Job ID = 10043497 sra ファイルのダウンロード中... Completed: 643702K bytes transferred in 18 seconds (282286K bits/sec), in 2 files, 3 directories. 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 8918051 spots for /home/okishinya/chipatlas/results/dm3/SRX2165279/SRR4244787.sra Written 8918051 spots total Written 7544460 spots for /home/okishinya/chipatlas/results/dm3/SRX2165279/SRR4244788.sra Written 7544460 spots total 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: 00:07:47 16462511 reads; of these: 16462511 (100.00%) were unpaired; of these: 3078669 (18.70%) aligned 0 times 9595139 (58.28%) aligned exactly 1 time 3788703 (23.01%) aligned >1 times 81.30% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 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] 3529594 / 13383842 = 0.2637 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, 02 Oct 2017 03:40:44: # Command line: callpeak -t SRX2165279.bam -f BAM -g dm -n SRX2165279.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2165279.10 # format = BAM # ChIP-seq file = ['SRX2165279.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 # Paired-End mode is off INFO @ Mon, 02 Oct 2017 03:40:44: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:40:44: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:40:44: # Command line: callpeak -t SRX2165279.bam -f BAM -g dm -n SRX2165279.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2165279.20 # format = BAM # ChIP-seq file = ['SRX2165279.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 # Paired-End mode is off INFO @ Mon, 02 Oct 2017 03:40:44: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:40:44: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:40:44: # Command line: callpeak -t SRX2165279.bam -f BAM -g dm -n SRX2165279.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2165279.05 # format = BAM # ChIP-seq file = ['SRX2165279.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 # Paired-End mode is off INFO @ Mon, 02 Oct 2017 03:40:44: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:40:44: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:40:52: 1000000 INFO @ Mon, 02 Oct 2017 03:40:53: 1000000 INFO @ Mon, 02 Oct 2017 03:40:53: 1000000 INFO @ Mon, 02 Oct 2017 03:41:00: 2000000 INFO @ Mon, 02 Oct 2017 03:41:02: 2000000 INFO @ Mon, 02 Oct 2017 03:41:02: 2000000 INFO @ Mon, 02 Oct 2017 03:41:07: 3000000 INFO @ Mon, 02 Oct 2017 03:41:10: 3000000 INFO @ Mon, 02 Oct 2017 03:41:10: 3000000 INFO @ Mon, 02 Oct 2017 03:41:15: 4000000 INFO @ Mon, 02 Oct 2017 03:41:19: 4000000 INFO @ Mon, 02 Oct 2017 03:41:19: 4000000 INFO @ Mon, 02 Oct 2017 03:41:23: 5000000 INFO @ Mon, 02 Oct 2017 03:41:28: 5000000 INFO @ Mon, 02 Oct 2017 03:41:28: 5000000 INFO @ Mon, 02 Oct 2017 03:41:31: 6000000 INFO @ Mon, 02 Oct 2017 03:41:37: 6000000 INFO @ Mon, 02 Oct 2017 03:41:37: 6000000 INFO @ Mon, 02 Oct 2017 03:41:39: 7000000 INFO @ Mon, 02 Oct 2017 03:41:45: 7000000 INFO @ Mon, 02 Oct 2017 03:41:45: 7000000 INFO @ Mon, 02 Oct 2017 03:41:47: 8000000 INFO @ Mon, 02 Oct 2017 03:41:54: 8000000 INFO @ Mon, 02 Oct 2017 03:41:54: 8000000 INFO @ Mon, 02 Oct 2017 03:41:54: 9000000 INFO @ Mon, 02 Oct 2017 03:42:01: #1 tag size is determined as 75 bps INFO @ Mon, 02 Oct 2017 03:42:01: #1 tag size = 75 INFO @ Mon, 02 Oct 2017 03:42:01: #1 total tags in treatment: 9854248 INFO @ Mon, 02 Oct 2017 03:42:01: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:42:01: #1 tags after filtering in treatment: 9854248 INFO @ Mon, 02 Oct 2017 03:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:42:01: #1 finished! INFO @ Mon, 02 Oct 2017 03:42:01: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:42:02: #2 number of paired peaks: 292 WARNING @ Mon, 02 Oct 2017 03:42:02: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Mon, 02 Oct 2017 03:42:02: start model_add_line... INFO @ Mon, 02 Oct 2017 03:42:02: start X-correlation... INFO @ Mon, 02 Oct 2017 03:42:02: end of X-cor INFO @ Mon, 02 Oct 2017 03:42:02: #2 finished! INFO @ Mon, 02 Oct 2017 03:42:02: #2 predicted fragment length is 100 bps INFO @ Mon, 02 Oct 2017 03:42:02: #2 alternative fragment length(s) may be 100 bps INFO @ Mon, 02 Oct 2017 03:42:02: #2.2 Generate R script for model : SRX2165279.10_model.r WARNING @ Mon, 02 Oct 2017 03:42:02: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:42:02: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Mon, 02 Oct 2017 