Job ID = 9029894 sra ファイルのダウンロード中... Completed: 424082K bytes transferred in 6 seconds (504889K 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 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1063 0 --:--:-- 0:00:07 --:--:-- 9483 100 31765 0 31765 0 0 3874 0 --:--:-- 0:00:08 --:--:-- 17617 100 87765 0 87765 0 0 9544 0 --:--:-- 0:00:09 --:--:-- 31367 100 120k 0 120k 0 0 12875 0 --:--:-- 0:00:09 --:--:-- 38860 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 18916953 spots for /home/okishinya/chipatlas/results/dm3/SRX2564130/SRR5259250.sra Written 18916953 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: 00:03:34 18916953 reads; of these: 18916953 (100.00%) were unpaired; of these: 13699541 (72.42%) aligned 0 times 4045213 (21.38%) aligned exactly 1 time 1172199 (6.20%) aligned >1 times 27.58% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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_rmdupse_core] 2515594 / 5217412 = 0.4822 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 @ Sat, 03 Jun 2017 15:43:18: # Command line: callpeak -t SRX2564130.bam -f BAM -g dm -n SRX2564130.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2564130.10 # format = BAM # ChIP-seq file = ['SRX2564130.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 @ Sat, 03 Jun 2017 15:43:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:43:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:43:18: # Command line: callpeak -t SRX2564130.bam -f BAM -g dm -n SRX2564130.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2564130.20 # format = BAM # ChIP-seq file = ['SRX2564130.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 @ Sat, 03 Jun 2017 15:43:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:43:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:43:18: # Command line: callpeak -t SRX2564130.bam -f BAM -g dm -n SRX2564130.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2564130.05 # format = BAM # ChIP-seq file = ['SRX2564130.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 @ Sat, 03 Jun 2017 15:43:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:43:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:43:25: 1000000 INFO @ Sat, 03 Jun 2017 15:43:25: 1000000 INFO @ Sat, 03 Jun 2017 15:43:25: 1000000 INFO @ Sat, 03 Jun 2017 15:43:31: 2000000 INFO @ Sat, 03 Jun 2017 15:43:32: 2000000 INFO @ Sat, 03 Jun 2017 15:43:32: 2000000 INFO @ Sat, 03 Jun 2017 15:43:36: #1 tag size is determined as 42 bps INFO @ Sat, 03 Jun 2017 15:43:36: #1 tag size = 42 INFO @ Sat, 03 Jun 2017 15:43:36: #1 total tags in treatment: 2701818 INFO @ Sat, 03 Jun 2017 15:43:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:43:36: #1 tags after filtering in treatment: 2697951 INFO @ Sat, 03 Jun 2017 15:43:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:36: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:36: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:37: #1 tag size is determined as 42 bps INFO @ Sat, 03 Jun 2017 15:43:37: #1 tag size = 42 INFO @ Sat, 03 Jun 2017 15:43:37: #1 total tags in treatment: 2701818 INFO @ Sat, 03 Jun 2017 15:43:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:43:37: #1 tag size is determined as 42 bps INFO @ Sat, 03 Jun 2017 15:43:37: #1 tag size = 42 INFO @ Sat, 03 Jun 2017 15:43:37: #1 total tags in treatment: 2701818 INFO @ Sat, 03 Jun 2017 15:43:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 15:43:37: #1 tags after filtering in treatment: 2697951 INFO @ Sat, 03 Jun 2017 15:43:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:37: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:37: #1 tags after filtering in treatment: 2697951 INFO @ Sat, 03 Jun 2017 15:43:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:37: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:37: #2 number of paired peaks: 4476 INFO @ Sat, 03 Jun 2017 15:43:37: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:38: #2 number of paired peaks: 4476 INFO @ Sat, 03 Jun 2017 15:43:38: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:38: #2 number of paired peaks: 4476 INFO @ Sat, 03 Jun 2017 15:43:38: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:46: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:46: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:46: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:46: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 15:43:46: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 03 Jun 2017 15:43:46: #2.2 Generate R script for model : SRX2564130.05_model.r WARNING @ Sat, 03 Jun 2017 15:43:46: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:43:46: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 03 Jun 2017 15:43:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 15:43:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:43:46: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:46: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:46: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:46: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 15:43:46: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 03 Jun 2017 15:43:46: #2.2 Generate R script for model : SRX2564130.10_model.r WARNING @ Sat, 03 Jun 2017 15:43:46: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:43:46: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 03 Jun 2017 15:43:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 15:43:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:43:46: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:46: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:46: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:46: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 15:43:46: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 03 Jun 2017 15:43:46: #2.2 Generate R script for model : SRX2564130.20_model.r WARNING @ Sat, 03 Jun 2017 15:43:46: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:43:46: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 03 Jun 2017 15:43:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 15:43:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:44:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:44:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:44:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:44:14: #4 Write output xls file... SRX2564130.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:44:14: #4 Write peak in narrowPeak format file... SRX2564130.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:44:14: #4 Write summits bed file... SRX2564130.20_summits.bed INFO @ Sat, 03 Jun 2017 15:44:14: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (439 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:44:15: #4 Write output xls file... SRX2564130.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:44:15: #4 Write peak in narrowPeak format file... SRX2564130.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:44:15: #4 Write summits bed file... SRX2564130.05_summits.bed INFO @ Sat, 03 Jun 2017 15:44:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6381 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:44:16: #4 Write output xls file... SRX2564130.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:44:16: #4 Write peak in narrowPeak format file... SRX2564130.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:44:16: #4 Write summits bed file... SRX2564130.10_summits.bed INFO @ Sat, 03 Jun 2017 15:44:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1708 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。