Job ID = 8696863 sra ファイルのダウンロード中... Completed: 891018K bytes transferred in 12 seconds (585238K 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 --:--:-- 0:00:06 --:--:-- 0 100 18919 0 18919 0 0 2445 0 --:--:-- 0:00:07 --:--:-- 14908 100 31396 0 31396 0 0 3801 0 --:--:-- 0:00:08 --:--:-- 17520 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 32551830 spots for /home/okishinya/chipatlas/results/dm3/SRX110794/SRR388376.sra Written 32551830 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: 00:16:32 32551830 reads; of these: 32551830 (100.00%) were unpaired; of these: 3138665 (9.64%) aligned 0 times 25192478 (77.39%) aligned exactly 1 time 4220687 (12.97%) aligned >1 times 90.36% overall alignment rate Time searching: 00:16:32 Overall time: 00:16:32 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] 4229532 / 29413165 = 0.1438 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 12:59:00: # Command line: callpeak -t SRX110794.bam -f BAM -g dm -n SRX110794.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110794.05 # format = BAM # ChIP-seq file = ['SRX110794.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 12:59:00: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:59:00: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:59:00: # Command line: callpeak -t SRX110794.bam -f BAM -g dm -n SRX110794.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110794.20 # format = BAM # ChIP-seq file = ['SRX110794.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 12:59:00: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:59:00: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:59:00: # Command line: callpeak -t SRX110794.bam -f BAM -g dm -n SRX110794.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110794.10 # format = BAM # ChIP-seq file = ['SRX110794.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 12:59:00: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:59:00: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:59:12: 1000000 INFO @ Fri, 10 Mar 2017 12:59:13: 1000000 INFO @ Fri, 10 Mar 2017 12:59:13: 1000000 INFO @ Fri, 10 Mar 2017 12:59:25: 2000000 INFO @ Fri, 10 Mar 2017 12:59:26: 2000000 INFO @ Fri, 10 Mar 2017 12:59:26: 2000000 INFO @ Fri, 10 Mar 2017 12:59:37: 3000000 INFO @ Fri, 10 Mar 2017 12:59:38: 3000000 INFO @ Fri, 10 Mar 2017 12:59:39: 3000000 INFO @ Fri, 10 Mar 2017 12:59:49: 4000000 INFO @ Fri, 10 Mar 2017 12:59:49: 4000000 INFO @ Fri, 10 Mar 2017 12:59:50: 4000000 INFO @ Fri, 10 Mar 2017 13:00:00: 5000000 INFO @ Fri, 10 Mar 2017 13:00:01: 5000000 INFO @ Fri, 10 Mar 2017 13:00:01: 5000000 INFO @ Fri, 10 Mar 2017 13:00:11: 6000000 INFO @ Fri, 10 Mar 2017 13:00:11: 6000000 INFO @ Fri, 10 Mar 2017 13:00:16: 6000000 INFO @ Fri, 10 Mar 2017 13:00:21: 7000000 INFO @ Fri, 10 Mar 2017 13:00:21: 7000000 INFO @ Fri, 10 Mar 2017 13:00:29: 7000000 INFO @ Fri, 10 Mar 2017 13:00:30: 8000000 INFO @ Fri, 10 Mar 2017 13:00:31: 8000000 INFO @ Fri, 10 Mar 2017 13:00:38: 9000000 INFO @ Fri, 10 Mar 2017 13:00:39: 8000000 INFO @ Fri, 10 Mar 2017 13:00:40: 9000000 INFO @ Fri, 10 Mar 2017 13:00:46: 10000000 INFO @ Fri, 10 Mar 2017 13:00:49: 9000000 INFO @ Fri, 10 Mar 2017 13:00:49: 10000000 INFO @ Fri, 10 Mar 2017 13:00:54: 11000000 INFO @ Fri, 10 Mar 2017 13:00:58: 11000000 INFO @ Fri, 10 Mar 2017 13:00:59: 10000000 INFO @ Fri, 10 Mar 2017 13:01:02: 12000000 INFO @ Fri, 10 Mar 2017 13:01:06: 12000000 INFO @ Fri, 10 Mar 2017 13:01:09: 11000000 INFO @ Fri, 10 Mar 2017 13:01:10: 13000000 INFO @ Fri, 10 Mar 2017 13:01:16: 13000000 INFO @ Fri, 10 Mar 2017 13:01:19: 14000000 INFO @ Fri, 10 Mar 2017 13:01:20: 12000000 INFO @ Fri, 10 Mar 2017 13:01:24: 