Job ID = 9028924 sra ファイルのダウンロード中... Completed: 327601K bytes transferred in 8 seconds (323272K 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 --:--:-- 0:00:07 --:--:-- 0 100 22318 0 22318 0 0 2643 0 --:--:-- 0:00:08 --:--:-- 11037 100 50792 0 50792 0 0 5380 0 --:--:-- 0:00:09 --:--:-- 16829 100 52663 0 52663 0 0 5529 0 --:--:-- 0:00:09 --:--:-- 16982 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 14118317 spots for /home/okishinya/chipatlas/results/ce10/SRX982111/SRR1956601.sra Written 14118317 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: 00:03:34 14118317 reads; of these: 14118317 (100.00%) were unpaired; of these: 1984687 (14.06%) aligned 0 times 10203068 (72.27%) aligned exactly 1 time 1930562 (13.67%) aligned >1 times 85.94% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 898404 / 12133630 = 0.0740 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 12:31:09: # Command line: callpeak -t SRX982111.bam -f BAM -g ce -n SRX982111.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982111.05 # format = BAM # ChIP-seq file = ['SRX982111.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 12:31:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:31:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:31:09: # Command line: callpeak -t SRX982111.bam -f BAM -g ce -n SRX982111.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982111.20 # format = BAM # ChIP-seq file = ['SRX982111.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 12:31:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:31:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:31:09: # Command line: callpeak -t SRX982111.bam -f BAM -g ce -n SRX982111.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982111.10 # format = BAM # ChIP-seq file = ['SRX982111.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 12:31:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:31:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:31:16: 1000000 INFO @ Sat, 03 Jun 2017 12:31:16: 1000000 INFO @ Sat, 03 Jun 2017 12:31:16: 1000000 INFO @ Sat, 03 Jun 2017 12:31:22: 2000000 INFO @ Sat, 03 Jun 2017 12:31:23: 2000000 INFO @ Sat, 03 Jun 2017 12:31:23: 2000000 INFO @ Sat, 03 Jun 2017 12:31:29: 3000000 INFO @ Sat, 03 Jun 2017 12:31:31: 3000000 INFO @ Sat, 03 Jun 2017 12:31:31: 3000000 INFO @ Sat, 03 Jun 2017 12:31:36: 4000000 INFO @ Sat, 03 Jun 2017 12:31:38: 4000000 INFO @ Sat, 03 Jun 2017 12:31:38: 4000000 INFO @ Sat, 03 Jun 2017 12:31:43: 5000000 INFO @ Sat, 03 Jun 2017 12:31:45: 5000000 INFO @ Sat, 03 Jun 2017 12:31:45: 5000000 INFO @ Sat, 03 Jun 2017 12:31:50: 6000000 INFO @ Sat, 03 Jun 2017 12:31:53: 6000000 INFO @ Sat, 03 Jun 2017 12:31:53: 6000000 INFO @ Sat, 03 Jun 2017 12:31:57: 7000000 INFO @ Sat, 03 Jun 2017 12:32:00: 7000000 INFO @ Sat, 03 Jun 2017 12:32:00: 7000000 INFO @ Sat, 03 Jun 2017 12:32:03: 8000000 INFO @ Sat, 03 Jun 2017 12:32:07: 8000000 INFO @ Sat, 03 Jun 2017 12:32:07: 8000000 INFO @ Sat, 03 Jun 2017 12:32:10: 9000000 INFO @ Sat, 03 Jun 2017 12:32:15: 9000000 INFO @ Sat, 03 Jun 2017 12:32:15: 9000000 INFO @ Sat, 03 Jun 2017 12:32:17: 10000000 INFO @ Sat, 03 Jun 2017 12:32:22: 10000000 INFO @ Sat, 03 Jun 2017 12:32:22: 10000000 INFO @ Sat, 03 Jun 2017 12:32:24: 11000000 INFO @ Sat, 03 Jun 2017 12:32:25: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:32:25: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:32:25: #1 total tags in treatment: 11235226 INFO @ Sat, 03 Jun 2017 12:32:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:32:25: #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 12:32:28: #1 tags after filtering in treatment: 11233954 INFO @ Sat, 03 Jun 2017 12:32:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:32:28: #1 finished! INFO @ Sat, 03 Jun 2017 12:32:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:32:29: 11000000 INFO @ Sat, 03 Jun 2017 12:32:29: 11000000 INFO @ Sat, 03 Jun 2017 12:32:30: #2 number of paired peaks: 296 WARNING @ Sat, 03 Jun 2017 12:32:30: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sat, 03 Jun 2017 12:32:30: start model_add_line... INFO @ Sat, 03 Jun 2017 12:32:31: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:32:31: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:32:31: #1 total tags in treatment: 11235226 INFO @ Sat, 03 Jun 2017 12:32:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:32:31: #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 