Job ID = 9029893 sra ファイルのダウンロード中... Completed: 500180K bytes transferred in 8 seconds (466901K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 22317 0 22317 0 0 2657 0 --:--:-- 0:00:08 --:--:-- 11175 100 50517 0 50517 0 0 5377 0 --:--:-- 0:00:09 --:--:-- 16884 100 114k 0 114k 0 0 11425 0 --:--:-- 0:00:10 --:--:-- 30372 100 135k 0 135k 0 0 13099 0 --:--:-- 0:00:10 --:--:-- 33302 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 22142303 spots for /home/okishinya/chipatlas/results/dm3/SRX2564128/SRR5259249.sra Written 22142303 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: 00:03:36 22142303 reads; of these: 22142303 (100.00%) were unpaired; of these: 16623726 (75.08%) aligned 0 times 3901731 (17.62%) aligned exactly 1 time 1616846 (7.30%) aligned >1 times 24.92% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 1649798 / 5518577 = 0.2990 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 15:43:17: # Command line: callpeak -t SRX2564128.bam -f BAM -g dm -n SRX2564128.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2564128.05 # format = BAM # ChIP-seq file = ['SRX2564128.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 15:43:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:43:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:43:17: # Command line: callpeak -t SRX2564128.bam -f BAM -g dm -n SRX2564128.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2564128.10 # format = BAM # ChIP-seq file = ['SRX2564128.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 15:43:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:43:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:43:17: # Command line: callpeak -t SRX2564128.bam -f BAM -g dm -n SRX2564128.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2564128.20 # format = BAM # ChIP-seq file = ['SRX2564128.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 15:43:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:43:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:43:24: 1000000 INFO @ Sat, 03 Jun 2017 15:43:24: 1000000 INFO @ Sat, 03 Jun 2017 15:43:24: 1000000 INFO @ Sat, 03 Jun 2017 15:43:31: 2000000 INFO @ Sat, 03 Jun 2017 15:43:31: 2000000 INFO @ Sat, 03 Jun 2017 15:43:31: 2000000 INFO @ Sat, 03 Jun 2017 15:43:37: 3000000 INFO @ Sat, 03 Jun 2017 15:43:38: 3000000 INFO @ Sat, 03 Jun 2017 15:43:38: 3000000 INFO @ Sat, 03 Jun 2017 15:43:42: #1 tag size is determined as 42 bps INFO @ Sat, 03 Jun 2017 15:43:42: #1 tag size = 42 INFO @ Sat, 03 Jun 2017 15:43:42: #1 total tags in treatment: 3868779 INFO @ Sat, 03 Jun 2017 15:43:42: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:42: #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 15:43:43: #1 tags after filtering in treatment: 3866113 INFO @ Sat, 03 Jun 2017 15:43:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:43: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:44: #2 number of paired peaks: 1163 INFO @ Sat, 03 Jun 2017 15:43:44: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:45: #1 tag size is determined as 42 bps INFO @ Sat, 03 Jun 2017 15:43:45: #1 tag size = 42 INFO @ Sat, 03 Jun 2017 15:43:45: #1 total tags in treatment: 3868779 INFO @ Sat, 03 Jun 2017 15:43:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:45: #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 15:43:45: #1 tag size is determined as 42 bps INFO @ Sat, 03 Jun 2017 15:43:45: #1 tag size = 42 INFO @ Sat, 03 Jun 2017 15:43:45: #1 total tags in treatment: 3868779 INFO @ Sat, 03 Jun 2017 15:43:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:45: #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 15:43:45: #1 tags after filtering in treatment: 3866113 INFO @ Sat, 03 Jun 2017 15:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:45: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:46: #1 tags after filtering in treatment: 3866113 INFO @ Sat, 03 Jun 2017 15:43:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:46: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:46: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:46: #2 number of paired peaks: 1163 INFO @ Sat, 03 Jun 2017 15:43:46: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:47: #2 number of paired peaks: 1163 INFO @ Sat, 03 Jun 2017 15:43:47: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:47: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:47: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:47: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:47: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 15:43:47: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 15:43:47: #2.2 Generate R script for model : SRX2564128.20_model.r WARNING @ Sat, 03 Jun 2017 15:43:47: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:43:47: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 15:43:47: #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 15:43:47: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:43:50: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:50: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:50: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:50: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 15:43:50: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 15:43:50: #2.2 Generate R script for model : SRX2564128.05_model.r WARNING @ Sat, 03 Jun 2017 15:43:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:43:50: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 15:43:50: #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 15:43:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:43:50: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:50: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:50: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:50: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 15:43:50: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 15:43:50: #2.2 Generate R script for model : SRX2564128.10_model.r WARNING @ Sat, 03 Jun 2017 15:43:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:43:50: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 15:43:50: #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 15:43:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:44:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:44:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:44:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:44:26: #4 Write output xls file... SRX2564128.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:44:26: #4 Write peak in narrowPeak format file... SRX2564128.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:44:26: #4 Write summits bed file... SRX2564128.20_summits.bed INFO @ Sat, 03 Jun 2017 15:44:26: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (534 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:44:28: #4 Write output xls file... SRX2564128.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:44:28: #4 Write peak in narrowPeak format file... SRX2564128.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:44:29: #4 Write summits bed file... SRX2564128.05_summits.bed INFO @ Sat, 03 Jun 2017 15:44:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3730 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:44:33: #4 Write output xls file... SRX2564128.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:44:33: #4 Write peak in narrowPeak format file... SRX2564128.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:44:33: #4 Write summits bed file... SRX2564128.10_summits.bed INFO @ Sat, 03 Jun 2017 15:44:33: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1558 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。