Job ID = 9029762 sra ファイルのダウンロード中... Completed: 378055K bytes transferred in 6 seconds (465752K 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 14324 0 14324 0 0 1909 0 --:--:-- 0:00:07 --:--:-- 13933 100 50839 0 50839 0 0 6102 0 --:--:-- 0:00:08 --:--:-- 27347 100 52710 0 52710 0 0 6326 0 --:--:-- 0:00:08 --:--:-- 28338 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 17888908 spots for /home/okishinya/chipatlas/results/dm3/SRX2055946/SRR4069178.sra Written 17888908 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: 00:09:38 17888908 reads; of these: 17888908 (100.00%) were unpaired; of these: 509780 (2.85%) aligned 0 times 10360745 (57.92%) aligned exactly 1 time 7018383 (39.23%) aligned >1 times 97.15% overall alignment rate Time searching: 00:09:38 Overall time: 00:09:38 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] 2544532 / 17379128 = 0.1464 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 15:19:39: # Command line: callpeak -t SRX2055946.bam -f BAM -g dm -n SRX2055946.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055946.20 # format = BAM # ChIP-seq file = ['SRX2055946.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 15:19:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:19:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:19:39: # Command line: callpeak -t SRX2055946.bam -f BAM -g dm -n SRX2055946.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055946.10 # format = BAM # ChIP-seq file = ['SRX2055946.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 15:19:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:19:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:19:39: # Command line: callpeak -t SRX2055946.bam -f BAM -g dm -n SRX2055946.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055946.05 # format = BAM # ChIP-seq file = ['SRX2055946.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 15:19:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:19:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:19:45: 1000000 INFO @ Sat, 03 Jun 2017 15:19:46: 1000000 INFO @ Sat, 03 Jun 2017 15:19:46: 1000000 INFO @ Sat, 03 Jun 2017 15:19:52: 2000000 INFO @ Sat, 03 Jun 2017 15:19:52: 2000000 INFO @ Sat, 03 Jun 2017 15:19:52: 2000000 INFO @ Sat, 03 Jun 2017 15:19:59: 3000000 INFO @ Sat, 03 Jun 2017 15:19:59: 3000000 INFO @ Sat, 03 Jun 2017 15:19:59: 3000000 INFO @ Sat, 03 Jun 2017 15:20:06: 4000000 INFO @ Sat, 03 Jun 2017 15:20:06: 4000000 INFO @ Sat, 03 Jun 2017 15:20:06: 4000000 INFO @ Sat, 03 Jun 2017 15:20:12: 5000000 INFO @ Sat, 03 Jun 2017 15:20:12: 5000000 INFO @ Sat, 03 Jun 2017 15:20:13: 5000000 INFO @ Sat, 03 Jun 2017 15:20:18: 6000000 INFO @ Sat, 03 Jun 2017 15:20:20: 6000000 INFO @ Sat, 03 Jun 2017 15:20:20: 6000000 INFO @ Sat, 03 Jun 2017 15:20:24: 7000000 INFO @ Sat, 03 Jun 2017 15:20:27: 7000000 INFO @ Sat, 03 Jun 2017 15:20:27: 7000000 INFO @ Sat, 03 Jun 2017 15:20:31: 8000000 INFO @ Sat, 03 Jun 2017 15:20:34: 8000000 INFO @ Sat, 03 Jun 2017 15:20:35: 8000000 INFO @ Sat, 03 Jun 2017 15:20:37: 9000000 INFO @ Sat, 03 Jun 2017 15:20:41: 9000000 INFO @ Sat, 03 Jun 2017 15:20:42: 9000000 INFO @ Sat, 03 Jun 2017 15:20:43: 10000000 INFO @ Sat, 03 Jun 2017 15:20:49: 10000000 INFO @ Sat, 03 Jun 2017 15:20:49: 10000000 INFO @ Sat, 03 Jun 2017 15:20:49: 11000000 INFO @ Sat, 03 Jun 2017 15:20:56: 12000000 INFO @ Sat, 03 Jun 2017 15:20:56: 11000000 INFO @ Sat, 03 Jun 2017 15:20:57: 11000000 INFO @ Sat, 03 Jun 2017 15:21:02: 13000000 INFO @ Sat, 03 Jun 2017 15:21:04: 12000000 INFO @ Sat, 03 Jun 2017 15:21:04: 12000000 INFO @ Sat, 03 Jun 2017 15:21:08: 14000000 INFO @ Sat, 03 Jun 2017 15:21:11: 13000000 INFO @ Sat, 03 Jun 2017 15:21:12: 13000000 INFO @ Sat, 03 Jun 2017 15:21:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:21:14: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:21:14: #1 total tags in treatment: 14834596 INFO @ Sat, 03 Jun 2017 15:21:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:21:14: #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 15:21:17: #1 tags after filtering in treatment: 14830739 INFO @ Sat, 03 Jun 2017 15:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:21:17: #1 finished! INFO @ Sat, 03 Jun 2017 15:21:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:21:19: 14000000 INFO @ Sat, 03 Jun 2017 15:21:20: #2 number of paired peaks: 1269 INFO @ Sat, 03 Jun 2017 15:21:20: start model_add_line... INFO @ Sat, 03 Jun 2017 15:21:20: 14000000 INFO @ Sat, 03 Jun 2017 15:21:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:21:25: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:21:25: #1 total tags in