14000000 INFO @ Fri, 10 Mar 2017 13:01:28: 15000000 INFO @ Fri, 10 Mar 2017 13:01:32: 13000000 INFO @ Fri, 10 Mar 2017 13:01:34: 15000000 INFO @ Fri, 10 Mar 2017 13:01:38: 16000000 INFO @ Fri, 10 Mar 2017 13:01:43: 16000000 INFO @ Fri, 10 Mar 2017 13:01:46: 14000000 INFO @ Fri, 10 Mar 2017 13:01:48: 17000000 INFO @ Fri, 10 Mar 2017 13:01:52: 17000000 INFO @ Fri, 10 Mar 2017 13:01:57: 18000000 INFO @ Fri, 10 Mar 2017 13:01:58: 15000000 INFO @ Fri, 10 Mar 2017 13:02:02: 18000000 INFO @ Fri, 10 Mar 2017 13:02:06: 19000000 INFO @ Fri, 10 Mar 2017 13:02:11: 19000000 INFO @ Fri, 10 Mar 2017 13:02:12: 16000000 INFO @ Fri, 10 Mar 2017 13:02:16: 20000000 INFO @ Fri, 10 Mar 2017 13:02:21: 20000000 INFO @ Fri, 10 Mar 2017 13:02:24: 17000000 INFO @ Fri, 10 Mar 2017 13:02:27: 21000000 INFO @ Fri, 10 Mar 2017 13:02:31: 21000000 INFO @ Fri, 10 Mar 2017 13:02:34: 18000000 INFO @ Fri, 10 Mar 2017 13:02:37: 22000000 INFO @ Fri, 10 Mar 2017 13:02:42: 22000000 INFO @ Fri, 10 Mar 2017 13:02:45: 19000000 INFO @ Fri, 10 Mar 2017 13:02:47: 23000000 INFO @ Fri, 10 Mar 2017 13:02:53: 23000000 INFO @ Fri, 10 Mar 2017 13:02:54: 20000000 INFO @ Fri, 10 Mar 2017 13:02:59: 24000000 INFO @ Fri, 10 Mar 2017 13:03:02: 21000000 INFO @ Fri, 10 Mar 2017 13:03:03: 24000000 INFO @ Fri, 10 Mar 2017 13:03:09: 25000000 INFO @ Fri, 10 Mar 2017 13:03:11: 22000000 INFO @ Fri, 10 Mar 2017 13:03:11: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 13:03:11: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 13:03:11: #1 total tags in treatment: 25183633 INFO @ Fri, 10 Mar 2017 13:03:11: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:03:11: #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 13:03:12: 25000000 INFO @ Fri, 10 Mar 2017 13:03:15: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 13:03:15: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 13:03:15: #1 total tags in treatment: 25183633 INFO @ Fri, 10 Mar 2017 13:03:15: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:03:15: #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 13:03:17: #1 tags after filtering in treatment: 25179634 INFO @ Fri, 10 Mar 2017 13:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:03:17: #1 finished! INFO @ Fri, 10 Mar 2017 13:03:17: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:03:20: 23000000 INFO @ Fri, 10 Mar 2017 13:03:21: #1 tags after filtering in treatment: 25179634 INFO @ Fri, 10 Mar 2017 13:03:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:03:21: #1 finished! INFO @ Fri, 10 Mar 2017 13:03:21: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:03:22: #2 number of paired peaks: 145 WARNING @ Fri, 10 Mar 2017 13:03:22: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 10 Mar 2017 13:03:22: start model_add_line... INFO @ Fri, 10 Mar 2017 13:03:27: #2 number of paired peaks: 145 WARNING @ Fri, 10 Mar 2017 13:03:27: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 10 Mar 2017 13:03:27: start model_add_line... INFO @ Fri, 10 Mar 2017 13:03:27: start X-correlation... INFO @ Fri, 10 Mar 2017 13:03:27: end of X-cor INFO @ Fri, 10 Mar 2017 13:03:27: #2 finished! INFO @ Fri, 10 Mar 2017 13:03:27: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Mar 2017 13:03:27: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 10 Mar 2017 13:03:27: #2.2 Generate R script for model : SRX110794.05_model.r WARNING @ Fri, 10 Mar 2017 13:03:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 13:03:27: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 10 Mar 2017 13:03:27: #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 13:03:27: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:03:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:03:28: 