Job ID = 3001499 sra ファイルのダウンロード中... Completed: 14276K bytes transferred in 4 seconds (26794K 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 4007 0 4007 0 0 7251 0 --:--:-- --:--:-- --:--:-- 11069 100 14953 0 14953 0 0 8583 0 --:--:-- 0:00:01 --:--:-- 9640 100 14953 0 14953 0 0 5451 0 --:--:-- 0:00:02 --:--:-- 5859 100 14953 0 14953 0 0 3992 0 --:--:-- 0:00:03 --:--:-- 4207 100 14953 0 14953 0 0 3150 0 --:--:-- 0:00:04 --:--:-- 3282 100 14953 0 14953 0 0 2601 0 --:--:-- 0:00:05 --:--:-- 2107 100 14953 0 14953 0 0 2215 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1929 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1708 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1533 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1390 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 0 580 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 0 502 0 --:--:-- 0:00:29 --:--:-- 0 100 16407 0 16407 0 0 536 0 --:--:-- 0:00:30 --:--:-- 301 100 32550 0 32550 0 0 1057 0 --:--:-- 0:00:30 --:--:-- 4390 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 883655 spots for /home/okishinya/chipatlas/results/ce10/SRX005633/SRR017602.sra Written 883655 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: 00:00:06 883655 reads; of these: 883655 (100.00%) were unpaired; of these: 417173 (47.21%) aligned 0 times 394773 (44.68%) aligned exactly 1 time 71709 (8.12%) aligned >1 times 52.79% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 11802 / 466482 = 0.0253 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 18:45:26: # Command line: callpeak -t SRX005633.bam -f BAM -g ce -n SRX005633.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005633.20 # format = BAM # ChIP-seq file = ['SRX005633.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 18:45:26: # Command line: callpeak -t SRX005633.bam -f BAM -g ce -n SRX005633.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005633.05 # format = BAM # ChIP-seq file = ['SRX005633.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 18:45:26: # Command line: callpeak -t SRX005633.bam -f BAM -g ce -n SRX005633.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005633.10 # format = BAM # ChIP-seq file = ['SRX005633.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 18:45:26: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:26: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:26: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:26: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:26: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:26: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:28: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:28: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:28: #1 total tags in treatment: 454680 INFO @ Mon, 07 Sep 2015 18:45:28: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:28: #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 18:45:29: #1 tags after filtering in treatment: 454680 INFO @ Mon, 07 Sep 2015 18:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:29: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:29: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:29: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:29: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:29: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:45:29: #1 total tags in treatment: 454680 INFO @ Mon, 07 Sep 2015 18:45:29: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:45:29: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:29: #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 18:45:29: #1 total tags in treatment: 454680 INFO @ Mon, 07 Sep 2015 18:45:29: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:29: #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 18:45:29: #2 number of paired peaks: 359 WARNING @ Mon, 07 Sep 2015 18:45:29: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:29: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:29: #1 tags after filtering in treatment: 454680 INFO @ Mon, 07 Sep 2015 18:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:29: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:29: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:29: #1 tags after filtering in treatment: 454680 INFO @ Mon, 07 Sep 2015 18:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:29: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:29: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:29: #2 number of paired peaks: 359 WARNING @ Mon, 07 Sep 2015 18:45:29: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:29: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:29: #2 number of paired peaks: 359 WARNING @ Mon, 07 Sep 2015 18:45:29: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:29: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:29: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:29: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:29: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:29: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:29: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:29: #2 predicted fragment length is 34 bps INFO @ Mon, 07 Sep 2015 18:45:29: #2 alternative fragment length(s) may be 34,112,167,243,445,449,583 bps INFO @ Mon, 07 Sep 2015 18:45:29: #2.2 Generate R script for model : SRX005633.20_model.r INFO @ Mon, 07 Sep 2015 18:45:29: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:29: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:29: #2 predicted fragment length is 34 bps INFO @ Mon, 07 Sep 2015 18:45:29: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:29: #2 alternative fragment length(s) may be 34,112,167,243,445,449,583 bps INFO @ Mon, 07 Sep 2015 18:45:29: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:29: #2.2 Generate R script for model : SRX005633.10_model.r INFO @ Mon, 07 Sep 2015 18:45:29: #2 predicted fragment length is 34 bps INFO @ Mon, 07 Sep 2015 18:45:29: #2 alternative fragment length(s) may be 34,112,167,243,445,449,583 bps INFO @ Mon, 07 Sep 2015 18:45:29: #2.2 Generate R script for model : SRX005633.05_model.r WARNING @ Mon, 07 Sep 2015 18:45:29: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:29: #2 You may need to consider one of the other alternative d(s): 34,112,167,243,445,449,583 WARNING @ Mon, 07 Sep 2015 18:45:29: #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 18:45:29: #3 Call peaks... WARNING @ Mon, 07 Sep 2015 18:45:29: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:29: #2 You may need to consider one of the other alternative d(s): 34,112,167,243,445,449,583 WARNING @ Mon, 07 Sep 2015 18:45:29: #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 18:45:29: #3 Call peaks... WARNING @ Mon, 07 Sep 2015 18:45:29: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:45:29: #2 You may need to consider one of the other alternative d(s): 34,112,167,243,445,449,583 WARNING @ Mon, 07 Sep 2015 18:45:29: #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 18:45:29: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:32: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:32: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:32: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:34: #4 Write output xls file... SRX005633.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:34: #4 Write output xls file... SRX005633.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:34: #4 Write output xls file... SRX005633.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:34: #4 Write peak in narrowPeak format file... SRX005633.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:34: #4 Write peak in narrowPeak format file... SRX005633.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:34: #4 Write summits bed file... SRX005633.20_summits.bed BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 07 Sep 2015 18:45:34: #4 Write peak in narrowPeak format file... SRX005633.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:34: #4 Write summits bed file... SRX005633.05_summits.bed INFO @ Mon, 07 Sep 2015 18:45:34: Done! INFO @ Mon, 07 Sep 2015 18:45:35: Done! INFO @ Mon, 07 Sep 2015 18:45:35: #4 Write summits bed file... SRX005633.10_summits.bed INFO @ Mon, 07 Sep 2015 18:45:35: Done! pass1 - making usageList (5 chroms): 3 millis pass2 - checking and writing primary data (9 records, 4 fields): 4 millis pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。