Job ID = 9029363 sra ファイルのダウンロード中... Completed: 1283940K bytes transferred in 13 seconds (801484K 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 12695 0 12695 0 0 1706 0 --:--:-- 0:00:07 --:--:-- 14200 100 47622 0 47622 0 0 5644 0 --:--:-- 0:00:08 --:--:-- 25196 100 65441 0 65441 0 0 7606 0 --:--:-- 0:00:08 --:--:-- 31844 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 23384087 spots for /home/okishinya/chipatlas/results/dm3/SRX1600295/SRR3187787.sra Written 23384087 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: 00:07:27 23384087 reads; of these: 23384087 (100.00%) were unpaired; of these: 4329868 (18.52%) aligned 0 times 17304802 (74.00%) aligned exactly 1 time 1749417 (7.48%) aligned >1 times 81.48% overall alignment rate Time searching: 00:07:27 Overall time: 00:07:27 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] 9905215 / 19054219 = 0.5198 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 13:31:36: # Command line: callpeak -t SRX1600295.bam -f BAM -g dm -n SRX1600295.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1600295.10 # format = BAM # ChIP-seq file = ['SRX1600295.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 13:31:36: # Command line: callpeak -t SRX1600295.bam -f BAM -g dm -n SRX1600295.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1600295.20 # format = BAM # ChIP-seq file = ['SRX1600295.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 13:31:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:31:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:31:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:31:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:31:36: # Command line: callpeak -t SRX1600295.bam -f BAM -g dm -n SRX1600295.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1600295.05 # format = BAM # ChIP-seq file = ['SRX1600295.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 13:31:36: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:31:36: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:31:43: 1000000 INFO @ Sat, 03 Jun 2017 13:31:43: 1000000 INFO @ Sat, 03 Jun 2017 13:31:43: 1000000 INFO @ Sat, 03 Jun 2017 13:31:50: 2000000 INFO @ Sat, 03 Jun 2017 13:31:50: 2000000 INFO @ Sat, 03 Jun 2017 13:31:51: 2000000 INFO @ Sat, 03 Jun 2017 13:31:57: 3000000 INFO @ Sat, 03 Jun 2017 13:31:57: 3000000 INFO @ Sat, 03 Jun 2017 13:31:59: 3000000 INFO @ Sat, 03 Jun 2017 13:32:04: 4000000 INFO @ Sat, 03 Jun 2017 13:32:05: 4000000 INFO @ Sat, 03 Jun 2017 13:32:07: 4000000 INFO @ Sat, 03 Jun 2017 13:32:12: 5000000 INFO @ Sat, 03 Jun 2017 13:32:12: 5000000 INFO @ Sat, 03 Jun 2017 13:32:15: 5000000 INFO @ Sat, 03 Jun 2017 13:32:19: 6000000 INFO @ Sat, 03 Jun 2017 13:32:20: 6000000 INFO @ Sat, 03 Jun 2017 13:32:23: 6000000 INFO @ Sat, 03 Jun 2017 13:32:27: 7000000 INFO @ Sat, 03 Jun 2017 13:32:28: 7000000 INFO @ Sat, 03 Jun 2017 13:32:31: 7000000 INFO @ Sat, 03 Jun 2017 13:32:35: 8000000 INFO @ Sat, 03 Jun 2017 13:32:36: 8000000 INFO @ Sat, 03 Jun 2017 13:32:39: 8000000 INFO @ Sat, 03 Jun 2017 13:32:42: 9000000 INFO @ Sat, 03 Jun 2017 13:32:43: 9000000 INFO @ Sat, 03 Jun 2017 13:32:44: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 13:32:44: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 13:32:44: #1 total tags in treatment: 9149004 INFO @ Sat, 03 Jun 2017 13:32:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:32:44: #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 13:32:45: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 13:32:45: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 13:32:45: #1 total tags in treatment: 9149004 INFO @ Sat, 03 Jun 2017 13:32:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:32:45: #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 13:32:45: #1 tags after filtering in treatment: 9138178 INFO @ Sat, 03 Jun 2017 13:32:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:32:45: #1 finished! INFO @ Sat, 03 Jun 2017 13:32:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:32:47: #1 tags after filtering in treatment: 9138178 INFO @ Sat, 03 Jun 2017 13:32:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:32:47: #1 finished! INFO @ Sat, 03 Jun 2017 13:32:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:32:47: 9000000 INFO @ Sat, 03 Jun 2017 13:32:48: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 13:32:48: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 