Job ID = 3001484 sra ファイルのダウンロード中... Completed: 524021K bytes transferred in 11 seconds (369056K 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 8765 0 --:--:-- 0:00:01 --:--:-- 9935 100 14953 0 14953 0 0 5522 0 --:--:-- 0:00:02 --:--:-- 5964 100 14953 0 14953 0 0 4030 0 --:--:-- 0:00:03 --:--:-- 4261 100 14953 0 14953 0 0 3174 0 --:--:-- 0:00:04 --:--:-- 3315 100 14953 0 14953 0 0 2617 0 --:--:-- 0:00:05 --:--:-- 2712 100 14953 0 14953 0 0 2227 0 --:--:-- 0:00:06 --:--:-- 0 100 16407 0 16407 0 0 2160 0 --:--:-- 0:00:07 --:--:-- 297 100 19327 0 19327 0 0 2463 0 --:--:-- 0:00:07 --:--:-- 1057 100 40368 0 40368 0 0 4999 0 --:--:-- 0:00:08 --:--:-- 7552 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 2362213 spots for /home/okishinya/chipatlas/results/ce10/SRX003827/SRR015067.sra Written 2362213 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 2362213 reads; of these: 2362213 (100.00%) were unpaired; of these: 1591022 (67.35%) aligned 0 times 561576 (23.77%) aligned exactly 1 time 209615 (8.87%) aligned >1 times 32.65% 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] 168288 / 771191 = 0.2182 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 18:44:54: # Command line: callpeak -t SRX003827.bam -f BAM -g ce -n SRX003827.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003827.10 # format = BAM # ChIP-seq file = ['SRX003827.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 18:44:54: # Command line: callpeak -t SRX003827.bam -f BAM -g ce -n SRX003827.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003827.20 # format = BAM # ChIP-seq file = ['SRX003827.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 18:44:54: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:44:54: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:44:54: # Command line: callpeak -t SRX003827.bam -f BAM -g ce -n SRX003827.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003827.05 # format = BAM # ChIP-seq file = ['SRX003827.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 18:44:54: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:44:54: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:44:54: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:44:54: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:44:57: #1 tag size is determined as 33 bps INFO @ Mon, 07 Sep 2015 18:44:57: #1 tag size = 33 INFO @ Mon, 07 Sep 2015 18:44:57: #1 total tags in treatment: 602903 INFO @ Mon, 07 Sep 2015 18:44:57: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:44:57: #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 18:44:57: #1 tag size is determined as 33 bps INFO @ Mon, 07 Sep 2015 18:44:57: #1 tag size = 33 INFO @ Mon, 07 Sep 2015 18:44:57: #1 total tags in treatment: 602903 INFO @ Mon, 07 Sep 2015 18:44:57: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:44:57: #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 18:44:57: #1 tag size is determined as 33 bps INFO @ Mon, 07 Sep 2015 18:44:57: #1 tag size = 33 INFO @ Mon, 07 Sep 2015 18:44:57: #1 total tags in treatment: 602903 INFO @ Mon, 07 Sep 2015 18:44:57: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:44:57: #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 18:44:57: #1 tags after filtering in treatment: 602575 INFO @ Mon, 07 Sep 2015 18:44:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:44:57: #1 finished! INFO @ Mon, 07 Sep 2015 18:44:57: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:44:57: #1 tags after filtering in treatment: 602575 INFO @ Mon, 07 Sep 2015 18:44:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:44:57: #1 finished! INFO @ Mon, 07 Sep 2015 18:44:57: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:44:57: #1 tags after filtering in treatment: 602575 INFO @ Mon, 07 Sep 2015 18:44:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:44:57: #1 finished! INFO @ Mon, 07 Sep 2015 18:44:57: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:44:58: #2 number of paired peaks: 497 WARNING @ Mon, 07 Sep 2015 18:44:58: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Mon, 07 Sep 2015 18:44:58: start model_add_line... INFO @ Mon, 07 Sep 2015 18:44:58: #2 number of paired