Job ID = 2161206 sra ファイルのダウンロード中... Completed: 216001K bytes transferred in 6 seconds (289100K 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 34473 0 34473 0 0 49133 0 --:--:-- --:--:-- --:--:-- 67594 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 7632922 spots for /home/okishinya/chipatlas/results/dm3/SRX013054/SRR030320.sra Written 7632922 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: 00:01:55 7632922 reads; of these: 7632922 (100.00%) were unpaired; of these: 586272 (7.68%) aligned 0 times 5778221 (75.70%) aligned exactly 1 time 1268429 (16.62%) aligned >1 times 92.32% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 431146 / 7046650 = 0.0612 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 @ Tue, 21 Apr 2015 12:05:58: # Command line: callpeak -t SRX013054.bam -f BAM -g dm -n SRX013054.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013054.05 # format = BAM # ChIP-seq file = ['SRX013054.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:05:58: # Command line: callpeak -t SRX013054.bam -f BAM -g dm -n SRX013054.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013054.10 # format = BAM # ChIP-seq file = ['SRX013054.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:05:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:05:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:05:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:05:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:05:58: # Command line: callpeak -t SRX013054.bam -f BAM -g dm -n SRX013054.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013054.20 # format = BAM # ChIP-seq file = ['SRX013054.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:05:58: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:05:58: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:06:03: 1000000 INFO @ Tue, 21 Apr 2015 12:06:03: 1000000 INFO @ Tue, 21 Apr 2015 12:06:03: 1000000 INFO @ Tue, 21 Apr 2015 12:06:08: 2000000 INFO @ Tue, 21 Apr 2015 12:06:08: 2000000 INFO @ Tue, 21 Apr 2015 12:06:08: 2000000 INFO @ Tue, 21 Apr 2015 12:06:13: 3000000 INFO @ Tue, 21 Apr 2015 12:06:13: 3000000 INFO @ Tue, 21 Apr 2015 12:06:13: 3000000 INFO @ Tue, 21 Apr 2015 12:06:18: 4000000 INFO @ Tue, 21 Apr 2015 12:06:18: 4000000 INFO @ Tue, 21 Apr 2015 12:06:19: 4000000 INFO @ Tue, 21 Apr 2015 12:06:23: 5000000 INFO @ Tue, 21 Apr 2015 12:06:24: 5000000 INFO @ Tue, 21 Apr 2015 12:06:24: 5000000 INFO @ Tue, 21 Apr 2015 12:06:29: 6000000 INFO @ Tue, 21 Apr 2015 12:06:29: 6000000 INFO @ Tue, 21 Apr 2015 12:06:30: 6000000 INFO @ Tue, 21 Apr 2015 12:06:32: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:06:32: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:06:32: #1 total tags in treatment: 6615504 INFO @ Tue, 21 Apr 2015 12:06:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:06:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:06:32: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:06:32: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:06:32: #1 total tags in treatment: 6615504 INFO @ Tue, 21 Apr 2015 12:06:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:06:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:06:33: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:06:33: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:06:33: #1 total tags in treatment: 6615504 INFO @ Tue, 21 Apr 2015 12:06:33: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:06:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:06:33: #1 tags after filtering in treatment: 6614665 INFO @ Tue, 21 Apr 2015 12:06:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:06:33: #1 finished! INFO @ Tue, 21 Apr 2015 12:06:33: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:06:33: #1 tags after filtering in treatment: 6614665 INFO @ Tue, 21 Apr 2015 12:06:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:06:33: #1 finished! INFO @ Tue, 21 Apr 2015 12:06:33: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:06:34: #1 tags after filtering in treatment: 6614665 INFO @ Tue, 21 Apr 2015 12:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:06:34: #1 finished! INFO @ Tue, 21 Apr 2015 12:06:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:06:34: #2 number of paired peaks: 111 WARNING @ Tue, 21 Apr 2015 12:06:34: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 21 Apr 2015 12:06:34: start model_add_line... INFO @ Tue, 21 Apr 2015 12:06:34: #2 number of paired peaks: 111 WARNING @ Tue, 21 Apr 2015 12:06:34: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 21 Apr 2015 12:06:34: start model_add_line... INFO @ Tue, 21 Apr 2015 12:06:35: start X-correlation... INFO @ Tue, 21 Apr 2015 12:06:35: end of X-cor INFO @ Tue, 21 Apr 2015 12:06:35: #2 finished! INFO @ Tue, 21 Apr 2015 12:06:35: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 12:06:35: #2 alternative fragment length(s) may be 46,518 bps INFO @ Tue, 21 Apr 2015 12:06:35: #2.2 Generate R script for model : SRX013054.05_model.r WARNING @ Tue, 21 Apr 2015 12:06:35: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:06:35: #2 You may need to consider one of the other alternative d(s): 46,518 WARNING @ Tue, 21 Apr 2015 12:06:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:06:35: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:06:35: start X-correlation... INFO @ Tue, 21 Apr 2015 12:06:35: end of X-cor INFO @ Tue, 21 Apr 2015 12:06:35: #2 finished! INFO @ Tue, 21 Apr 2015 12:06:35: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 12:06:35: #2 alternative fragment length(s) may be 46,518 bps INFO @ Tue, 21 Apr 2015 12:06:35: #2.2 Generate R script for model : SRX013054.20_model.r WARNING @ Tue, 21 Apr 2015 12:06:35: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:06:35: #2 You may need to consider one of the other alternative d(s): 46,518 WARNING @ Tue, 21 Apr 2015 12:06:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:06:35: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:06:35: #2 number of paired peaks: 111 WARNING @ Tue, 21 Apr 2015 12:06:35: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 21 Apr 2015 12:06:35: start model_add_line... INFO @ Tue, 21 Apr 2015 12:06:36: start X-correlation... INFO @ Tue, 21 Apr 2015 12:06:36: end of X-cor INFO @ Tue, 21 Apr 2015 12:06:36: #2 finished! INFO @ Tue, 21 Apr 2015 12:06:36: #2 predicted fragment length is 46 bps INFO @ Tue, 21 Apr 2015 12:06:36: #2 alternative fragment length(s) may be 46,518 bps INFO @ Tue, 21 Apr 2015 12:06:36: #2.2 Generate R script for model : SRX013054.10_model.r WARNING @ Tue, 21 Apr 2015 12:06:36: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:06:36: #2 You may need to consider one of the other alternative d(s): 46,518 WARNING @ Tue, 21 Apr 2015 12:06:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:06:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:06:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:07:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:07:12: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:07:13: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:07:36: #4 Write output xls file... SRX013054.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:07:36: #4 Write peak in narrowPeak format file... SRX013054.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:07:36: #4 Write summits bed file... SRX013054.10_summits.bed INFO @ Tue, 21 Apr 2015 12:07:36: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (398 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:07:37: #4 Write output xls file... SRX013054.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:07:37: #4 Write peak in narrowPeak format file... SRX013054.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:07:37: #4 Write summits bed file... SRX013054.20_summits.bed INFO @ Tue, 21 Apr 2015 12:07:37: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:07:41: #4 Write output xls file... SRX013054.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:07:41: #4 Write peak in narrowPeak format file... SRX013054.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:07:41: #4 Write summits bed file... SRX013054.05_summits.bed INFO @ Tue, 21 Apr 2015 12:07:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (967 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。