Job ID = 2162415 sra ファイルのダウンロード中... Completed: 559540K bytes transferred in 8 seconds (551540K 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 35549 0 35549 0 0 49851 0 --:--:-- --:--:-- --:--:-- 68232 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 21810536 spots for /home/okishinya/chipatlas/results/dm3/SRX085410/SRR317188.sra Written 21810536 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: 00:00:01 Multiseed full-index search: 00:10:21 21810536 reads; of these: 21810536 (100.00%) were unpaired; of these: 6126247 (28.09%) aligned 0 times 10656098 (48.86%) aligned exactly 1 time 5028191 (23.05%) aligned >1 times 71.91% overall alignment rate Time searching: 00:10:23 Overall time: 00:10:23 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4202904 / 15684289 = 0.2680 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 14:06:12: # Command line: callpeak -t SRX085410.bam -f BAM -g dm -n SRX085410.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX085410.05 # format = BAM # ChIP-seq file = ['SRX085410.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 14:06:12: # Command line: callpeak -t SRX085410.bam -f BAM -g dm -n SRX085410.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX085410.10 # format = BAM # ChIP-seq file = ['SRX085410.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 14:06:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:06:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:06:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:06:12: # Command line: callpeak -t SRX085410.bam -f BAM -g dm -n SRX085410.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX085410.20 # format = BAM # ChIP-seq file = ['SRX085410.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 14:06:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:06:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:06:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:06:18: 1000000 INFO @ Tue, 21 Apr 2015 14:06:18: 1000000 INFO @ Tue, 21 Apr 2015 14:06:18: 1000000 INFO @ Tue, 21 Apr 2015 14:06:23: 2000000 INFO @ Tue, 21 Apr 2015 14:06:23: 2000000 INFO @ Tue, 21 Apr 2015 14:06:23: 2000000 INFO @ Tue, 21 Apr 2015 14:06:29: 3000000 INFO @ Tue, 21 Apr 2015 14:06:29: 3000000 INFO @ Tue, 21 Apr 2015 14:06:29: 3000000 INFO @ Tue, 21 Apr 2015 14:06:35: 4000000 INFO @ Tue, 21 Apr 2015 14:06:35: 4000000 INFO @ Tue, 21 Apr 2015 14:06:35: 4000000 INFO @ Tue, 21 Apr 2015 14:06:41: 5000000 INFO @ Tue, 21 Apr 2015 14:06:41: 5000000 INFO @ Tue, 21 Apr 2015 14:06:41: 5000000 INFO @ Tue, 21 Apr 2015 14:06:46: 6000000 INFO @ Tue, 21 Apr 2015 14:06:46: 6000000 INFO @ Tue, 21 Apr 2015 14:06:47: 6000000 INFO @ Tue, 21 Apr 2015 14:06:52: 7000000 INFO @ Tue, 21 Apr 2015 14:06:52: 7000000 INFO @ Tue, 21 Apr 2015 14:06:53: 7000000 INFO @ Tue, 21 Apr 2015 14:06:58: 8000000 INFO @ Tue, 21 Apr 2015 14:06:58: 8000000 INFO @ Tue, 21 Apr 2015 14:06:59: 8000000 INFO @ Tue, 21 Apr 2015 14:07:04: 9000000 INFO @ Tue, 21 Apr 2015 14:07:04: 9000000 INFO @ Tue, 21 Apr 2015 14:07:05: 9000000 INFO @ Tue, 21 Apr 2015 14:07:10: 10000000 INFO @ Tue, 21 Apr 2015 14:07:10: 10000000 INFO @ Tue, 21 Apr 2015 14:07:11: 10000000 INFO @ Tue, 21 Apr 2015 14:07:15: 11000000 INFO @ Tue, 21 Apr 2015 14:07:16: 11000000 INFO @ Tue, 21 Apr 2015 14:07:17: 11000000 INFO @ Tue, 21 Apr 2015 14:07:18: #1 tag size is determined as 54 bps INFO @ Tue, 21 Apr 2015 14:07:18: #1 tag size = 54 INFO @ Tue, 21 Apr 2015 14:07:18: #1 total tags in treatment: 11481385 INFO @ Tue, 21 Apr 2015 14:07:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:18: #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 14:07:19: #1 tag size is determined as 54 bps INFO @ Tue, 21 Apr 2015 14:07:19: #1 tag size = 54 INFO @ Tue, 21 Apr 2015 14:07:19: #1 total tags in treatment: 11481385 INFO @ Tue, 21 Apr 2015 14:07:19: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:19: #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 14:07:20: #1 tag size is determined as 54 bps INFO @ Tue, 21 Apr 2015 14:07:20: #1 tag size = 54 INFO @ Tue, 21 Apr 2015 14:07:20: #1 total tags in treatment: 11481385 INFO @ Tue, 21 Apr 2015 14:07:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:20: #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 14:07:20: #1 tags after filtering in treatment: 11433127 INFO @ Tue, 21 Apr 2015 14:07:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:20: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:20: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:21: #1 tags after filtering in treatment: 11433127 INFO @ Tue, 21 Apr 2015 14:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:21: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:22: #1 tags after filtering in treatment: 11433127 INFO @ Tue, 21 Apr 2015 14:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:22: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:22: #2 number of paired peaks: 373 WARNING @ Tue, 21 Apr 2015 14:07:22: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Tue, 21 Apr 2015 14:07:22: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:23: #2 number of paired peaks: 373 WARNING @ Tue, 21 Apr 2015 14:07:23: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Tue, 21 Apr 2015 14:07:23: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:24: #2 number of paired peaks: 373 WARNING @ Tue, 21 Apr 2015 14:07:24: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Tue, 21 Apr 2015 14:07:24: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:26: start X-correlation... INFO @ Tue, 21 Apr 2015 14:07:26: end of X-cor INFO @ Tue, 21 Apr 2015 14:07:26: #2 finished! INFO @ Tue, 21 Apr 2015 14:07:26: #2 predicted fragment length is 50 bps INFO @ Tue, 21 Apr 2015 14:07:26: #2 alternative fragment length(s) may be 3,50,536 bps INFO @ Tue, 21 Apr 2015 14:07:26: #2.2 Generate R script for model : SRX085410.20_model.r WARNING @ Tue, 21 Apr 2015 14:07:26: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:07:26: #2 You may need to consider one of the other alternative d(s): 3,50,536 WARNING @ Tue, 21 Apr 2015 14:07:26: #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 14:07:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:07:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:07:27: start X-correlation... INFO @ Tue, 21 Apr 2015 14:07:27: end of X-cor INFO @ Tue, 21 Apr 2015 14:07:27: #2 finished! INFO @ Tue, 21 Apr 2015 14:07:27: #2 predicted fragment length is 50 bps INFO @ Tue, 21 Apr 2015 14:07:27: #2 alternative fragment length(s) may be 3,50,536 bps INFO @ Tue, 21 Apr 2015 14:07:27: #2.2 Generate R script for model : SRX085410.05_model.r WARNING @ Tue, 21 Apr 2015 14:07:27: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:07:27: #2 You may need to consider one of the other alternative d(s): 3,50,536 WARNING @ Tue, 21 Apr 2015 14:07:27: #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 14:07:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:07:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:07:28: start X-correlation... INFO @ Tue, 21 Apr 2015 14:07:28: end of X-cor INFO @ Tue, 21 Apr 2015 14:07:28: #2 finished! INFO @ Tue, 21 Apr 2015 14:07:28: #2 predicted fragment length is 50 bps INFO @ Tue, 21 Apr 2015 14:07:28: #2 alternative fragment length(s) may be 3,50,536 bps INFO @ Tue, 21 Apr 2015 14:07:28: #2.2 Generate R script for model : SRX085410.10_model.r WARNING @ Tue, 21 Apr 2015 14:07:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:07:28: #2 You may need to consider one of the other alternative d(s): 3,50,536 WARNING @ Tue, 21 Apr 2015 14:07:28: #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 14:07:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:08:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:08:29: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:08:29: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:09:11: #4 Write output xls file... SRX085410.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:09:11: #4 Write peak in narrowPeak format file... SRX085410.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:09:11: #4 Write summits bed file... SRX085410.20_summits.bed INFO @ Tue, 21 Apr 2015 14:09:11: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (725 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:09:14: #4 Write output xls file... SRX085410.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:09:14: #4 Write peak in narrowPeak format file... SRX085410.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:09:14: #4 Write summits bed file... SRX085410.05_summits.bed INFO @ Tue, 21 Apr 2015 14:09:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2650 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:09:14: #4 Write output xls file... SRX085410.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:09:14: #4 Write peak in narrowPeak format file... SRX085410.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:09:14: #4 Write summits bed file... SRX085410.10_summits.bed INFO @ Tue, 21 Apr 2015 14:09:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1455 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。