12:32:31: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:32:31: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:32:31: #1 total tags in treatment: 11235226 INFO @ Sat, 03 Jun 2017 12:32:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:32:31: #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 12:32:33: #1 tags after filtering in treatment: 11233954 INFO @ Sat, 03 Jun 2017 12:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:32:33: #1 finished! INFO @ Sat, 03 Jun 2017 12:32:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:32:33: #1 tags after filtering in treatment: 11233954 INFO @ Sat, 03 Jun 2017 12:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:32:33: #1 finished! INFO @ Sat, 03 Jun 2017 12:32:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:32:35: #2 number of paired peaks: 296 WARNING @ Sat, 03 Jun 2017 12:32:35: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sat, 03 Jun 2017 12:32:35: start model_add_line... INFO @ Sat, 03 Jun 2017 12:32:35: #2 number of paired peaks: 296 WARNING @ Sat, 03 Jun 2017 12:32:35: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sat, 03 Jun 2017 12:32:35: start model_add_line... INFO @ Sat, 03 Jun 2017 12:32:35: start X-correlation... INFO @ Sat, 03 Jun 2017 12:32:35: end of X-cor INFO @ Sat, 03 Jun 2017 12:32:35: #2 finished! INFO @ Sat, 03 Jun 2017 12:32:35: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 12:32:35: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 12:32:35: #2.2 Generate R script for model : SRX982111.10_model.r WARNING @ Sat, 03 Jun 2017 12:32:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:32:35: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 12:32:35: #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 12:32:35: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:32:39: start X-correlation... INFO @ Sat, 03 Jun 2017 12:32:39: end of X-cor INFO @ Sat, 03 Jun 2017 12:32:39: #2 finished! INFO @ Sat, 03 Jun 2017 12:32:39: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 12:32:39: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 12:32:39: #2.2 Generate R script for model : SRX982111.05_model.r WARNING @ Sat, 03 Jun 2017 12:32:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:32:39: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 12:32:39: #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 12:32:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:32:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:32:39: start X-correlation... INFO @ Sat, 03 Jun 2017 12:32:39: end of X-cor INFO @ Sat, 03 Jun 2017 12:32:39: #2 finished! INFO @ Sat, 03 Jun 2017 12:32:39: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 12:32:39: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 12:32:39: #2.2 Generate R script for model : SRX982111.20_model.r WARNING @ Sat, 03 Jun 2017 12:32:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:32:39: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 12:32:39: #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 12:32:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:32:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:33:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:33:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:33:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:34:15: #4 Write output xls file... SRX982111.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:34:15: #4 Write peak in narrowPeak format file... SRX982111.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:34:15: #4 Write summits bed file... SRX982111.10_summits.bed INFO @ Sat, 03 Jun 2017 12:34:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (403 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:34:24: #4 Write output xls file... SRX982111.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:34:24: #4 Write peak in narrowPeak format file... SRX982111.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:34:24: #4 Write summits bed file... SRX982111.05_summits.bed INFO @ Sat, 03 Jun 2017 12:34:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:34:26: #4 Write output xls file... SRX982111.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:34:26: #4 Write peak in narrowPeak format file... SRX982111.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:34:26: #4 Write summits bed file... SRX982111.20_summits.bed INFO @ Sat, 03 Jun 2017 12:34:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (165 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。