Job ID = 9730458 sra ファイルのダウンロード中... Completed: 610915K bytes transferred in 38 seconds (131243K bits/sec), in 1 file, 2 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 19779275 spots for /home/okishinya/chipatlas/results/dm3/SRX2829098/SRR5569908.sra Written 19779275 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: 00:06:57 19779275 reads; of these: 19779275 (100.00%) were unpaired; of these: 3514581 (17.77%) aligned 0 times 10442680 (52.80%) aligned exactly 1 time 5822014 (29.43%) aligned >1 times 82.23% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:58 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] 8796004 / 16264694 = 0.5408 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 @ Sun, 03 Sep 2017 01:06:25: # Command line: callpeak -t SRX2829098.bam -f BAM -g dm -n SRX2829098.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2829098.20 # format = BAM # ChIP-seq file = ['SRX2829098.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 @ Sun, 03 Sep 2017 01:06:25: # Command line: callpeak -t SRX2829098.bam -f BAM -g dm -n SRX2829098.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2829098.05 # format = BAM # ChIP-seq file = ['SRX2829098.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 @ Sun, 03 Sep 2017 01:06:25: # Command line: callpeak -t SRX2829098.bam -f BAM -g dm -n SRX2829098.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2829098.10 # format = BAM # ChIP-seq file = ['SRX2829098.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 @ Sun, 03 Sep 2017 01:06:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:06:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:06:25: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:06:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:06:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:06:25: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:06:31: 1000000 INFO @ Sun, 03 Sep 2017 01:06:32: 1000000 INFO @ Sun, 03 Sep 2017 01:06:32: 1000000 INFO @ Sun, 03 Sep 2017 01:06:38: 2000000 INFO @ Sun, 03 Sep 2017 01:06:39: 2000000 INFO @ Sun, 03 Sep 2017 01:06:39: 2000000 INFO @ Sun, 03 Sep 2017 01:06:44: 3000000 INFO @ Sun, 03 Sep 2017 01:06:47: 3000000 INFO @ Sun, 03 Sep 2017 01:06:47: 3000000 INFO @ Sun, 03 Sep 2017 01:06:51: 4000000 INFO @ Sun, 03 Sep 2017 01:06:54: 4000000 INFO @ Sun, 03 Sep 2017 01:06:54: 4000000 INFO @ Sun, 03 Sep 2017 01:06:58: 5000000 INFO @ Sun, 03 Sep 2017 01:07:01: 5000000 INFO @ Sun, 03 Sep 2017 01:07:01: 5000000 INFO @ Sun, 03 Sep 2017 01:07:04: 6000000 INFO @ Sun, 03 Sep 2017 01:07:09: 6000000 INFO @ Sun, 03 Sep 2017 01:07:09: 6000000 INFO @ Sun, 03 Sep 2017 01:07:11: 7000000 INFO @ Sun, 03 Sep 2017 01:07:14: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:07:14: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:07:14: #1 total tags in treatment: 7468690 INFO @ Sun, 03 Sep 2017 01:07:14: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:07:14: #1 tags after filtering in treatment: 7468690 INFO @ Sun, 03 Sep 2017 01:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:14: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:14: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:15: #2 number of paired peaks: 624 WARNING @ Sun, 03 Sep 2017 01:07:15: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:15: start model_add_line... INFO @ Sun, 03 Sep 2017 01:07:15: start X-correlation... INFO @ Sun, 03 Sep 2017 01:07:15: end of X-cor INFO @ Sun, 03 Sep 2017 01:07:15: #2 finished! INFO @ Sun, 03 Sep 2017 01:07:15: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Sep 2017 01:07:15: #2 alternative fragment length(s) may be 47 bps INFO @ Sun, 03 Sep 2017 01:07:15: #2.2 Generate R script for model : SRX2829098.20_model.r WARNING @ Sun, 03 Sep 2017 01:07:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:07:15: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sun, 03 Sep 2017 01:07:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:07:15: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:07:16: 7000000 INFO @ Sun, 03 Sep 2017 01:07:16: 7000000 INFO @ Sun, 03 Sep 2017 01:07:19: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:07:19: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:07:19: #1 total tags in treatment: 7468690 INFO @ Sun, 03 Sep 2017 01:07:19: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:07:19: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:07:19: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:07:19: #1 total tags in treatment: 7468690 INFO @ Sun, 03 Sep 2017 01:07:19: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:07:19: #1 tags after filtering in treatment: 7468690 INFO @ Sun, 03 Sep 2017 01:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:19: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:19: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:19: #1 tags after filtering in treatment: 7468690 INFO @ Sun, 03 Sep 2017 01:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:19: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:19: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:20: #2 number of paired peaks: 624 WARNING @ Sun, 03 Sep 2017 01:07:20: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:20: start model_add_line... INFO @ Sun, 03 Sep 2017 01:07:20: #2 number of paired peaks: 624 WARNING @ Sun, 03 Sep 2017 01:07:20: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:20: start model_add_line... INFO @ Sun, 03 Sep 2017 01:07:20: start X-correlation... INFO @ Sun, 03 Sep 2017 01:07:20: end of X-cor INFO @ Sun, 03 Sep 2017 01:07:20: #2 finished! INFO @ Sun, 03 Sep 2017 01:07:20: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Sep 2017 01:07:20: #2 alternative fragment length(s) may be 47 bps INFO @ Sun, 03 Sep 2017 01:07:20: #2.2 Generate R script for model : SRX2829098.10_model.r INFO @ Sun, 03 Sep 2017 01:07:20: start X-correlation... INFO @ Sun, 03 Sep 2017 01:07:20: end of X-cor INFO @ Sun, 03 Sep 2017 01:07:20: #2 finished! INFO @ Sun, 03 Sep 2017 01:07:20: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Sep 2017 01:07:20: #2 alternative fragment length(s) may be 47 bps INFO @ Sun, 03 Sep 2017 01:07:20: #2.2 Generate R script for model : SRX2829098.05_model.r WARNING @ Sun, 03 Sep 2017 01:07:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:07:20: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sun, 03 Sep 2017 01:07:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:07:20: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:07:20: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 03 Sep 2017 01:07:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:07:20: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sun, 03 Sep 2017 01:07:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:07:20: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:07:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:07:32: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:07:37: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:07:37: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:07:41: #4 Write output xls file... SRX2829098.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:07:41: #4 Write peak in narrowPeak format file... SRX2829098.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:07:41: #4 Write summits bed file... SRX2829098.20_summits.bed INFO @ Sun, 03 Sep 2017 01:07:41: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1086 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:07:47: #4 Write output xls file... SRX2829098.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:07:47: #4 Write peak in narrowPeak format file... SRX2829098.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:07:47: #4 Write summits bed file... SRX2829098.05_summits.bed INFO @ Sun, 03 Sep 2017 01:07:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2247 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:07:47: #4 Write output xls file... SRX2829098.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:07:47: #4 Write peak in narrowPeak format file... SRX2829098.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:07:47: #4 Write summits bed file... SRX2829098.10_summits.bed INFO @ Sun, 03 Sep 2017 01:07:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1582 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。