Job ID = 9157977 sra ファイルのダウンロード中... Completed: 5232454K bytes transferred in 199 seconds (214448K 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 83847447 spots for /home/okishinya/chipatlas/results/dm3/SRX2788639/SRR5515259.sra Written 83847447 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: 00:29:33 83847447 reads; of these: 83847447 (100.00%) were unpaired; of these: 51230901 (61.10%) aligned 0 times 27538515 (32.84%) aligned exactly 1 time 5078031 (6.06%) aligned >1 times 38.90% overall alignment rate Time searching: 00:29:33 Overall time: 00:29:33 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 16 files... [bam_rmdupse_core] 29347365 / 32616546 = 0.8998 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 15:05:28: # Command line: callpeak -t SRX2788639.bam -f BAM -g dm -n SRX2788639.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2788639.05 # format = BAM # ChIP-seq file = ['SRX2788639.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 15:05:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:05:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:05:28: # Command line: callpeak -t SRX2788639.bam -f BAM -g dm -n SRX2788639.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2788639.10 # format = BAM # ChIP-seq file = ['SRX2788639.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 15:05:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:05:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:05:28: # Command line: callpeak -t SRX2788639.bam -f BAM -g dm -n SRX2788639.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2788639.20 # format = BAM # ChIP-seq file = ['SRX2788639.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 15:05:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:05:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:05:39: 1000000 INFO @ Tue, 27 Jun 2017 15:05:39: 1000000 INFO @ Tue, 27 Jun 2017 15:05:40: 1000000 INFO @ Tue, 27 Jun 2017 15:05:50: 2000000 INFO @ Tue, 27 Jun 2017 15:05:50: 2000000 INFO @ Tue, 27 Jun 2017 15:05:51: 2000000 INFO @ Tue, 27 Jun 2017 15:06:01: 3000000 INFO @ Tue, 27 Jun 2017 15:06:01: 3000000 INFO @ Tue, 27 Jun 2017 15:06:02: 3000000 INFO @ Tue, 27 Jun 2017 15:06:04: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 15:06:04: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 15:06:04: #1 total tags in treatment: 3269181 INFO @ Tue, 27 Jun 2017 15:06:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:06:04: #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 15:06:04: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 15:06:04: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 15:06:04: #1 total tags in treatment: 3269181 INFO @ Tue, 27 Jun 2017 15:06:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:06:04: #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 15:06:04: #1 tags after filtering in treatment: 3269181 INFO @ Tue, 27 Jun 2017 15:06:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:06:04: #1 finished! INFO @ Tue, 27 Jun 2017 15:06:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:06:04: #1 tags after filtering in treatment: 3269181 INFO @ Tue, 27 Jun 2017 15:06:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:06:04: #1 finished! INFO @ Tue, 27 Jun 2017 15:06:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:06:04: #2 number of paired peaks: 3941 INFO @ Tue, 27 Jun 2017 15:06:04: start model_add_line... INFO @ Tue, 27 Jun 2017 15:06:04: #2 number of paired peaks: 3941 INFO @ Tue, 27 Jun 2017 15:06:04: start model_add_line... INFO @ Tue, 27 Jun 2017 15:06:04: start X-correlation... INFO @ Tue, 27 Jun 2017 15:06:04: end of X-cor INFO @ Tue, 27 Jun 2017 15:06:04: #2 finished! INFO @ Tue, 27 Jun 2017 15:06:04: #2 predicted fragment length is 104 bps INFO @ Tue, 27 Jun 2017 15:06:04: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 27 Jun 2017 15:06:04: #2.2 Generate R script for model : SRX2788639.10_model.r INFO @ Tue, 27 Jun 2017 15:06:04: start X-correlation... WARNING @ Tue, 27 Jun 2017 15:06:04: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:06:04: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Tue, 27 Jun 2017 15:06:04: #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 15:06:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:06:04: end of X-cor INFO @ Tue, 27 Jun 2017 15:06:04: #2 finished! INFO @ Tue, 27 Jun 2017 15:06:04: #2 predicted fragment length is 104 bps INFO @ Tue, 27 Jun 2017 15:06:04: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 27 Jun 2017 15:06:04: #2.2 Generate R script for model : SRX2788639.05_model.r WARNING @ Tue, 27 Jun 2017 15:06:04: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:06:04: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Tue, 27 Jun 2017 15:06:04: #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 15:06:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:06:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:06:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:06:05: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 15:06:05: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 15:06:05: #1 total tags in treatment: 3269181 INFO @ Tue, 27 Jun 2017 15:06:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:06:05: #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 15:06:05: #1 tags after filtering in treatment: 3269181 INFO @ Tue, 27 Jun 2017 15:06:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:06:05: #1 finished! INFO @ Tue, 27 Jun 2017 15:06:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:06:06: #2 number of paired peaks: 3941 INFO @ Tue, 27 Jun 2017 15:06:06: start model_add_line... INFO @ Tue, 27 Jun 2017 15:06:06: start X-correlation... INFO @ Tue, 27 Jun 2017 15:06:06: end of X-cor INFO @ Tue, 27 Jun 2017 15:06:06: #2 finished! INFO @ Tue, 27 Jun 2017 15:06:06: #2 predicted fragment length is 104 bps INFO @ Tue, 27 Jun 2017 15:06:06: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 27 Jun 2017 15:06:06: #2.2 Generate R script for model : SRX2788639.20_model.r WARNING @ Tue, 27 Jun 2017 15:06:06: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:06:06: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Tue, 27 Jun 2017 15:06:06: #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 15:06:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:06:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:06:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:06:15: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:06:17: #4 Write output xls file... SRX2788639.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:06:17: #4 Write peak in narrowPeak format file... SRX2788639.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:06:17: #4 Write summits bed file... SRX2788639.05_summits.bed INFO @ Tue, 27 Jun 2017 15:06:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6446 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:06:18: #4 Write output xls file... SRX2788639.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:06:18: #4 Write peak in narrowPeak format file... SRX2788639.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:06:18: #4 Write summits bed file... SRX2788639.10_summits.bed INFO @ Tue, 27 Jun 2017 15:06:18: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3818 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:06:19: #4 Write output xls file... SRX2788639.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:06:19: #4 Write peak in narrowPeak format file... SRX2788639.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:06:19: #4 Write summits bed file... SRX2788639.20_summits.bed INFO @ Tue, 27 Jun 2017 15:06:19: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1767 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。