Job ID = 9029776 sra ファイルのダウンロード中... Completed: 535818K bytes transferred in 8 seconds (541902K 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 22318 0 22318 0 0 2802 0 --:--:-- 0:00:07 --:--:-- 16780 100 30915 0 30915 0 0 3727 0 --:--:-- 0:00:08 --:--:-- 18601 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 22969101 spots for /home/okishinya/chipatlas/results/dm3/SRX2055958/SRR4069190.sra Written 22969101 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: 00:09:34 22969101 reads; of these: 22969101 (100.00%) were unpaired; of these: 5231812 (22.78%) aligned 0 times 11814007 (51.43%) aligned exactly 1 time 5923282 (25.79%) aligned >1 times 77.22% overall alignment rate Time searching: 00:09:34 Overall time: 00:09:34 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] 2663018 / 17737289 = 0.1501 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 15:24:11: # Command line: callpeak -t SRX2055958.bam -f BAM -g dm -n SRX2055958.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055958.05 # format = BAM # ChIP-seq file = ['SRX2055958.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 15:24:11: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:24:11: # Command line: callpeak -t SRX2055958.bam -f BAM -g dm -n SRX2055958.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055958.10 # format = BAM # ChIP-seq file = ['SRX2055958.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 15:24:11: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:24:11: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:24:11: # Command line: callpeak -t SRX2055958.bam -f BAM -g dm -n SRX2055958.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055958.20 # format = BAM # ChIP-seq file = ['SRX2055958.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 15:24:11: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:24:11: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:24:11: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:24:17: 1000000 INFO @ Sat, 03 Jun 2017 15:24:17: 1000000 INFO @ Sat, 03 Jun 2017 15:24:17: 1000000 INFO @ Sat, 03 Jun 2017 15:24:23: 2000000 INFO @ Sat, 03 Jun 2017 15:24:23: 2000000 INFO @ Sat, 03 Jun 2017 15:24:23: 2000000 INFO @ Sat, 03 Jun 2017 15:24:29: 3000000 INFO @ Sat, 03 Jun 2017 15:24:29: 3000000 INFO @ Sat, 03 Jun 2017 15:24:29: 3000000 INFO @ Sat, 03 Jun 2017 15:24:34: 4000000 INFO @ Sat, 03 Jun 2017 15:24:36: 4000000 INFO @ Sat, 03 Jun 2017 15:24:36: 4000000 INFO @ Sat, 03 Jun 2017 15:24:40: 5000000 INFO @ Sat, 03 Jun 2017 15:24:42: 5000000 INFO @ Sat, 03 Jun 2017 15:24:42: 5000000 INFO @ Sat, 03 Jun 2017 15:24:46: 6000000 INFO @ Sat, 03 Jun 2017 15:24:48: 6000000 INFO @ Sat, 03 Jun 2017 15:24:48: 6000000 INFO @ Sat, 03 Jun 2017 15:24:52: 7000000 INFO @ Sat, 03 Jun 2017 15:24:54: 7000000 INFO @ Sat, 03 Jun 2017 15:24:54: 7000000 INFO @ Sat, 03 Jun 2017 15:24:58: 8000000 INFO @ Sat, 03 Jun 2017 15:25:00: 8000000 INFO @ Sat, 03 Jun 2017 15:25:00: 8000000 INFO @ Sat, 03 Jun 2017 15:25:04: 9000000 INFO @ Sat, 03 Jun 2017 15:25:06: 9000000 INFO @ Sat, 03 Jun 2017 15:25:07: 9000000 INFO @ Sat, 03 Jun 2017 15:25:10: 10000000 INFO @ Sat, 03 Jun 2017 15:25:12: 10000000 INFO @ Sat, 03 Jun 2017 15:25:13: 10000000 INFO @ Sat, 03 Jun 2017 15:25:17: 11000000 INFO @ Sat, 03 Jun 2017 15:25:18: 11000000 INFO @ Sat, 03 Jun 2017 15:25:19: 11000000 INFO @ Sat, 03 Jun 2017 15:25:23: 12000000 INFO @ Sat, 03 Jun 2017 15:25:24: 12000000 INFO @ Sat, 03 Jun 2017 15:25:26: 12000000 INFO @ Sat, 03 Jun 2017 15:25:29: 13000000 INFO @ Sat, 03 Jun 2017 15:25:29: 13000000 INFO @ Sat, 03 Jun 2017 15:25:32: 13000000 INFO @ Sat, 03 Jun 2017 15:25:35: 14000000 INFO @ Sat, 03 Jun 2017 15:25:36: 14000000 INFO @ Sat, 03 Jun 2017 15:25:38: 14000000 INFO @ Sat, 03 Jun 2017 15:25:41: 15000000 INFO @ Sat, 03 Jun 2017 15:25:42: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:25:42: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:25:42: #1 total tags in treatment: 15074271 INFO @ Sat, 03 Jun 2017 15:25:42: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:25:42: #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 15:25:42: 15000000 INFO @ Sat, 03 Jun 2017 15:25:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:25:43: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:25:43: #1 total tags in treatment: 15074271 INFO @ Sat, 03 Jun 2017 15:25:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:25:43: #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 15:25:44: 15000000 INFO @ Sat, 03 Jun 2017 15:25:44: #1 tags after filtering in treatment: 15070157 INFO @ Sat, 03 Jun 2017 15:25:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:25:44: #1 finished! INFO @ Sat, 03 Jun 2017 15:25:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:25:45: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:25:45: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:25:45: #1 total tags in treatment: 15074271 INFO @ Sat, 03 Jun 2017 15:25:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:25:45: #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 15:25:45: #1 tags after filtering in treatment: 15070157 INFO @ Sat, 03 Jun 2017 15:25:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:25:45: #1 finished! INFO @ Sat, 03 Jun 2017 15:25:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:25:47: #2 number of paired peaks: 905 WARNING @ Sat, 03 Jun 2017 15:25:47: Fewer paired peaks (905) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 905 pairs to build model! INFO @ Sat, 03 Jun 2017 15:25:47: start model_add_line... INFO @ Sat, 03 Jun 2017 15:25:48: #1 tags after filtering in treatment: 15070157 INFO @ Sat, 03 Jun 2017 15:25:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:25:48: #1 finished! INFO @ Sat, 03 Jun 2017 15:25:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:25:48: #2 number of paired peaks: 905 WARNING @ Sat, 03 Jun 2017 15:25:48: Fewer paired peaks (905) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 905 pairs to build model! INFO @ Sat, 03 Jun 2017 15:25:48: start model_add_line... INFO @ Sat, 03 Jun 2017 15:25:50: #2 number of paired peaks: 905 WARNING @ Sat, 03 Jun 2017 15:25:50: Fewer paired peaks (905) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 905 pairs to build model! INFO @ Sat, 03 Jun 2017 15:25:50: start model_add_line... INFO @ Sat, 03 Jun 2017 15:25:56: start X-correlation... INFO @ Sat, 03 Jun 2017 15:25:56: end of X-cor INFO @ Sat, 03 Jun 2017 15:25:56: #2 finished! INFO @ Sat, 03 Jun 2017 15:25:56: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 15:25:56: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Jun 2017 15:25:56: #2.2 Generate R script for model : SRX2055958.10_model.r WARNING @ Sat, 03 Jun 2017 15:25:56: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:25:56: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Jun 2017 15:25:56: #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 15:25:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:25:57: start X-correlation... INFO @ Sat, 03 Jun 2017 15:25:57: end of X-cor INFO @ Sat, 03 Jun 2017 15:25:57: #2 finished! INFO @ Sat, 03 Jun 2017 15:25:57: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 15:25:57: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Jun 2017 15:25:57: #2.2 Generate R script for model : SRX2055958.20_model.r WARNING @ Sat, 03 Jun 2017 15:25:57: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:25:57: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Jun 2017 15:25:57: #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 15:25:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:25:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:25:59: start X-correlation... INFO @ Sat, 03 Jun 2017 15:25:59: end of X-cor INFO @ Sat, 03 Jun 2017 15:25:59: #2 finished! INFO @ Sat, 03 Jun 2017 15:25:59: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 15:25:59: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Jun 2017 15:25:59: #2.2 Generate R script for model : SRX2055958.05_model.r WARNING @ Sat, 03 Jun 2017 15:25:59: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:25:59: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Jun 2017 15:25:59: #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 15:25:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:27:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:27:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:27:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:28:07: #4 Write output xls file... SRX2055958.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:28:07: #4 Write peak in narrowPeak format file... SRX2055958.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:28:07: #4 Write summits bed file... SRX2055958.20_summits.bed INFO @ Sat, 03 Jun 2017 15:28:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1551 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:28:19: #4 Write output xls file... SRX2055958.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:28:19: #4 Write peak in narrowPeak format file... SRX2055958.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:28:19: #4 Write summits bed file... SRX2055958.10_summits.bed INFO @ Sat, 03 Jun 2017 15:28:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2826 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:28:25: #4 Write output xls file... SRX2055958.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:28:25: #4 Write peak in narrowPeak format file... SRX2055958.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:28:25: #4 Write summits bed file... SRX2055958.05_summits.bed INFO @ Sat, 03 Jun 2017 15:28:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4261 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。