Job ID = 9029538 sra ファイルのダウンロード中... Completed: 652743K bytes transferred in 9 seconds (574201K 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 14324 0 14324 0 0 1864 0 --:--:-- 0:00:07 --:--:-- 13615 100 38317 0 38317 0 0 4415 0 --:--:-- 0:00:08 --:--:-- 18718 100 86317 0 86317 0 0 8923 0 --:--:-- 0:00:09 --:--:-- 28375 100 95590 0 95590 0 0 9880 0 --:--:-- 0:00:09 --:--:-- 31402 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 9027732 spots for /home/okishinya/chipatlas/results/dm3/SRX1837978/SRR3658919.sra Written 9027732 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: 00:31:38 9027732 reads; of these: 9027732 (100.00%) were unpaired; of these: 924325 (10.24%) aligned 0 times 4247973 (47.05%) aligned exactly 1 time 3855434 (42.71%) aligned >1 times 89.76% overall alignment rate Time searching: 00:31:38 Overall time: 00:31:39 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] 3177569 / 8103407 = 0.3921 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 14:40:44: # Command line: callpeak -t SRX1837978.bam -f BAM -g dm -n SRX1837978.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1837978.05 # format = BAM # ChIP-seq file = ['SRX1837978.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 14:40:44: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:40:44: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:40:44: # Command line: callpeak -t SRX1837978.bam -f BAM -g dm -n SRX1837978.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1837978.20 # format = BAM # ChIP-seq file = ['SRX1837978.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 14:40:44: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:40:44: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:40:44: # Command line: callpeak -t SRX1837978.bam -f BAM -g dm -n SRX1837978.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1837978.10 # format = BAM # ChIP-seq file = ['SRX1837978.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 14:40:44: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:40:44: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:40:55: 1000000 INFO @ Sat, 03 Jun 2017 14:40:55: 1000000 INFO @ Sat, 03 Jun 2017 14:40:55: 1000000 INFO @ Sat, 03 Jun 2017 14:41:06: 2000000 INFO @ Sat, 03 Jun 2017 14:41:06: 2000000 INFO @ Sat, 03 Jun 2017 14:41:06: 2000000 INFO @ Sat, 03 Jun 2017 14:41:16: 3000000 INFO @ Sat, 03 Jun 2017 14:41:16: 3000000 INFO @ Sat, 03 Jun 2017 14:41:16: 3000000 INFO @ Sat, 03 Jun 2017 14:41:27: 4000000 INFO @ Sat, 03 Jun 2017 14:41:27: 4000000 INFO @ Sat, 03 Jun 2017 14:41:27: 4000000 INFO @ Sat, 03 Jun 2017 14:41:37: #1 tag size is determined as 145 bps INFO @ Sat, 03 Jun 2017 14:41:37: #1 tag size = 145 INFO @ Sat, 03 Jun 2017 14:41:37: #1 total tags in treatment: 4925838 INFO @ Sat, 03 Jun 2017 14:41:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:41:37: #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 14:41:37: #1 tag size is determined as 145 bps INFO @ Sat, 03 Jun 2017 14:41:37: #1 tag size = 145 INFO @ Sat, 03 Jun 2017 14:41:37: #1 total tags in treatment: 4925838 INFO @ Sat, 03 Jun 2017 14:41:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:41:37: #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 14:41:37: #1 tag size is determined as 145 bps INFO @ Sat, 03 Jun 2017 14:41:37: #1 tag size = 145 INFO @ Sat, 03 Jun 2017 14:41:37: #1 total tags in treatment: 4925838 INFO @ Sat, 03 Jun 2017 14:41:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:41:37: #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 14:41:38: #1 tags after filtering in treatment: 4904614 INFO @ Sat, 03 Jun 2017 14:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:41:38: #1 finished! INFO @ Sat, 03 Jun 2017 14:41:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:41:38: #1 tags after filtering in treatment: 4904614 INFO @ Sat, 03 Jun 2017 14:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:41:38: #1 finished! INFO @ Sat, 03 Jun 2017 14:41:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:41:38: #1 tags after filtering in treatment: 4904614 INFO @ Sat, 03 Jun 2017 14:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:41:38: #1 finished! INFO @ Sat, 03 Jun 2017 14:41:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:41:39: #2 number of paired peaks: 3316 INFO @ Sat, 03 Jun 2017 14:41:39: start model_add_line... INFO @ Sat, 03 Jun 2017 14:41:39: #2 number of paired peaks: 3316 INFO @ Sat, 03 Jun 2017 14:41:39: start model_add_line... INFO @ Sat, 03 Jun 2017 14:41:39: #2 number of paired peaks: 3316 INFO @ Sat, 03 Jun 2017 14:41:39: start model_add_line... INFO @ Sat, 03 Jun 2017 14:41:49: start X-correlation... INFO @ Sat, 03 Jun 2017 14:41:49: end of X-cor INFO @ Sat, 03 Jun 2017 14:41:49: #2 finished! INFO @ Sat, 03 Jun 2017 14:41:49: #2 predicted fragment length is 159 bps INFO @ Sat, 03 Jun 2017 14:41:49: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 03 Jun 2017 14:41:49: #2.2 Generate R script for model : SRX1837978.20_model.r WARNING @ Sat, 03 Jun 2017 14:41:49: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:41:49: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Sat, 03 Jun 2017 14:41:49: #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 14:41:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:41:49: start X-correlation... INFO @ Sat, 03 Jun 2017 14:41:49: end of X-cor INFO @ Sat, 03 Jun 2017 14:41:49: #2 finished! INFO @ Sat, 03 Jun 2017 14:41:49: #2 predicted fragment length is 159 bps INFO @ Sat, 03 Jun 2017 14:41:49: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 03 Jun 2017 14:41:49: #2.2 Generate R script for model : SRX1837978.05_model.r WARNING @ Sat, 03 Jun 2017 14:41:49: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:41:49: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Sat, 03 Jun 2017 14:41:49: #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 14:41:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:41:50: start X-correlation... INFO @ Sat, 03 Jun 2017 14:41:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:41:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:41:50: #2 predicted fragment length is 159 bps INFO @ Sat, 03 Jun 2017 14:41:50: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 03 Jun 2017 14:41:50: #2.2 Generate R script for model : SRX1837978.10_model.r WARNING @ Sat, 03 Jun 2017 14:41:50: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:41:50: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Sat, 03 Jun 2017 14:41:50: #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 14:41:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:41:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:42:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:42:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:42:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:42:43: #4 Write output xls file... SRX1837978.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:42:43: #4 Write peak in narrowPeak format file... SRX1837978.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:42:43: #4 Write summits bed file... SRX1837978.20_summits.bed INFO @ Sat, 03 Jun 2017 14:42:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3610 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:42:49: #4 Write output xls file... SRX1837978.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:42:49: #4 Write peak in narrowPeak format file... SRX1837978.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:42:49: #4 Write summits bed file... SRX1837978.05_summits.bed INFO @ Sat, 03 Jun 2017 14:42:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10371 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:42:50: #4 Write output xls file... SRX1837978.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:42:50: #4 Write peak in narrowPeak format file... SRX1837978.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:42:50: #4 Write summits bed file... SRX1837978.10_summits.bed INFO @ Sat, 03 Jun 2017 14:42:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6751 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。