Job ID = 3001473 sra ファイルのダウンロード中... Completed: 2858859K bytes transferred in 25 seconds (935491K 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 7813 0 --:--:-- --:--:-- --:--:-- 12482 100 14953 0 14953 0 0 8774 0 --:--:-- 0:00:01 --:--:-- 9889 100 14953 0 14953 0 0 5525 0 --:--:-- 0:00:02 --:--:-- 5947 100 14953 0 14953 0 0 4033 0 --:--:-- 0:00:03 --:--:-- 4254 100 14953 0 14953 0 0 3175 0 --:--:-- 0:00:04 --:--:-- 3311 100 14953 0 14953 0 0 2618 0 --:--:-- 0:00:05 --:--:-- 2106 100 14953 0 14953 0 0 2227 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1938 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1715 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1538 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1395 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1275 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1175 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1089 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1015 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 950 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 893 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 843 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 798 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 757 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 721 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 687 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 657 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 629 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 604 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 580 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 559 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 538 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 520 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 502 0 --:--:-- 0:00:29 --:--:-- 0 100 22947 0 22947 0 0 750 0 --:--:-- 0:00:30 --:--:-- 1657 100 40589 0 40589 0 0 1319 0 --:--:-- 0:00:30 --:--:-- 6391 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 11736857 spots for /home/okishinya/chipatlas/results/ce10/SRX003816/SRR015056.sra Written 11736857 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: 00:01:34 11736857 reads; of these: 11736857 (100.00%) were unpaired; of these: 5159951 (43.96%) aligned 0 times 5411406 (46.11%) aligned exactly 1 time 1165500 (9.93%) aligned >1 times 56.04% overall alignment rate Time searching: 00:01:34 Overall time: 00:01:34 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_rmdupse_core] 450253 / 6576906 = 0.0685 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 18:48:26: # Command line: callpeak -t SRX003816.bam -f BAM -g ce -n SRX003816.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003816.10 # format = BAM # ChIP-seq file = ['SRX003816.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 18:48:26: # Command line: callpeak -t SRX003816.bam -f BAM -g ce -n SRX003816.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003816.20 # format = BAM # ChIP-seq file = ['SRX003816.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 18:48:26: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:48:26: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:48:26: # Command line: callpeak -t SRX003816.bam -f BAM -g ce -n SRX003816.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003816.05 # format = BAM # ChIP-seq file = ['SRX003816.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 18:48:26: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:48:26: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:48:26: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:48:26: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:48:32: 1000000 INFO @ Mon, 07 Sep 2015 18:48:32: 1000000 INFO @ Mon, 07 Sep 2015 18:48:32: 1000000 INFO @ Mon, 07 Sep 2015 18:48:37: 2000000 INFO @ Mon, 07 Sep 2015 18:48:37: 2000000 INFO @ Mon, 07 Sep 2015 18:48:37: 2000000 INFO @ Mon, 07 Sep 2015 18:48:42: 3000000 INFO @ Mon, 07 Sep 2015 18:48:42: 3000000 INFO @ Mon, 07 Sep 2015 18:48:43: 3000000 INFO @ Mon, 07 Sep 2015 18:48:48: 4000000 INFO @ Mon, 07 Sep 2015 18:48:48: 4000000 INFO @ Mon, 07 Sep 2015 18:48:48: 4000000 INFO @ Mon, 07 Sep 2015 18:48:53: 5000000 INFO @ Mon, 07 Sep 2015 18:48:53: 5000000 INFO @ Mon, 07 Sep 2015 18:48:54: 5000000 INFO @ Mon, 07 Sep 2015 18:48:58: 6000000 INFO @ Mon, 07 Sep 2015 18:48:58: 6000000 INFO @ Mon, 07 Sep 2015 18:48:59: 6000000 INFO @ Mon, 07 Sep 2015 18:48:59: #1 tag size is determined as 33 bps INFO @ Mon, 07 Sep 2015 18:48:59: #1 tag size = 33 INFO @ Mon, 07 Sep 2015 18:48:59: #1 total tags in treatment: 6126653 INFO @ Mon, 07 Sep 2015 18:48:59: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:48:59: #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 18:48:59: #1 tag size is determined as 33 bps INFO @ Mon, 07 Sep 2015 18:48:59: #1 tag size = 33 INFO @ Mon, 07 Sep 2015 18:48:59: #1 total tags in treatment: 6126653 INFO @ Mon, 07 Sep 2015 18:48:59: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:48:59: #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 18:49:00: #1 tag size is determined as 33 bps INFO @ Mon, 07 Sep 2015 18:49:00: #1 tag size = 