treatment: 14834596 INFO @ Sat, 03 Jun 2017 15:21:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:21:25: #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 15:21:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:21:26: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:21:26: #1 total tags in treatment: 14834596 INFO @ Sat, 03 Jun 2017 15:21:26: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:21:26: #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 15:21:28: #1 tags after filtering in treatment: 14830739 INFO @ Sat, 03 Jun 2017 15:21:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:21:28: #1 finished! INFO @ Sat, 03 Jun 2017 15:21:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:21:29: #1 tags after filtering in treatment: 14830739 INFO @ Sat, 03 Jun 2017 15:21:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:21:29: #1 finished! INFO @ Sat, 03 Jun 2017 15:21:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:21:30: #2 number of paired peaks: 1269 INFO @ Sat, 03 Jun 2017 15:21:30: start model_add_line... INFO @ Sat, 03 Jun 2017 15:21:31: start X-correlation... INFO @ Sat, 03 Jun 2017 15:21:31: end of X-cor INFO @ Sat, 03 Jun 2017 15:21:31: #2 finished! INFO @ Sat, 03 Jun 2017 15:21:31: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 15:21:31: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 15:21:31: #2.2 Generate R script for model : SRX2055946.05_model.r WARNING @ Sat, 03 Jun 2017 15:21:31: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:21:31: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 15:21:31: #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 15:21:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:21:32: #2 number of paired peaks: 1269 INFO @ Sat, 03 Jun 2017 15:21:32: start model_add_line... INFO @ Sat, 03 Jun 2017 15:21:42: start X-correlation... INFO @ Sat, 03 Jun 2017 15:21:42: end of X-cor INFO @ Sat, 03 Jun 2017 15:21:42: #2 finished! INFO @ Sat, 03 Jun 2017 15:21:42: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 15:21:42: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 15:21:42: #2.2 Generate R script for model : SRX2055946.10_model.r WARNING @ Sat, 03 Jun 2017 15:21:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:21:42: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 15:21:42: #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 15:21:42: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:21:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:21:44: start X-correlation... INFO @ Sat, 03 Jun 2017 15:21:44: end of X-cor INFO @ Sat, 03 Jun 2017 15:21:44: #2 finished! INFO @ Sat, 03 Jun 2017 15:21:44: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 15:21:44: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 15:21:44: #2.2 Generate R script for model : SRX2055946.20_model.r WARNING @ Sat, 03 Jun 2017 15:21:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:21:44: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 15:21:44: #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 15:21:44: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:21:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:22:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:23:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:23:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:23:54: #4 Write output xls file... SRX2055946.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:23:54: #4 Write peak in narrowPeak format file... SRX2055946.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:23:54: #4 Write summits bed file... SRX2055946.05_summits.bed INFO @ Sat, 03 Jun 2017 15:23:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3688 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:24:02: #4 Write output xls file... SRX2055946.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:24:02: #4 Write peak in narrowPeak format file... SRX2055946.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:24:03: #4 Write summits bed file... SRX2055946.20_summits.bed INFO @ Sat, 03 Jun 2017 15:24:03: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1452 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:24:06: #4 Write output xls file... SRX2055946.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:24:06: #4 Write peak in narrowPeak format file... SRX2055946.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:24:06: #4 Write summits bed file... SRX2055946.10_summits.bed INFO @ Sat, 03 Jun 2017 15:24:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2734 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。