Job ID = 8697013 sra ファイルのダウンロード中... Completed: 526090K bytes transferred in 11 seconds (377409K 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 0 977 0 --:--:-- 0:00:07 --:--:-- 7534 100 28797 0 28797 0 0 3304 0 --:--:-- 0:00:08 --:--:-- 15228 100 30668 0 30668 0 0 3518 0 --:--:-- 0:00:08 --:--:-- 16192 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 22513168 spots for /home/okishinya/chipatlas/results/dm3/SRX119302/SRR407386.sra Written 22513168 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: 00:14:23 22513168 reads; of these: 22513168 (100.00%) were unpaired; of these: 1437329 (6.38%) aligned 0 times 17497978 (77.72%) aligned exactly 1 time 3577861 (15.89%) aligned >1 times 93.62% overall alignment rate Time searching: 00:14:23 Overall time: 00:14:23 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 12 files... [bam_rmdupse_core] 11323715 / 21075839 = 0.5373 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 @ Fri, 10 Mar 2017 13:41:47: # Command line: callpeak -t SRX119302.bam -f BAM -g dm -n SRX119302.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX119302.20 # format = BAM # ChIP-seq file = ['SRX119302.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 @ Fri, 10 Mar 2017 13:41:47: #1 read tag files... INFO @ Fri, 10 Mar 2017 13:41:47: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 13:41:48: # Command line: callpeak -t SRX119302.bam -f BAM -g dm -n SRX119302.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX119302.10 # format = BAM # ChIP-seq file = ['SRX119302.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 @ Fri, 10 Mar 2017 13:41:48: #1 read tag files... INFO @ Fri, 10 Mar 2017 13:41:48: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 13:41:48: # Command line: callpeak -t SRX119302.bam -f BAM -g dm -n SRX119302.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX119302.05 # format = BAM # ChIP-seq file = ['SRX119302.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 @ Fri, 10 Mar 2017 13:41:48: #1 read tag files... INFO @ Fri, 10 Mar 2017 13:41:48: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 13:41:56: 1000000 INFO @ Fri, 10 Mar 2017 13:41:56: 1000000 INFO @ Fri, 10 Mar 2017 13:42:04: 2000000 INFO @ Fri, 10 Mar 2017 13:42:05: 2000000 INFO @ Fri, 10 Mar 2017 13:42:12: 3000000 INFO @ Fri, 10 Mar 2017 13:42:14: 3000000 INFO @ Fri, 10 Mar 2017 13:42:20: 4000000 INFO @ Fri, 10 Mar 2017 13:42:22: 4000000 INFO @ Fri, 10 Mar 2017 13:42:29: 5000000 INFO @ Fri, 10 Mar 2017 13:42:31: 5000000 INFO @ Fri, 10 Mar 2017 13:42:31: 1000000 INFO @ Fri, 10 Mar 2017 13:42:38: 6000000 INFO @ Fri, 10 Mar 2017 13:42:40: 6000000 INFO @ Fri, 10 Mar 2017 13:42:47: 7000000 INFO @ Fri, 10 Mar 2017 13:42:48: 7000000 INFO @ Fri, 10 Mar 2017 13:42:56: 8000000 INFO @ Fri, 10 Mar 2017 13:42:56: 8000000 INFO @ Fri, 10 Mar 2017 13:43:03: 9000000 INFO @ Fri, 10 Mar 2017 13:43:06: 9000000 INFO @ Fri, 10 Mar 2017 13:43:09: #1 tag size is determined as 54 bps INFO @ Fri, 10 Mar 2017 13:43:09: #1 tag size = 54 INFO @ Fri, 10 Mar 2017 13:43:09: #1 total tags in treatment: 9752124 INFO @ Fri, 10 Mar 2017 13:43:09: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:43:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 13:43:11: #1 tags after filtering in treatment: 9748719 INFO @ Fri, 10 Mar 2017 13:43:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:43:11: #1 finished! INFO @ Fri, 10 Mar 2017 13:43:11: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:43:13: #1 tag size is determined as 54 bps INFO @ Fri, 10 Mar 2017 13:43:13: #1 tag size = 54 INFO @ Fri, 10 Mar 2017 13:43:13: #1 total tags in treatment: 9752124 INFO @ Fri, 10 Mar 2017 13:43:13: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:43:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 13:43:13: 2000000 INFO @ Fri, 10 Mar 2017 13:43:14: #2 number of paired peaks: 3007 INFO @ Fri, 10 Mar 2017 13:43:14: start model_add_line... INFO @ Fri, 10 Mar 2017 13:43:15: #1 tags after filtering in treatment: 9748719 INFO @ Fri, 10 Mar 2017 13:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:43:15: #1 finished! INFO @ Fri, 10 Mar 2017 13:43:15: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:43:18: #2 number of paired peaks: 3007 INFO @ Fri, 10 Mar 2017 13:43:18: start model_add_line... INFO @ Fri, 10 Mar 2017 13:43:37: start X-correlation... INFO @ Fri, 10 Mar 2017 13:43:37: end of X-cor INFO @ Fri, 10 Mar 2017 13:43:37: #2 