33 INFO @ Mon, 07 Sep 2015 18:49:00: #1 total tags in treatment: 6126653 INFO @ Mon, 07 Sep 2015 18:49:00: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:49:00: #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 18:49:00: #1 tags after filtering in treatment: 6126346 INFO @ Mon, 07 Sep 2015 18:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:49:00: #1 finished! INFO @ Mon, 07 Sep 2015 18:49:00: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:49:00: #1 tags after filtering in treatment: 6126346 INFO @ Mon, 07 Sep 2015 18:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:49:00: #1 finished! INFO @ Mon, 07 Sep 2015 18:49:00: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:49:01: #1 tags after filtering in treatment: 6126346 INFO @ Mon, 07 Sep 2015 18:49:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:49:01: #1 finished! INFO @ Mon, 07 Sep 2015 18:49:01: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:49:01: #2 number of paired peaks: 342 WARNING @ Mon, 07 Sep 2015 18:49:01: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Mon, 07 Sep 2015 18:49:01: start model_add_line... INFO @ Mon, 07 Sep 2015 18:49:01: #2 number of paired peaks: 342 WARNING @ Mon, 07 Sep 2015 18:49:01: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Mon, 07 Sep 2015 18:49:01: start model_add_line... INFO @ Mon, 07 Sep 2015 18:49:02: #2 number of paired peaks: 342 WARNING @ Mon, 07 Sep 2015 18:49:02: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Mon, 07 Sep 2015 18:49:02: start model_add_line... INFO @ Mon, 07 Sep 2015 18:49:04: start X-correlation... INFO @ Mon, 07 Sep 2015 18:49:05: start X-correlation... INFO @ Mon, 07 Sep 2015 18:49:05: end of X-cor INFO @ Mon, 07 Sep 2015 18:49:05: end of X-cor INFO @ Mon, 07 Sep 2015 18:49:05: #2 finished! INFO @ Mon, 07 Sep 2015 18:49:05: #2 finished! INFO @ Mon, 07 Sep 2015 18:49:05: #2 predicted fragment length is 31 bps INFO @ Mon, 07 Sep 2015 18:49:05: #2 predicted fragment length is 31 bps INFO @ Mon, 07 Sep 2015 18:49:05: #2 alternative fragment length(s) may be 4,31,523,542 bps INFO @ Mon, 07 Sep 2015 18:49:05: #2 alternative fragment length(s) may be 4,31,523,542 bps INFO @ Mon, 07 Sep 2015 18:49:05: #2.2 Generate R script for model : SRX003816.10_model.r INFO @ Mon, 07 Sep 2015 18:49:05: #2.2 Generate R script for model : SRX003816.20_model.r WARNING @ Mon, 07 Sep 2015 18:49:05: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:49:05: #2 You may need to consider one of the other alternative d(s): 4,31,523,542 WARNING @ Mon, 07 Sep 2015 18:49:05: #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 18:49:05: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:49:05: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 07 Sep 2015 18:49:05: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:49:05: #2 You may need to consider one of the other alternative d(s): 4,31,523,542 WARNING @ Mon, 07 Sep 2015 18:49:05: #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 18:49:05: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:49:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:49:06: start X-correlation... INFO @ Mon, 07 Sep 2015 18:49:06: end of X-cor INFO @ Mon, 07 Sep 2015 18:49:06: #2 finished! INFO @ Mon, 07 Sep 2015 18:49:06: #2 predicted fragment length is 31 bps INFO @ Mon, 07 Sep 2015 18:49:06: #2 alternative fragment length(s) may be 4,31,523,542 bps INFO @ Mon, 07 Sep 2015 18:49:06: #2.2 Generate R script for model : SRX003816.05_model.r WARNING @ Mon, 07 Sep 2015 18:49:06: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:49:06: #2 You may need to consider one of the other alternative d(s): 4,31,523,542 WARNING @ Mon, 07 Sep 2015 18:49:06: #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 18:49:06: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:49:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:49:37: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:49:39: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:49:41: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:50:02: #4 Write output xls file... SRX003816.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:50:02: #4 Write peak in narrowPeak format file... SRX003816.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:50:03: #4 Write output xls file... SRX003816.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:50:03: #4 Write summits bed file... SRX003816.10_summits.bed INFO @ Mon, 07 Sep 2015 18:50:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:50:03: #4 Write peak in narrowPeak format file... SRX003816.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:50:03: #4 Write summits bed file... SRX003816.20_summits.bed INFO @ Mon, 07 Sep 2015 18:50:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:50:05: #4 Write output xls file... SRX003816.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:50:05: #4 Write peak in narrowPeak format file... SRX003816.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:50:05: #4 Write summits bed file... SRX003816.05_summits.bed INFO @ Mon, 07 Sep 2015 18:50:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (484 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。