13:32:48: #1 total tags in treatment: 9149004 INFO @ Sat, 03 Jun 2017 13:32:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:32:48: #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 13:32:48: #2 number of paired peaks: 6668 INFO @ Sat, 03 Jun 2017 13:32:48: start model_add_line... INFO @ Sat, 03 Jun 2017 13:32:49: #2 number of paired peaks: 6668 INFO @ Sat, 03 Jun 2017 13:32:49: start model_add_line... INFO @ Sat, 03 Jun 2017 13:32:49: #1 tags after filtering in treatment: 9138178 INFO @ Sat, 03 Jun 2017 13:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:32:49: #1 finished! INFO @ Sat, 03 Jun 2017 13:32:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:32:52: #2 number of paired peaks: 6668 INFO @ Sat, 03 Jun 2017 13:32:52: start model_add_line... INFO @ Sat, 03 Jun 2017 13:33:24: start X-correlation... INFO @ Sat, 03 Jun 2017 13:33:24: end of X-cor INFO @ Sat, 03 Jun 2017 13:33:24: #2 finished! INFO @ Sat, 03 Jun 2017 13:33:24: #2 predicted fragment length is 124 bps INFO @ Sat, 03 Jun 2017 13:33:24: #2 alternative fragment length(s) may be 124 bps INFO @ Sat, 03 Jun 2017 13:33:24: #2.2 Generate R script for model : SRX1600295.10_model.r WARNING @ Sat, 03 Jun 2017 13:33:24: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:33:24: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sat, 03 Jun 2017 13:33:24: #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 13:33:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:33:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:33:26: start X-correlation... INFO @ Sat, 03 Jun 2017 13:33:26: end of X-cor INFO @ Sat, 03 Jun 2017 13:33:26: #2 finished! INFO @ Sat, 03 Jun 2017 13:33:26: #2 predicted fragment length is 124 bps INFO @ Sat, 03 Jun 2017 13:33:26: #2 alternative fragment length(s) may be 124 bps INFO @ Sat, 03 Jun 2017 13:33:26: #2.2 Generate R script for model : SRX1600295.20_model.r WARNING @ Sat, 03 Jun 2017 13:33:26: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:33:26: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sat, 03 Jun 2017 13:33:26: #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 13:33:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:33:27: start X-correlation... INFO @ Sat, 03 Jun 2017 13:33:27: end of X-cor INFO @ Sat, 03 Jun 2017 13:33:27: #2 finished! INFO @ Sat, 03 Jun 2017 13:33:27: #2 predicted fragment length is 124 bps INFO @ Sat, 03 Jun 2017 13:33:27: #2 alternative fragment length(s) may be 124 bps INFO @ Sat, 03 Jun 2017 13:33:27: #2.2 Generate R script for model : SRX1600295.05_model.r WARNING @ Sat, 03 Jun 2017 13:33:27: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:33:27: #2 You may need to consider one of the other alternative d(s): 124 WARNING @ Sat, 03 Jun 2017 13:33:27: #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 13:33:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:34:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:34:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:34:20: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:34:56: #4 Write output xls file... SRX1600295.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:34:56: #4 Write peak in narrowPeak format file... SRX1600295.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:34:56: #4 Write summits bed file... SRX1600295.20_summits.bed INFO @ Sat, 03 Jun 2017 13:34:56: Done! pass1 - making usageList (13 chroms): 9 millis pass2 - checking and writing primary data (4502 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:35:06: #4 Write output xls file... SRX1600295.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:35:06: #4 Write peak in narrowPeak format file... SRX1600295.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:35:06: #4 Write summits bed file... SRX1600295.10_summits.bed INFO @ Sat, 03 Jun 2017 13:35:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7952 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:35:14: #4 Write output xls file... SRX1600295.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:35:14: #4 Write peak in narrowPeak format file... SRX1600295.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:35:14: #4 Write summits bed file... SRX1600295.05_summits.bed INFO @ Sat, 03 Jun 2017 13:35:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10105 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。