Job ID = 9033414 sra ファイルのダウンロード中... Completed: 505844K bytes transferred in 10 seconds (377531K 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 30318 0 30318 0 0 3777 0 --:--:-- 0:00:08 --:--:-- 18936 100 56514 0 56514 0 0 6630 0 --:--:-- 0:00:08 --:--:-- 26937 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 23892783 spots for /home/okishinya/chipatlas/results/dm3/SRX969928/SRR1931644.sra Written 23892783 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: 00:09:08 23892783 reads; of these: 23892783 (100.00%) were unpaired; of these: 887393 (3.71%) aligned 0 times 17487962 (73.19%) aligned exactly 1 time 5517428 (23.09%) aligned >1 times 96.29% overall alignment rate Time searching: 00:09:08 Overall time: 00:09:08 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] 2692087 / 23005390 = 0.1170 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 @ Sun, 04 Jun 2017 00:28:34: # Command line: callpeak -t SRX969928.bam -f BAM -g dm -n SRX969928.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX969928.05 # format = BAM # ChIP-seq file = ['SRX969928.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 @ Sun, 04 Jun 2017 00:28:34: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:28:34: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:28:34: # Command line: callpeak -t SRX969928.bam -f BAM -g dm -n SRX969928.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX969928.20 # format = BAM # ChIP-seq file = ['SRX969928.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 @ Sun, 04 Jun 2017 00:28:34: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:28:34: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:28:34: # Command line: callpeak -t SRX969928.bam -f BAM -g dm -n SRX969928.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX969928.10 # format = BAM # ChIP-seq file = ['SRX969928.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 @ Sun, 04 Jun 2017 00:28:34: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:28:34: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:28:39: 1000000 INFO @ Sun, 04 Jun 2017 00:28:40: 1000000 INFO @ Sun, 04 Jun 2017 00:28:40: 1000000 INFO @ Sun, 04 Jun 2017 00:28:44: 2000000 INFO @ Sun, 04 Jun 2017 00:28:46: 2000000 INFO @ Sun, 04 Jun 2017 00:28:46: 2000000 INFO @ Sun, 04 Jun 2017 00:28:49: 3000000 INFO @ Sun, 04 Jun 2017 00:28:52: 3000000 INFO @ Sun, 04 Jun 2017 00:28:52: 3000000 INFO @ Sun, 04 Jun 2017 00:28:55: 4000000 INFO @ Sun, 04 Jun 2017 00:28:58: 4000000 INFO @ Sun, 04 Jun 2017 00:28:58: 4000000 INFO @ Sun, 04 Jun 2017 00:29:00: 5000000 INFO @ Sun, 04 Jun 2017 00:29:04: 5000000 INFO @ Sun, 04 Jun 2017 00:29:04: 5000000 INFO @ Sun, 04 Jun 2017 00:29:05: 6000000 INFO @ Sun, 04 Jun 2017 00:29:10: 6000000 INFO @ Sun, 04 Jun 2017 00:29:10: 6000000 INFO @ Sun, 04 Jun 2017 00:29:11: 7000000 INFO @ Sun, 04 Jun 2017 00:29:16: 8000000 INFO @ Sun, 04 Jun 2017 00:29:17: 7000000 INFO @ Sun, 04 Jun 2017 00:29:17: 7000000 INFO @ Sun, 04 Jun 2017 00:29:21: 9000000 INFO @ Sun, 04 Jun 2017 00:29:23: 8000000 INFO @ Sun, 04 Jun 2017 00:29:23: 8000000 INFO @ Sun, 04 Jun 2017 00:29:27: 10000000 INFO @ Sun, 04 Jun 2017 00:29:30: 9000000 INFO @ Sun, 04 Jun 2017 00:29:30: 9000000 INFO @ Sun, 04 Jun 2017 00:29:32: 11000000 INFO @ Sun, 04 Jun 2017 00:29:36: 10000000 INFO @ Sun, 04 Jun 2017 00:29:36: 10000000 INFO @ Sun, 04 Jun 2017 00:29:38: 12000000 INFO @ Sun, 04 Jun 2017 00:29:43: 11000000 INFO @ Sun, 04 Jun 2017 00:29:43: 11000000 INFO @ Sun, 04 Jun 2017 00:29:43: 13000000 INFO @ Sun, 04 Jun 2017 00:29:48: 14000000 INFO @ Sun, 04 Jun 2017 00:29:49: 12000000 INFO @ Sun, 04 Jun 2017 00:29:49: 12000000 INFO @ Sun, 04 Jun 2017 00:29:54: 15000000 INFO @ Sun, 04 Jun 2017 00:29:55: 13000000 INFO @ Sun, 04 Jun 2017 00:29:55: 13000000 INFO @ Sun, 04 Jun 2017 00:29:59: 16000000 INFO @ Sun, 04 Jun 2017 00:30:02: 14000000 INFO @ Sun, 04 Jun 2017 00:30:02: 14000000 INFO @ Sun, 04 Jun 2017 00:30:04: 17000000 INFO @ Sun, 04 Jun 2017 00:30:08: 15000000 INFO @ Sun, 04 Jun 2017 00:30:08: 15000000 INFO @ Sun, 04 Jun 2017 00:30:10: 18000000 INFO @ Sun, 04 Jun 2017 00:30:15: 16000000 INFO @ Sun, 04 Jun 2017 00:30:15: 16000000 INFO @ Sun, 04 Jun 2017 00:30:15: 19000000 INFO @ Sun, 04 Jun 2017 00:30:21: 20000000 INFO @ Sun, 04 Jun 2017 00:30:21: 17000000 INFO @ Sun, 04 Jun 2017 00:30:21: 17000000 INFO @ Sun, 04 Jun 2017 00:30:23: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:30:23: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:30:23: #1 total tags in treatment: 20313303 INFO @ Sun, 04 Jun 2017 00:30:23: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:30:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:30:27: #1 tags after filtering in treatment: 20308034 INFO @ Sun, 04 Jun 2017 00:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:30:27: #1 finished! INFO @ Sun, 04 Jun 2017 00:30:27: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:30:28: 18000000 INFO @ Sun, 04 Jun 2017 00:30:28: 18000000 INFO @ Sun, 04 Jun 2017 00:30:31: #2 number of paired peaks: 104 WARNING @ Sun, 04 Jun 2017 00:30:31: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sun, 04 Jun 2017 00:30:31: start model_add_line... INFO @ Sun, 04 Jun 2017 00:30:32: start X-correlation... INFO @ Sun, 04 Jun 2017 00:30:32: end of X-cor INFO @ Sun, 04 Jun 2017 00:30:32: #2 finished! INFO @ Sun, 04 Jun 2017 00:30:32: #2 predicted fragment length is 48 bps INFO @ Sun, 04 Jun 2017 00:30:32: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 04 Jun 2017 00:30:32: #2.2 Generate R script for model : SRX969928.10_model.r WARNING @ Sun, 04 Jun 2017 00:30:32: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:30:32: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 04 Jun 2017 00:30:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:30:32: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:30:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:30:34: 19000000 INFO @ Sun, 04 Jun 2017 00:30:34: 19000000 INFO @ Sun, 04 Jun 2017 00:30:41: 20000000 INFO @ Sun, 04 Jun 2017 00:30:41: 20000000 INFO @ Sun, 04 Jun 2017 00:30:43: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:30:43: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:30:43: #1 total tags in treatment: 20313303 INFO @ Sun, 04 Jun 2017 00:30:43: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:30:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:30:43: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:30:43: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:30:43: #1 total tags in treatment: 20313303 INFO @ Sun, 04 Jun 2017 00:30:43: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:30:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:30:47: #1 tags after filtering in treatment: 20308034 INFO @ Sun, 04 Jun 2017 00:30:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:30:47: #1 finished! INFO @ Sun, 04 Jun 2017 00:30:47: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:30:47: #1 tags after filtering in treatment: 20308034 INFO @ Sun, 04 Jun 2017 00:30:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:30:47: #1 finished! INFO @ Sun, 04 Jun 2017 00:30:47: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:30:50: #2 number of paired peaks: 104 WARNING @ Sun, 04 Jun 2017 00:30:50: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sun, 04 Jun 2017 00:30:50: start model_add_line... INFO @ Sun, 04 Jun 2017 00:30:50: #2 number of paired peaks: 104 WARNING @ Sun, 04 Jun 2017 00:30:50: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Sun, 04 Jun 2017 00:30:50: start model_add_line... INFO @ Sun, 04 Jun 2017 00:30:51: start X-correlation... INFO @ Sun, 04 Jun 2017 00:30:51: end of X-cor INFO @ Sun, 04 Jun 2017 00:30:51: #2 finished! INFO @ Sun, 04 Jun 2017 00:30:51: #2 predicted fragment length is 48 bps INFO @ Sun, 04 Jun 2017 00:30:51: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 04 Jun 2017 00:30:51: #2.2 Generate R script for model : SRX969928.05_model.r WARNING @ Sun, 04 Jun 2017 00:30:51: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:30:51: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 04 Jun 2017 00:30:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:30:51: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:30:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:30:51: start X-correlation... INFO @ Sun, 04 Jun 2017 00:30:51: end of X-cor INFO @ Sun, 04 Jun 2017 00:30:51: #2 finished! INFO @ Sun, 04 Jun 2017 00:30:51: #2 predicted fragment length is 48 bps INFO @ Sun, 04 Jun 2017 00:30:51: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 04 Jun 2017 00:30:51: #2.2 Generate R script for model : SRX969928.20_model.r WARNING @ Sun, 04 Jun 2017 00:30:51: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:30:51: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 04 Jun 2017 00:30:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:30:51: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:30:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:32:12: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:32:30: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:32:37: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:33:23: #4 Write output xls file... SRX969928.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:33:23: #4 Write peak in narrowPeak format file... SRX969928.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:33:23: #4 Write summits bed file... SRX969928.10_summits.bed INFO @ Sun, 04 Jun 2017 00:33:23: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1284 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:33:42: #4 Write output xls file... SRX969928.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:33:42: #4 Write peak in narrowPeak format file... SRX969928.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:33:42: #4 Write summits bed file... SRX969928.20_summits.bed INFO @ Sun, 04 Jun 2017 00:33:42: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1001 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:33:54: #4 Write output xls file... SRX969928.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:33:54: #4 Write peak in narrowPeak format file... SRX969928.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:33:54: #4 Write summits bed file... SRX969928.05_summits.bed INFO @ Sun, 04 Jun 2017 00:33:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1574 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。