Job ID = 3001486 sra ファイルのダウンロード中... Completed: 339061K bytes transferred in 9 seconds (299868K 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 --:--:-- --:--:-- --:--:-- 0 100 14953 0 14953 0 0 8577 0 --:--:-- 0:00:01 --:--:-- 9811 100 14953 0 14953 0 0 5446 0 --:--:-- 0:00:02 --:--:-- 5919 100 14953 0 14953 0 0 3990 0 --:--:-- 0:00:03 --:--:-- 4239 100 14953 0 14953 0 0 3149 0 --:--:-- 0:00:04 --:--:-- 3301 100 14953 0 14953 0 0 2600 0 --:--:-- 0:00:05 --:--:-- 2703 100 14953 0 14953 0 0 2214 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1928 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1707 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1532 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1389 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1271 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1171 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1086 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1012 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 948 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 891 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 841 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 796 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 756 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 719 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 686 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 656 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 628 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 603 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 579 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 558 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 538 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 519 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 501 0 --:--:-- 0:00:29 --:--:-- 0 100 16400 0 16400 0 0 536 0 --:--:-- 0:00:30 --:--:-- 302 100 40326 0 40326 0 0 1310 0 --:--:-- 0:00:30 --:--:-- 6383 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 1578355 spots for /home/okishinya/chipatlas/results/ce10/SRX003829/SRR015069.sra Written 1578355 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: 00:00:16 1578355 reads; of these: 1578355 (100.00%) were unpaired; of these: 666410 (42.22%) aligned 0 times 703695 (44.58%) aligned exactly 1 time 208250 (13.19%) aligned >1 times 57.78% overall alignment rate Time searching: 00:00:16 Overall time: 00:00:16 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_rmdupse_core] 68195 / 911945 = 0.0748 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 @ Mon, 07 Sep 2015 18:45:29: # Command line: callpeak -t SRX003829.bam -f BAM -g ce -n SRX003829.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003829.10 # format = BAM # ChIP-seq file = ['SRX003829.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 @ Mon, 07 Sep 2015 18:45:29: # Command line: callpeak -t SRX003829.bam -f BAM -g ce -n SRX003829.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003829.20 # format = BAM # ChIP-seq file = ['SRX003829.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 @ Mon, 07 Sep 2015 18:45:29: # Command line: callpeak -t SRX003829.bam -f BAM -g ce -n SRX003829.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003829.05 # format = BAM # ChIP-seq file = ['SRX003829.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 @ Mon, 07 Sep 2015 18:45:29: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:29: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:29: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:29: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:29: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:29: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:34: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:45:34: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:45:34: #1 total tags in treatment: 843750 INFO @ Mon, 07 Sep 2015 18:45:34: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:34: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:45:34: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:45:34: #1 total tags in treatment: 843750 INFO @ Mon, 07 Sep 2015 18:45:34: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:34: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:45:34: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:45:34: #1 total tags in treatment: 843750 INFO @ Mon, 07 Sep 2015 18:45:34: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:45:34: #1 tags after filtering in treatment: 843619 INFO @ Mon, 07 Sep 2015 18:45:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:34: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:34: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:34: #1 tags after filtering in treatment: 843619 INFO @ Mon, 07 Sep 2015 18:45:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:34: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:34: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:34: #1 tags after filtering in treatment: 843619 INFO @ Mon, 07 Sep 2015 18:45:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:34: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:34: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:35: #2 number of paired peaks: 491 WARNING @ Mon, 07 Sep 2015 18:45:35: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:35: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:35: #2 number of paired peaks: 491 WARNING @ Mon, 07 Sep 2015 18:45:35: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:35: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:35: #2 number of paired peaks: 491 WARNING @ Mon, 07 Sep 2015 18:45:35: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:35: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:35: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:35: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:35: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:35: #2 predicted fragment length is 46 bps INFO @ Mon, 07 Sep 2015 18:45:35: #2 alternative fragment length(s) may be 46,465 bps INFO @ Mon, 07 Sep 2015 18:45:35: #2.2 Generate R script for model : SRX003829.10_model.r WARNING @ Mon, 07 Sep 2015 18:45:35: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:35: #2 You may need to consider one of the other alternative d(s): 46,465 WARNING @ Mon, 07 Sep 2015 18:45:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 Sep 2015 18:45:35: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:35: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:35: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:35: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:35: #2 predicted fragment length is 46 bps INFO @ Mon, 07 Sep 2015 18:45:35: #2 alternative fragment length(s) may be 46,465 bps INFO @ Mon, 07 Sep 2015 18:45:35: #2.2 Generate R script for model : SRX003829.05_model.r WARNING @ Mon, 07 Sep 2015 18:45:35: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:35: #2 You may need to consider one of the other alternative d(s): 46,465 WARNING @ Mon, 07 Sep 2015 18:45:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 Sep 2015 18:45:35: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:35: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:35: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:35: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:35: #2 predicted fragment length is 46 bps INFO @ Mon, 07 Sep 2015 18:45:35: #2 alternative fragment length(s) may be 46,465 bps INFO @ Mon, 07 Sep 2015 18:45:35: #2.2 Generate R script for model : SRX003829.20_model.r WARNING @ Mon, 07 Sep 2015 18:45:35: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:35: #2 You may need to consider one of the other alternative d(s): 46,465 WARNING @ Mon, 07 Sep 2015 18:45:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 Sep 2015 18:45:35: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:40: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:40: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:40: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write output xls file... SRX003829.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write peak in narrowPeak format file... SRX003829.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write summits bed file... SRX003829.20_summits.bed INFO @ Mon, 07 Sep 2015 18:45:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write output xls file... SRX003829.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write peak in narrowPeak format file... SRX003829.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write summits bed file... SRX003829.10_summits.bed INFO @ Mon, 07 Sep 2015 18:45:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (81 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write output xls file... SRX003829.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write peak in narrowPeak format file... SRX003829.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:44: #4 Write summits bed file... SRX003829.05_summits.bed INFO @ Mon, 07 Sep 2015 18:45:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (228 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。