03:42:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:42:02: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:42:02: 9000000 INFO @ Mon, 02 Oct 2017 03:42:02: 9000000 INFO @ Mon, 02 Oct 2017 03:42:10: #1 tag size is determined as 75 bps INFO @ Mon, 02 Oct 2017 03:42:10: #1 tag size = 75 INFO @ Mon, 02 Oct 2017 03:42:10: #1 total tags in treatment: 9854248 INFO @ Mon, 02 Oct 2017 03:42:10: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:42:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:42:10: #1 tag size is determined as 75 bps INFO @ Mon, 02 Oct 2017 03:42:10: #1 tag size = 75 INFO @ Mon, 02 Oct 2017 03:42:10: #1 total tags in treatment: 9854248 INFO @ Mon, 02 Oct 2017 03:42:10: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:42:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:42:10: #1 tags after filtering in treatment: 9854248 INFO @ Mon, 02 Oct 2017 03:42:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:42:10: #1 finished! INFO @ Mon, 02 Oct 2017 03:42:10: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:42:10: #1 tags after filtering in treatment: 9854248 INFO @ Mon, 02 Oct 2017 03:42:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:42:10: #1 finished! INFO @ Mon, 02 Oct 2017 03:42:10: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:42:10: #2 number of paired peaks: 292 WARNING @ Mon, 02 Oct 2017 03:42:10: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Mon, 02 Oct 2017 03:42:10: start model_add_line... INFO @ Mon, 02 Oct 2017 03:42:10: #2 number of paired peaks: 292 WARNING @ Mon, 02 Oct 2017 03:42:10: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Mon, 02 Oct 2017 03:42:10: start model_add_line... INFO @ Mon, 02 Oct 2017 03:42:11: start X-correlation... INFO @ Mon, 02 Oct 2017 03:42:11: end of X-cor INFO @ Mon, 02 Oct 2017 03:42:11: #2 finished! INFO @ Mon, 02 Oct 2017 03:42:11: #2 predicted fragment length is 100 bps INFO @ Mon, 02 Oct 2017 03:42:11: #2 alternative fragment length(s) may be 100 bps INFO @ Mon, 02 Oct 2017 03:42:11: #2.2 Generate R script for model : SRX2165279.20_model.r WARNING @ Mon, 02 Oct 2017 03:42:11: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:42:11: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Mon, 02 Oct 2017 03:42:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:42:11: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:42:11: start X-correlation... INFO @ Mon, 02 Oct 2017 03:42:11: end of X-cor INFO @ Mon, 02 Oct 2017 03:42:11: #2 finished! INFO @ Mon, 02 Oct 2017 03:42:11: #2 predicted fragment length is 100 bps INFO @ Mon, 02 Oct 2017 03:42:11: #2 alternative fragment length(s) may be 100 bps INFO @ Mon, 02 Oct 2017 03:42:11: #2.2 Generate R script for model : SRX2165279.05_model.r WARNING @ Mon, 02 Oct 2017 03:42:11: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:42:11: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Mon, 02 Oct 2017 03:42:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:42:11: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:42:24: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:42:34: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:42:34: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:42:37: #4 Write output xls file... SRX2165279.10_peaks.xls INFO @ Mon, 02 Oct 2017 03:42:37: #4 Write peak in narrowPeak format file... SRX2165279.10_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:42:37: #4 Write summits bed file... SRX2165279.10_summits.bed INFO @ Mon, 02 Oct 2017 03:42:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1805 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:42:46: #4 Write output xls file... SRX2165279.20_peaks.xls INFO @ Mon, 02 Oct 2017 03:42:46: #4 Write peak in narrowPeak format file... SRX2165279.20_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:42:46: #4 Write summits bed file... SRX2165279.20_summits.bed INFO @ Mon, 02 Oct 2017 03:42:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (997 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:42:47: #4 Write output xls file... SRX2165279.05_peaks.xls INFO @ Mon, 02 Oct 2017 03:42:47: #4 Write peak in narrowPeak format file... SRX2165279.05_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:42:47: #4 Write summits bed file... SRX2165279.05_summits.bed INFO @ Mon, 02 Oct 2017 03:42:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3056 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。