Job ID = 9157989 sra ファイルのダウンロード中... Completed: 805749K bytes transferred in 40 seconds (161653K 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 14693698 spots for /home/okishinya/chipatlas/results/dm3/SRX2788646/SRR5515266.sra Written 14693698 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: 00:06:54 14693698 reads; of these: 14693698 (100.00%) were unpaired; of these: 2191647 (14.92%) aligned 0 times 10889356 (74.11%) aligned exactly 1 time 1612695 (10.98%) aligned >1 times 85.08% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 7294387 / 12502051 = 0.5835 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, 27 Jun 2017 14:32:37: # Command line: callpeak -t SRX2788646.bam -f BAM -g dm -n SRX2788646.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2788646.20 # format = BAM # ChIP-seq file = ['SRX2788646.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 @ Tue, 27 Jun 2017 14:32:37: # Command line: callpeak -t SRX2788646.bam -f BAM -g dm -n SRX2788646.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2788646.10 # format = BAM # ChIP-seq file = ['SRX2788646.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 @ Tue, 27 Jun 2017 14:32:37: # Command line: callpeak -t SRX2788646.bam -f BAM -g dm -n SRX2788646.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2788646.05 # format = BAM # ChIP-seq file = ['SRX2788646.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 @ Tue, 27 Jun 2017 14:32:37: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:32:37: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:32:37: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:32:37: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:32:37: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:32:37: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:32:47: 1000000 INFO @ Tue, 27 Jun 2017 14:32:48: 1000000 INFO @ Tue, 27 Jun 2017 14:32:48: 1000000 INFO @ Tue, 27 Jun 2017 14:32:56: 2000000 INFO @ Tue, 27 Jun 2017 14:32:58: 2000000 INFO @ Tue, 27 Jun 2017 14:32:58: 2000000 INFO @ Tue, 27 Jun 2017 14:33:06: 3000000 INFO @ Tue, 27 Jun 2017 14:33:08: 3000000 INFO @ Tue, 27 Jun 2017 14:33:08: 3000000 INFO @ Tue, 27 Jun 2017 14:33:16: 4000000 INFO @ Tue, 27 Jun 2017 14:33:19: 4000000 INFO @ Tue, 27 Jun 2017 14:33:19: 4000000 INFO @ Tue, 27 Jun 2017 14:33:25: 5000000 INFO @ Tue, 27 Jun 2017 14:33:27: #1 tag size is determined as 98 bps INFO @ Tue, 27 Jun 2017 14:33:27: #1 tag size = 98 INFO @ Tue, 27 Jun 2017 14:33:27: #1 total tags in treatment: 5207664 INFO @ Tue, 27 Jun 2017 14:33:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:33:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:33:27: #1 tags after filtering in treatment: 5207664 INFO @ Tue, 27 Jun 2017 14:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:33:27: #1 finished! INFO @ Tue, 27 Jun 2017 14:33:27: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:33:28: #2 number of paired peaks: 5936 INFO @ Tue, 27 Jun 2017 14:33:28: start model_add_line... INFO @ Tue, 27 Jun 2017 14:33:28: start X-correlation... INFO @ Tue, 27 Jun 2017 14:33:28: end of X-cor INFO @ Tue, 27 Jun 2017 14:33:28: #2 finished! INFO @ Tue, 27 Jun 2017 14:33:28: #2 predicted fragment length is 180 bps INFO @ Tue, 27 Jun 2017 14:33:28: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 27 Jun 2017 14:33:28: #2.2 Generate R script for model : SRX2788646.10_model.r WARNING @ Tue, 27 Jun 2017 14:33:28: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:33:28: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Tue, 27 Jun 2017 14:33:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 14:33:28: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:33:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:33:29: 5000000 INFO @ Tue, 27 Jun 2017 14:33:29: 5000000 INFO @ Tue, 27 Jun 2017 14:33:31: #1 tag size is determined as 98 bps INFO @ Tue, 27 Jun 2017 14:33:31: #1 tag size = 98 INFO @ Tue, 27 Jun 2017 14:33:31: #1 total tags in treatment: 5207664 INFO @ Tue, 27 Jun 2017 14:33:31: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:33:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:33:31: #1 tag size is determined as 98 bps INFO @ Tue, 27 Jun 2017 14:33:31: #1 tag size = 98 INFO @ Tue, 27 Jun 2017 14:33:31: #1 total tags in treatment: 5207664 INFO @ Tue, 27 Jun 2017 14:33:31: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:33:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:33:31: #1 tags after filtering in treatment: 5207664 INFO @ Tue, 27 Jun 2017 14:33:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:33:31: #1 finished! INFO @ Tue, 27 Jun 2017 14:33:31: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:33:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:33:31: #1 tags after filtering in treatment: 5207664 INFO @ Tue, 27 Jun 2017 14:33:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:33:31: #1 finished! INFO @ Tue, 27 Jun 2017 14:33:31: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:33:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:33:31: #2 number of paired peaks: 5936 INFO @ Tue, 27 Jun 2017 14:33:31: start model_add_line... INFO @ Tue, 27 Jun 2017 14:33:31: #2 number of paired peaks: 5936 INFO @ Tue, 27 Jun 2017 14:33:31: start model_add_line... INFO @ Tue, 27 Jun 2017 14:33:32: start X-correlation... INFO @ Tue, 27 Jun 2017 14:33:32: end of X-cor INFO @ Tue, 27 Jun 2017 14:33:32: #2 finished! INFO @ Tue, 27 Jun 2017 14:33:32: #2 predicted fragment length is 180 bps INFO @ Tue, 27 Jun 2017 14:33:32: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 27 Jun 2017 14:33:32: #2.2 Generate R script for model : SRX2788646.05_model.r INFO @ Tue, 27 Jun 2017 14:33:32: start X-correlation... INFO @ Tue, 27 Jun 2017 14:33:32: end of X-cor INFO @ Tue, 27 Jun 2017 14:33:32: #2 finished! WARNING @ Tue, 27 Jun 2017 14:33:32: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Tue, 27 Jun 2017 14:33:32: #2 predicted fragment length is 180 bps WARNING @ Tue, 27 Jun 2017 14:33:32: #2 You may need to consider one of the other alternative d(s): 180 INFO @ Tue, 27 Jun 2017 14:33:32: #2 alternative fragment length(s) may be 180 bps WARNING @ Tue, 27 Jun 2017 14:33:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 14:33:32: #2.2 Generate R script for model : SRX2788646.20_model.r INFO @ Tue, 27 Jun 2017 14:33:32: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:33:32: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 27 Jun 2017 14:33:32: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:33:32: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Tue, 27 Jun 2017 14:33:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 14:33:32: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:33:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:33:45: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:33:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:33:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:33:53: #4 Write output xls file... SRX2788646.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:33:53: #4 Write peak in narrowPeak format file... SRX2788646.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:33:53: #4 Write summits bed file... SRX2788646.10_summits.bed INFO @ Tue, 27 Jun 2017 14:33:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4950 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:33:56: #4 Write output xls file... SRX2788646.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:33:56: #4 Write peak in narrowPeak format file... SRX2788646.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:33:56: #4 Write summits bed file... SRX2788646.20_summits.bed INFO @ Tue, 27 Jun 2017 14:33:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3673 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:33:56: #4 Write output xls file... SRX2788646.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:33:56: #4 Write peak in narrowPeak format file... SRX2788646.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:33:56: #4 Write summits bed file... SRX2788646.05_summits.bed INFO @ Tue, 27 Jun 2017 14:33:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5991 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。