Job ID = 9029233 sra ファイルのダウンロード中... Completed: 1042472K bytes transferred in 14 seconds (582607K 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 1963 0 --:--:-- 0:00:07 --:--:-- 14098 100 38317 0 38317 0 0 4621 0 --:--:-- 0:00:08 --:--:-- 19044 100 91061 0 91061 0 0 9803 0 --:--:-- 0:00:09 --:--:-- 30262 100 174k 0 174k 0 0 17410 0 --:--:-- 0:00:10 --:--:-- 44709 100 199k 0 199k 0 0 19536 0 --:--:-- 0:00:10 --:--:-- 48941 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 43421345 spots for /home/okishinya/chipatlas/results/dm3/SRX1433373/SRR2919838.sra Written 43421345 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:39 43421345 reads; of these: 43421345 (100.00%) were unpaired; of these: 28711360 (66.12%) aligned 0 times 9110252 (20.98%) aligned exactly 1 time 5599733 (12.90%) aligned >1 times 33.88% overall alignment rate Time searching: 00:12:40 Overall time: 00:12:40 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] 8593279 / 14709985 = 0.5842 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 13:10:54: # Command line: callpeak -t SRX1433373.bam -f BAM -g dm -n SRX1433373.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433373.10 # format = BAM # ChIP-seq file = ['SRX1433373.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 13:10:54: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:10:54: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:10:54: # Command line: callpeak -t SRX1433373.bam -f BAM -g dm -n SRX1433373.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433373.05 # format = BAM # ChIP-seq file = ['SRX1433373.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 13:10:54: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:10:54: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:10:54: # Command line: callpeak -t SRX1433373.bam -f BAM -g dm -n SRX1433373.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433373.20 # format = BAM # ChIP-seq file = ['SRX1433373.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 13:10:54: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:10:54: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:10:59: 1000000 INFO @ Sat, 03 Jun 2017 13:10:59: 1000000 INFO @ Sat, 03 Jun 2017 13:10:59: 1000000 INFO @ Sat, 03 Jun 2017 13:11:05: 2000000 INFO @ Sat, 03 Jun 2017 13:11:06: 2000000 INFO @ Sat, 03 Jun 2017 13:11:06: 2000000 INFO @ Sat, 03 Jun 2017 13:11:12: 3000000 INFO @ Sat, 03 Jun 2017 13:11:12: 3000000 INFO @ Sat, 03 Jun 2017 13:11:13: 3000000 INFO @ Sat, 03 Jun 2017 13:11:18: 4000000 INFO @ Sat, 03 Jun 2017 13:11:19: 4000000 INFO @ Sat, 03 Jun 2017 13:11:20: 4000000 INFO @ Sat, 03 Jun 2017 13:11:24: 5000000 INFO @ Sat, 03 Jun 2017 13:11:25: 5000000 INFO @ Sat, 03 Jun 2017 13:11:27: 5000000 INFO @ Sat, 03 Jun 2017 13:11:30: 6000000 INFO @ Sat, 03 Jun 2017 13:11:31: 6000000 INFO @ Sat, 03 Jun 2017 13:11:31: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:31: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:31: #1 total tags in treatment: 6116706 INFO @ Sat, 03 Jun 2017 13:11:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:31: #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 13:11:32: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:32: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:32: #1 total tags in treatment: 6116706 INFO @ Sat, 03 Jun 2017 13:11:32: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:32: #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 13:11:32: #1 tags after filtering in treatment: 6115061 INFO @ Sat, 03 Jun 2017 13:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:32: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:32: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:33: #1 tags after filtering in treatment: 6115061 INFO @ Sat, 03 Jun 2017 13:11:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:33: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:34: 6000000 INFO @ Sat, 03 Jun 2017 13:11:34: #2 number of paired peaks: 1989 INFO @ Sat, 03 Jun 2017 13:11:34: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:34: #2 number of paired peaks: 1989 INFO @ Sat, 03 Jun 2017 13:11:34: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:34: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:34: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:34: #1 total tags in treatment: 6116706 INFO @ Sat, 03 Jun 2017 13:11:34: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:34: #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 13:11:35: #1 tags after filtering in treatment: 6115061 INFO @ Sat, 03 Jun 2017 13:11:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:35: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:35: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:37: #2 number of paired peaks: 1989 INFO @ Sat, 03 Jun 2017 13:11:37: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:42: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:42: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:42: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:42: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 13:11:42: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 03 Jun 2017 13:11:42: #2.2 Generate R script for model : SRX1433373.20_model.r WARNING @ Sat, 03 Jun 2017 13:11:42: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:42: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 03 Jun 2017 13:11:42: #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 13:11:42: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:43: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:43: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:43: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:43: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 13:11:43: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 03 Jun 2017 13:11:43: #2.2 Generate R script for model : SRX1433373.10_model.r WARNING @ Sat, 03 Jun 2017 13:11:43: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:43: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 03 Jun 2017 13:11:43: #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 13:11:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:45: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:45: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:45: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:45: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 13:11:45: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 03 Jun 2017 13:11:45: #2.2 Generate R script for model : SRX1433373.05_model.r WARNING @ Sat, 03 Jun 2017 13:11:45: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:45: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 03 Jun 2017 13:11:45: #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 13:11:45: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:12:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:12:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:12:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:12:46: #4 Write output xls file... SRX1433373.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:46: #4 Write peak in narrowPeak format file... SRX1433373.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:46: #4 Write summits bed file... SRX1433373.20_summits.bed INFO @ Sat, 03 Jun 2017 13:12:46: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1793 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:12:50: #4 Write output xls file... SRX1433373.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:50: #4 Write peak in narrowPeak format file... SRX1433373.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:50: #4 Write summits bed file... SRX1433373.10_summits.bed INFO @ Sat, 03 Jun 2017 13:12:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2677 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:12:56: #4 Write output xls file... SRX1433373.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:56: #4 Write peak in narrowPeak format file... SRX1433373.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:56: #4 Write summits bed file... SRX1433373.05_summits.bed INFO @ Sat, 03 Jun 2017 13:12:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3740 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。