Job ID = 9029252 sra ファイルのダウンロード中... Completed: 623164K bytes transferred in 12 seconds (420486K 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 14324 0 14324 0 0 1941 0 --:--:-- 0:00:07 --:--:-- 12892 100 41829 0 41829 0 0 4994 0 --:--:-- 0:00:08 --:--:-- 19852 100 91821 0 91821 0 0 9798 0 --:--:-- 0:00:09 --:--:-- 29600 100 109k 0 109k 0 0 11731 0 --:--:-- 0:00:09 --:--:-- 34230 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 29185176 spots for /home/okishinya/chipatlas/results/dm3/SRX1433401/SRR2919817.sra Written 29185176 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: 00:09:01 29185176 reads; of these: 29185176 (100.00%) were unpaired; of these: 2848781 (9.76%) aligned 0 times 20138305 (69.00%) aligned exactly 1 time 6198090 (21.24%) aligned >1 times 90.24% overall alignment rate Time searching: 00:09:01 Overall time: 00:09:01 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] 8078127 / 26336395 = 0.3067 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 13:09:29: # Command line: callpeak -t SRX1433401.bam -f BAM -g dm -n SRX1433401.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433401.20 # format = BAM # ChIP-seq file = ['SRX1433401.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 13:09:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:09:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:09:29: # Command line: callpeak -t SRX1433401.bam -f BAM -g dm -n SRX1433401.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433401.10 # format = BAM # ChIP-seq file = ['SRX1433401.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 13:09:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:09:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:09:29: # Command line: callpeak -t SRX1433401.bam -f BAM -g dm -n SRX1433401.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433401.05 # format = BAM # ChIP-seq file = ['SRX1433401.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 13:09:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:09:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:09:35: 1000000 INFO @ Sat, 03 Jun 2017 13:09:35: 1000000 INFO @ Sat, 03 Jun 2017 13:09:35: 1000000 INFO @ Sat, 03 Jun 2017 13:09:41: 2000000 INFO @ Sat, 03 Jun 2017 13:09:41: 2000000 INFO @ Sat, 03 Jun 2017 13:09:41: 2000000 INFO @ Sat, 03 Jun 2017 13:09:47: 3000000 INFO @ Sat, 03 Jun 2017 13:09:48: 3000000 INFO @ Sat, 03 Jun 2017 13:09:48: 3000000 INFO @ Sat, 03 Jun 2017 13:09:52: 4000000 INFO @ Sat, 03 Jun 2017 13:09:54: 4000000 INFO @ Sat, 03 Jun 2017 13:09:54: 4000000 INFO @ Sat, 03 Jun 2017 13:09:58: 5000000 INFO @ Sat, 03 Jun 2017 13:10:00: 5000000 INFO @ Sat, 03 Jun 2017 13:10:00: 5000000 INFO @ Sat, 03 Jun 2017 13:10:03: 6000000 INFO @ Sat, 03 Jun 2017 13:10:06: 6000000 INFO @ Sat, 03 Jun 2017 13:10:06: 6000000 INFO @ Sat, 03 Jun 2017 13:10:09: 7000000 INFO @ Sat, 03 Jun 2017 13:10:12: 7000000 INFO @ Sat, 03 Jun 2017 13:10:12: 7000000 INFO @ Sat, 03 Jun 2017 13:10:14: 8000000 INFO @ Sat, 03 Jun 2017 13:10:17: 8000000 INFO @ Sat, 03 Jun 2017 13:10:17: 8000000 INFO @ Sat, 03 Jun 2017 13:10:19: 9000000 INFO @ Sat, 03 Jun 2017 13:10:23: 9000000 INFO @ Sat, 03 Jun 2017 13:10:23: 9000000 INFO @ Sat, 03 Jun 2017 13:10:24: 10000000 INFO @ Sat, 03 Jun 2017 13:10:30: 10000000 INFO @ Sat, 03 Jun 2017 13:10:30: 10000000 INFO @ Sat, 03 Jun 2017 13:10:30: 11000000 INFO @ Sat, 03 Jun 2017 13:10:37: 12000000 INFO @ Sat, 03 Jun 2017 13:10:37: 11000000 INFO @ Sat, 03 Jun 2017 13:10:37: 11000000 INFO @ Sat, 03 Jun 2017 13:10:42: 13000000 INFO @ Sat, 03 Jun 2017 13:10:43: 12000000 INFO @ Sat, 03 Jun 2017 13:10:43: 12000000 INFO @ Sat, 03 Jun 2017 13:10:48: 14000000 INFO @ Sat, 03 Jun 2017 13:10:49: 13000000 INFO @ Sat, 03 Jun 2017 13:10:49: 13000000 INFO @ Sat, 03 Jun 2017 13:10:54: 15000000 INFO @ Sat, 03 Jun 2017 13:10:55: 14000000 INFO @ Sat, 03 Jun 2017 13:10:55: 14000000 INFO @ Sat, 03 Jun 2017 13:10:59: 16000000 INFO @ Sat, 03 Jun 2017 13:11:01: 15000000 INFO @ Sat, 03 Jun 2017 13:11:01: 15000000 INFO @ Sat, 03 Jun 2017 13:11:04: 17000000 INFO @ Sat, 03 Jun 2017 13:11:07: 16000000 INFO @ Sat, 03 Jun 2017 13:11:07: 16000000 INFO @ Sat, 03 Jun 2017 13:11:09: 18000000 INFO @ Sat, 03 Jun 2017 13:11:11: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:11:11: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:11:11: #1 total tags in treatment: 18258268 INFO @ Sat, 03 Jun 2017 13:11:11: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:11: #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 13:11:12: 17000000 INFO @ Sat, 03 Jun 2017 13:11:12: 17000000 INFO @ Sat, 03 Jun 2017 13:11:14: #1 tags after filtering in treatment: 18254087 INFO @ Sat, 03 Jun 2017 13:11:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:14: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:17: #2 number of paired peaks: 349 WARNING @ Sat, 03 Jun 