, 03 Jun 2017 12:04:18: 1000000 INFO @ Sat, 03 Jun 2017 12:04:25: 2000000 INFO @ Sat, 03 Jun 2017 12:04:28: 2000000 INFO @ Sat, 03 Jun 2017 12:04:28: 2000000 INFO @ Sat, 03 Jun 2017 12:04:33: 3000000 INFO @ Sat, 03 Jun 2017 12:04:37: 3000000 INFO @ Sat, 03 Jun 2017 12:04:37: 3000000 INFO @ Sat, 03 Jun 2017 12:04:41: 4000000 INFO @ Sat, 03 Jun 2017 12:04:47: 4000000 INFO @ Sat, 03 Jun 2017 12:04:47: 4000000 INFO @ Sat, 03 Jun 2017 12:04:48: 5000000 INFO @ Sat, 03 Jun 2017 12:04:56: 5000000 INFO @ Sat, 03 Jun 2017 12:04:56: 5000000 INFO @ Sat, 03 Jun 2017 12:04:56: 6000000 INFO @ Sat, 03 Jun 2017 12:05:06: 7000000 INFO @ Sat, 03 Jun 2017 12:05:07: 6000000 INFO @ Sat, 03 Jun 2017 12:05:07: 6000000 INFO @ Sat, 03 Jun 2017 12:05:18: 8000000 INFO @ Sat, 03 Jun 2017 12:05:18: 7000000 INFO @ Sat, 03 Jun 2017 12:05:18: 7000000 INFO @ Sat, 03 Jun 2017 12:05:29: 9000000 INFO @ Sat, 03 Jun 2017 12:05:29: 8000000 INFO @ Sat, 03 Jun 2017 12:05:29: 8000000 INFO @ Sat, 03 Jun 2017 12:05:40: 10000000 INFO @ Sat, 03 Jun 2017 12:05:41: 9000000 INFO @ Sat, 03 Jun 2017 12:05:41: 9000000 INFO @ Sat, 03 Jun 2017 12:05:42: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 12:05:42: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 12:05:42: #1 total tags in treatment: 10186334 INFO @ Sat, 03 Jun 2017 12:05:42: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:05:42: #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 12:05:45: #1 tags after filtering in treatment: 10183120 INFO @ Sat, 03 Jun 2017 12:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:05:45: #1 finished! INFO @ Sat, 03 Jun 2017 12:05:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:05:46: #2 number of paired peaks: 490 WARNING @ Sat, 03 Jun 2017 12:05:46: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Sat, 03 Jun 2017 12:05:46: start model_add_line... INFO @ Sat, 03 Jun 2017 12:05:50: 10000000 INFO @ Sat, 03 Jun 2017 12:05:50: 10000000 INFO @ Sat, 03 Jun 2017 12:05:52: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 12:05:52: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 12:05:52: #1 total tags in treatment: 10186334 INFO @ Sat, 03 Jun 2017 12:05:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:05:52: #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 12:05:52: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 12:05:52: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 12:05:52: #1 total tags in treatment: 10186334 INFO @ Sat, 03 Jun 2017 12:05:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:05:52: #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 12:05:53: start X-correlation... INFO @ Sat, 03 Jun 2017 12:05:53: end of X-cor INFO @ Sat, 03 Jun 2017 12:05:53: #2 finished! INFO @ Sat, 03 Jun 2017 12:05:53: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Jun 2017 12:05:53: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 03 Jun 2017 12:05:53: #2.2 Generate R script for model : SRX982060.05_model.r WARNING @ Sat, 03 Jun 2017 12:05:53: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:05:53: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 03 Jun 2017 12:05:53: #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 12:05:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:05:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:05:54: #1 tags after filtering in treatment: 10183120 INFO @ Sat, 03 Jun 2017 12:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:05:54: #1 finished! INFO @ Sat, 03 Jun 2017 12:05:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:05:54: #1 tags after filtering in treatment: 10183120 INFO @ Sat, 03 Jun 2017 12:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:05:54: #1 finished! INFO @ Sat, 03 Jun 2017 12:05:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:05:56: #2 number of paired peaks: 490 WARNING @ Sat, 03 Jun 2017 12:05:56: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Sat, 03 Jun 2017 12:05:56: start model_add_line... INFO @ Sat, 03 Jun 2017 12:05:56: #2 number of paired peaks: 490 WARNING @ Sat, 03 Jun 2017 12:05:56: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Sat, 03 Jun 2017 12:05:56: start model_add_line... INFO @ Sat, 03 Jun 2017 12:06:02: start X-correlation... INFO @ Sat, 03 Jun 2017 12:06:02: end of X-cor INFO @ Sat, 03 Jun 2017 12:06:02: #2 finished! INFO @ Sat, 03 Jun 2017 12:06:02: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Jun 2017 12:06:02: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 03 Jun 2017 12:06:02: #2.2 Generate R script for model : SRX982060.20_model.r WARNING @ Sat, 03 Jun 2017 12:06:02: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:06:02: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 03 Jun 2017 12:06:02: #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 12:06:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:06:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:06:02: start X-correlation... INFO @ Sat, 03 Jun 2017 12:06:02: end of X-cor INFO @ Sat, 03 Jun 2017 12:06:02: #2 finished! INFO @ Sat, 03 Jun 2017 12:06:02: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Jun 2017 12:06:02: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 03 Jun 2017 12:06:02: #2.2 Generate R script for model : SRX982060.10_model.r WARNING @ Sat, 03 Jun 2017 12:06:02: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:06:02: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 03 Jun 2017 12:06:02: #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 12:06:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:06:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:06:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:06:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:07:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:07:37: #4 Write output xls file... SRX982060.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:07:37: #4 Write peak in narrowPeak format file... SRX982060.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:07:37: #4 Write summits bed file... SRX982060.05_summits.bed INFO @ Sat, 03 Jun 2017 12:07:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1291 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:07:41: #4 Write output xls file... SRX982060.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:07:41: #4 Write peak in narrowPeak format file... SRX982060.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:07:41: #4 Write summits bed file... SRX982060.10_summits.bed INFO @ Sat, 03 Jun 2017 12:07:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (852 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:07:42: #4 Write output xls file... SRX982060.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:07:42: #4 Write peak in narrowPeak format file... SRX982060.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:07:42: #4 Write summits bed file... SRX982060.20_summits.bed INFO @ Sat, 03 Jun 2017 12:07:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (450 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。