24000000 INFO @ Fri, 10 Mar 2017 13:03:32: start X-correlation... INFO @ Fri, 10 Mar 2017 13:03:32: end of X-cor INFO @ Fri, 10 Mar 2017 13:03:32: #2 finished! INFO @ Fri, 10 Mar 2017 13:03:32: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Mar 2017 13:03:32: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 10 Mar 2017 13:03:32: #2.2 Generate R script for model : SRX110794.10_model.r WARNING @ Fri, 10 Mar 2017 13:03:32: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 13:03:32: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 10 Mar 2017 13:03:32: #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 13:03:32: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:03:37: 25000000 INFO @ Fri, 10 Mar 2017 13:03:39: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 13:03:39: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 13:03:39: #1 total tags in treatment: 25183633 INFO @ Fri, 10 Mar 2017 13:03:39: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 13:03:39: #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 13:03:45: #1 tags after filtering in treatment: 25179634 INFO @ Fri, 10 Mar 2017 13:03:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 13:03:45: #1 finished! INFO @ Fri, 10 Mar 2017 13:03:45: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 13:03:51: #2 number of paired peaks: 145 WARNING @ Fri, 10 Mar 2017 13:03:51: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 10 Mar 2017 13:03:51: start model_add_line... INFO @ Fri, 10 Mar 2017 13:03:56: start X-correlation... INFO @ Fri, 10 Mar 2017 13:03:56: end of X-cor INFO @ Fri, 10 Mar 2017 13:03:56: #2 finished! INFO @ Fri, 10 Mar 2017 13:03:56: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Mar 2017 13:03:56: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 10 Mar 2017 13:03:56: #2.2 Generate R script for model : SRX110794.20_model.r WARNING @ Fri, 10 Mar 2017 13:03:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 13:03:56: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 10 Mar 2017 13:03:56: #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 13:03:56: #3 Call peaks... INFO @ Fri, 10 Mar 2017 13:03:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:05:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:05:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:06:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:07:30: #4 Write output xls file... SRX110794.05_peaks.xls INFO @ Fri, 10 Mar 2017 13:07:31: #4 Write peak in narrowPeak format file... SRX110794.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:07:31: #4 Write summits bed file... SRX110794.05_summits.bed INFO @ Fri, 10 Mar 2017 13:07:31: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (13840 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 13:07:39: #4 Write output xls file... SRX110794.10_peaks.xls INFO @ Fri, 10 Mar 2017 13:07:39: #4 Write peak in narrowPeak format file... SRX110794.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:07:39: #4 Write summits bed file... SRX110794.10_summits.bed INFO @ Fri, 10 Mar 2017 13:07:39: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6124 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 13:08:02: #4 Write output xls file... SRX110794.20_peaks.xls INFO @ Fri, 10 Mar 2017 13:08:02: #4 Write peak in narrowPeak format file... SRX110794.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:08:02: #4 Write summits bed file... SRX110794.20_summits.bed INFO @ Fri, 10 Mar 2017 13:08:02: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1001 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。