2017 13:11:17: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:17: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:18: 18000000 INFO @ Sat, 03 Jun 2017 13:11:18: 18000000 INFO @ Sat, 03 Jun 2017 13:11:19: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:11:19: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:11:19: #1 total tags in treatment: 18258268 INFO @ Sat, 03 Jun 2017 13:11:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:19: #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 13:11:19: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:11:19: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:11:19: #1 total tags in treatment: 18258268 INFO @ Sat, 03 Jun 2017 13:11:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:19: #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 13:11:22: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:22: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:22: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:22: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 13:11:22: #2 alternative fragment length(s) may be 4,47 bps INFO @ Sat, 03 Jun 2017 13:11:22: #2.2 Generate R script for model : SRX1433401.10_model.r WARNING @ Sat, 03 Jun 2017 13:11:22: #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 13:11:22: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Sat, 03 Jun 2017 13:11:22: #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 13:11:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:24: #1 tags after filtering in treatment: 18254087 INFO @ Sat, 03 Jun 2017 13:11:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:24: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:24: #1 tags after filtering in treatment: 18254087 INFO @ Sat, 03 Jun 2017 13:11:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:24: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:27: #2 number of paired peaks: 349 WARNING @ Sat, 03 Jun 2017 13:11:27: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:27: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:27: #2 number of paired peaks: 349 WARNING @ Sat, 03 Jun 2017 13:11:27: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:27: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:32: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:32: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:32: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:32: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 13:11:32: #2 alternative fragment length(s) may be 4,47 bps INFO @ Sat, 03 Jun 2017 13:11:32: #2.2 Generate R script for model : SRX1433401.20_model.r WARNING @ Sat, 03 Jun 2017 13:11:32: #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 13:11:32: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Sat, 03 Jun 2017 13:11:32: #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 13:11:32: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:32: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:32: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:32: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:32: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 13:11:32: #2 alternative fragment length(s) may be 4,47 bps INFO @ Sat, 03 Jun 2017 13:11:32: #2.2 Generate R script for model : SRX1433401.05_model.r WARNING @ Sat, 03 Jun 2017 13:11:32: #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 13:11:32: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Sat, 03 Jun 2017 13:11:32: #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 13:11:32: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:14: #4 Write output xls file... SRX1433401.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:14: #4 Write peak in narrowPeak format file... SRX1433401.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:14: #4 Write summits bed file... SRX1433401.10_summits.bed INFO @ Sat, 03 Jun 2017 13:14:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2470 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:14:15: #4 Write output xls file... SRX1433401.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:15: #4 Write peak in narrowPeak format file... SRX1433401.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:15: #4 Write summits bed file... SRX1433401.05_summits.bed INFO @ Sat, 03 Jun 2017 13:14:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4553 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:14:17: #4 Write output xls file... SRX1433401.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:18: #4 Write peak in narrowPeak format file... SRX1433401.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:18: #4 Write summits bed file... SRX1433401.20_summits.bed INFO @ Sat, 03 Jun 2017 13:14:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1011 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。