finished! INFO @ Fri, 10 Mar 2017 13:43:37: #2 predicted fragment length is 103 bps INFO @ Fri, 10 Mar 2017 13:43:37: #2 alternative fragment length(s) may be 103 bps INFO @ Fri, 10 Mar 2017 13:43:37: #2.2 Generate R script for model : SRX119302.20_model.r WARNING @ Fri, 10 Mar 2017 13:43:37: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 13:43:37: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Fri, 10 Mar 2017 13:43:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 13:43:37: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:43:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:43:43: start X-correlation... INFO @ Fri, 10 Mar 2017 13:43:43: end of X-cor INFO @ Fri, 10 Mar 2017 13:43:43: #2 finished! INFO @ Fri, 10 Mar 2017 13:43:43: #2 predicted fragment length is 103 bps INFO @ Fri, 10 Mar 2017 13:43:43: #2 alternative fragment length(s) may be 103 bps INFO @ Fri, 10 Mar 2017 13:43:43: #2.2 Generate R script for model : SRX119302.10_model.r WARNING @ Fri, 10 Mar 2017 13:43:43: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 13:43:43: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Fri, 10 Mar 2017 13:43:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 13:43:43: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:43:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:43:44: 3000000 INFO @ Fri, 10 Mar 2017 13:44:14: 4000000 INFO @ Fri, 10 Mar 2017 13:44:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:44:44: 5000000 INFO @ Fri, 10 Mar 2017 13:44:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:45:31: #4 Write output xls file... SRX119302.20_peaks.xls INFO @ Fri, 10 Mar 2017 13:45:31: #4 Write peak in narrowPeak format file... SRX119302.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:45:31: #4 Write summits bed file... SRX119302.20_summits.bed INFO @ Fri, 10 Mar 2017 13:45:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4705 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 13:45:43: 6000000 INFO @ Fri, 10 Mar 2017 13:45:43: #4 Write output xls file... SRX119302.10_peaks.xls INFO @ Fri, 10 Mar 2017 13:45:44: #4 Write peak in narrowPeak format file... SRX119302.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:45:44: #4 Write summits bed file... SRX119302.10_summits.bed INFO @ Fri, 10 Mar 2017 13:45:44: Done! pass1 - making usageList (15 chroms): 9 millis pass2 - checking and writing primary data (6321 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 13:46:31: 7000000 INFO @ Fri, 10 Mar 2017 13:47:07: 8000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 10 Mar 2017 13:47:56: 9000000 INFO @ Fri, 10 Mar 2017 13:48:39: #1 tag size is determined as 54 bps INFO @ Fri, 10 Mar 2017 13:48:39: #1 tag size = 54 INFO @ Fri, 10 Mar 2017 13:48:39: #1 total tags in treatment: 9752124 INFO @ Fri, 10 Mar 2017 13:48:39: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:48:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 13:48:42: #1 tags after filtering in treatment: 9748719 INFO @ Fri, 10 Mar 2017 13:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:48:42: #1 finished! INFO @ Fri, 10 Mar 2017 13:48:42: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:48:47: #2 number of paired peaks: 3007 INFO @ Fri, 10 Mar 2017 13:48:47: start model_add_line... INFO @ Fri, 10 Mar 2017 13:49:29: start X-correlation... INFO @ Fri, 10 Mar 2017 13:49:29: end of X-cor INFO @ Fri, 10 Mar 2017 13:49:29: #2 finished! INFO @ Fri, 10 Mar 2017 13:49:29: #2 predicted fragment length is 103 bps INFO @ Fri, 10 Mar 2017 13:49:29: #2 alternative fragment length(s) may be 103 bps INFO @ Fri, 10 Mar 2017 13:49:29: #2.2 Generate R script for model : SRX119302.05_model.r WARNING @ Fri, 10 Mar 2017 13:49:29: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 13:49:29: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Fri, 10 Mar 2017 13:49:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 13:49:29: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:50:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:51:52: #4 Write output xls file... SRX119302.05_peaks.xls INFO @ Fri, 10 Mar 2017 13:51:52: #4 Write peak in narrowPeak format file... SRX119302.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:51:52: #4 Write summits bed file... SRX119302.05_summits.bed INFO @ Fri, 10 Mar 2017 13:51:52: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8490 records, 4 fields): 17 millis CompletedMACS2peakCalling