Job ID = 9025621 sra ファイルのダウンロード中... Completed: 391449K bytes transferred in 6 seconds (461530K 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 2802 0 --:--:-- 0:00:07 --:--:-- 16206 100 44725 0 44725 0 0 5086 0 --:--:-- 0:00:08 --:--:-- 20265 100 49591 0 49591 0 0 5535 0 --:--:-- 0:00:08 --:--:-- 20906 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 11756944 spots for /home/okishinya/chipatlas/results/ce10/SRX208763/SRR628897.sra Written 11756944 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: 00:04:16 11756944 reads; of these: 11756944 (100.00%) were unpaired; of these: 1169663 (9.95%) aligned 0 times 9229787 (78.50%) aligned exactly 1 time 1357494 (11.55%) aligned >1 times 90.05% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 6876497 / 10587281 = 0.6495 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 04:43:23: # Command line: callpeak -t SRX208763.bam -f BAM -g ce -n SRX208763.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208763.10 # format = BAM # ChIP-seq file = ['SRX208763.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 04:43:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:43:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:43:23: # Command line: callpeak -t SRX208763.bam -f BAM -g ce -n SRX208763.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208763.05 # format = BAM # ChIP-seq file = ['SRX208763.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 04:43:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:43:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:43:23: # Command line: callpeak -t SRX208763.bam -f BAM -g ce -n SRX208763.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208763.20 # format = BAM # ChIP-seq file = ['SRX208763.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 04:43:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:43:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:43:29: 1000000 INFO @ Sat, 03 Jun 2017 04:43:30: 1000000 INFO @ Sat, 03 Jun 2017 04:43:30: 1000000 INFO @ Sat, 03 Jun 2017 04:43:35: 2000000 INFO @ Sat, 03 Jun 2017 04:43:36: 2000000 INFO @ Sat, 03 Jun 2017 04:43:36: 2000000 INFO @ Sat, 03 Jun 2017 04:43:42: 3000000 INFO @ Sat, 03 Jun 2017 04:43:43: 3000000 INFO @ Sat, 03 Jun 2017 04:43:43: 3000000 INFO @ Sat, 03 Jun 2017 04:43:46: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:43:46: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:43:46: #1 total tags in treatment: 3710784 INFO @ Sat, 03 Jun 2017 04:43:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:43:46: #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 04:43:47: #1 tags after filtering in treatment: 3237577 INFO @ Sat, 03 Jun 2017 04:43:47: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Jun 2017 04:43:47: #1 finished! INFO @ Sat, 03 Jun 2017 04:43:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:43:47: #2 number of paired peaks: 528 WARNING @ Sat, 03 Jun 2017 04:43:47: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Sat, 03 Jun 2017 04:43:47: start model_add_line... INFO @ Sat, 03 Jun 2017 04:43:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:43:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:43:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:43:48: #1 total tags in treatment: 3710784 INFO @ Sat, 03 Jun 2017 04:43:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:43:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:43:48: #1 total tags in treatment: 3710784 INFO @ Sat, 03 Jun 2017 04:43:48: #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 04:43:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:43:48: #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 04:43:48: #1 tags after filtering in treatment: 3237577 INFO @ Sat, 03 Jun 2017 04:43:48: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Jun 2017 04:43:48: #1 finished! INFO @ Sat, 03 Jun 2017 04:43:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:43:48: #1 tags after filtering in treatment: 3237577 INFO @ Sat, 03 Jun 2017 04:43:48: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Jun 2017 04:43:48: #1 finished! INFO @ Sat, 03 Jun 2017 04:43:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:43:49: #2 number of paired peaks: 528 WARNING @ Sat, 03 Jun 2017 04:43:49: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Sat, 03 Jun 2017 04:43:49: start model_add_line... INFO @ Sat, 03 Jun 2017 04:43:49: #2 number of paired peaks: 528 WARNING @ Sat, 03 Jun 2017 04:43:49: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Sat, 03 Jun 2017 04:43:49: start model_add_line... INFO @ Sat, 03 Jun 2017 04:43:50: start X-correlation... INFO @ Sat, 03 Jun 2017 04:43:50: end of X-cor INFO @ Sat, 03 Jun 2017 04:43:50: #2 finished! INFO @ Sat, 03 Jun 2017 04:43:50: #2 predicted fragment length is 65 bps INFO @ Sat, 03 Jun 2017 04:43:50: #2 alternative fragment length(s) may be 3,65,127,182 bps INFO @ Sat, 03 Jun 2017 04:43:50: #2.2 Generate R script for model : SRX208763.20_model.r WARNING @ Sat, 03 Jun 2017 04:43:50: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:43:50: #2 You may need to consider one of the other alternative d(s): 3,65,127,182 WARNING @ Sat, 03 Jun 2017 04:43:50: #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 04:43:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:43:51: start X-correlation... INFO @ Sat, 03 Jun 2017 04:43:51: end of X-cor INFO @ Sat, 03 Jun 2017 04:43:51: #2 finished! INFO @ Sat, 03 Jun 2017 04:43:51: #2 predicted fragment length is 65 bps INFO @ Sat, 03 Jun 2017 04:43:51: #2 alternative fragment length(s) may be 3,65,127,182 bps INFO @ Sat, 03 Jun 2017 04:43:51: #2.2 Generate R script for model : SRX208763.10_model.r WARNING @ Sat, 03 Jun 2017 04:43:51: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:43:51: #2 You may need to consider one of the other alternative d(s): 3,65,127,182 WARNING @ Sat, 03 Jun 2017 04:43:51: #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 04:43:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:43:51: start X-correlation... INFO @ Sat, 03 Jun 2017 04:43:51: end of X-cor INFO @ Sat, 03 Jun 2017 04:43:51: #2 finished! INFO @ Sat, 03 Jun 2017 04:43:51: #2 predicted fragment length is 65 bps INFO @ Sat, 03 Jun 2017 04:43:51: #2 alternative fragment length(s) may be 3,65,127,182 bps INFO @ Sat, 03 Jun 2017 04:43:51: #2.2 Generate R script for model : SRX208763.05_model.r WARNING @ Sat, 03 Jun 2017 04:43:51: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:43:51: #2 You may need to consider one of the other alternative d(s): 3,65,127,182 WARNING @ Sat, 03 Jun 2017 04:43:51: #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 04:43:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:44:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:44:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:44:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:44:22: #4 Write output xls file... SRX208763.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:22: #4 Write peak in narrowPeak format file... SRX208763.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:22: #4 Write summits bed file... SRX208763.20_summits.bed INFO @ Sat, 03 Jun 2017 04:44:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (40 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:44:24: #4 Write output xls file... SRX208763.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:24: #4 Write peak in narrowPeak format file... SRX208763.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:24: #4 Write summits bed file... SRX208763.05_summits.bed INFO @ Sat, 03 Jun 2017 04:44:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:44:26: #4 Write output xls file... SRX208763.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:26: #4 Write peak in narrowPeak format file... SRX208763.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:26: #4 Write summits bed file... SRX208763.10_summits.bed INFO @ Sat, 03 Jun 2017 04:44:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (185 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。