peaks: 497 WARNING @ Mon, 07 Sep 2015 18:44:58: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Mon, 07 Sep 2015 18:44:58: start model_add_line... INFO @ Mon, 07 Sep 2015 18:44:58: #2 number of paired peaks: 497 WARNING @ Mon, 07 Sep 2015 18:44:58: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Mon, 07 Sep 2015 18:44:58: start model_add_line... INFO @ Mon, 07 Sep 2015 18:44:58: start X-correlation... INFO @ Mon, 07 Sep 2015 18:44:58: start X-correlation... INFO @ Mon, 07 Sep 2015 18:44:58: start X-correlation... INFO @ Mon, 07 Sep 2015 18:44:58: end of X-cor INFO @ Mon, 07 Sep 2015 18:44:58: end of X-cor INFO @ Mon, 07 Sep 2015 18:44:58: #2 finished! INFO @ Mon, 07 Sep 2015 18:44:58: #2 finished! INFO @ Mon, 07 Sep 2015 18:44:58: #2 predicted fragment length is 38 bps INFO @ Mon, 07 Sep 2015 18:44:58: #2 predicted fragment length is 38 bps INFO @ Mon, 07 Sep 2015 18:44:58: end of X-cor INFO @ Mon, 07 Sep 2015 18:44:58: #2 alternative fragment length(s) may be 38,63,143,543,578 bps INFO @ Mon, 07 Sep 2015 18:44:58: #2 alternative fragment length(s) may be 38,63,143,543,578 bps INFO @ Mon, 07 Sep 2015 18:44:58: #2 finished! INFO @ Mon, 07 Sep 2015 18:44:58: #2.2 Generate R script for model : SRX003827.10_model.r INFO @ Mon, 07 Sep 2015 18:44:58: #2.2 Generate R script for model : SRX003827.05_model.r INFO @ Mon, 07 Sep 2015 18:44:58: #2 predicted fragment length is 38 bps INFO @ Mon, 07 Sep 2015 18:44:58: #2 alternative fragment length(s) may be 38,63,143,543,578 bps INFO @ Mon, 07 Sep 2015 18:44:58: #2.2 Generate R script for model : SRX003827.20_model.r WARNING @ Mon, 07 Sep 2015 18:44:58: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:44:58: #2 You may need to consider one of the other alternative d(s): 38,63,143,543,578 WARNING @ Mon, 07 Sep 2015 18:44:58: #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 18:44:58: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:44:58: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 07 Sep 2015 18:44:58: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:44:58: #2 You may need to consider one of the other alternative d(s): 38,63,143,543,578 WARNING @ Mon, 07 Sep 2015 18:44:58: #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 18:44:58: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:44:58: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 07 Sep 2015 18:44:58: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 Sep 2015 18:44:58: #2 You may need to consider one of the other alternative d(s): 38,63,143,543,578 WARNING @ Mon, 07 Sep 2015 18:44:58: #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 18:44:58: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:44:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:02: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:02: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:02: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:05: #4 Write output xls file... SRX003827.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:05: #4 Write peak in narrowPeak format file... SRX003827.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:05: #4 Write summits bed file... SRX003827.20_summits.bed INFO @ Mon, 07 Sep 2015 18:45:05: #4 Write output xls file... SRX003827.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:05: Done! INFO @ Mon, 07 Sep 2015 18:45:05: #4 Write peak in narrowPeak format file... SRX003827.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:05: #4 Write summits bed file... SRX003827.10_summits.bed INFO @ Mon, 07 Sep 2015 18:45:05: Done! pass1 - making usageList (6 chroms): 3 millis INFO @ Mon, 07 Sep 2015 18:45:05: #4 Write output xls file... SRX003827.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:05: #4 Write peak in narrowPeak format file... SRX003827.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:05: #4 Write summits bed file... SRX003827.05_summits.bed INFO @ Mon, 07 Sep 2015 18:45:05: Done! pass2 - checking and writing primary data (155 records, 4 fields): 108 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 75 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (351 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。