Job ID = 9029765 sra ファイルのダウンロード中... Completed: 1418051K bytes transferred in 16 seconds (705868K 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 2948 0 --:--:-- 0:00:07 --:--:-- 19173 100 31049 0 31049 0 0 3929 0 --:--:-- 0:00:07 --:--:-- 20754 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 29198102 spots for /home/okishinya/chipatlas/results/dm3/SRX2055949/SRR4069181.sra Written 29198102 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: 00:15:05 29198102 reads; of these: 29198102 (100.00%) were unpaired; of these: 742544 (2.54%) aligned 0 times 16963068 (58.10%) aligned exactly 1 time 11492490 (39.36%) aligned >1 times 97.46% overall alignment rate Time searching: 00:15:05 Overall time: 00:15:05 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] 16803256 / 28455558 = 0.5905 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 15:28:12: # Command line: callpeak -t SRX2055949.bam -f BAM -g dm -n SRX2055949.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055949.10 # format = BAM # ChIP-seq file = ['SRX2055949.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 15:28:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:28:12: # Command line: callpeak -t SRX2055949.bam -f BAM -g dm -n SRX2055949.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055949.05 # format = BAM # ChIP-seq file = ['SRX2055949.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 15:28:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:28:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:28:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:28:12: # Command line: callpeak -t SRX2055949.bam -f BAM -g dm -n SRX2055949.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055949.20 # format = BAM # ChIP-seq file = ['SRX2055949.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 15:28:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:28:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:28:18: 1000000 INFO @ Sat, 03 Jun 2017 15:28:19: 1000000 INFO @ Sat, 03 Jun 2017 15:28:19: 1000000 INFO @ Sat, 03 Jun 2017 15:28:24: 2000000 INFO @ Sat, 03 Jun 2017 15:28:25: 2000000 INFO @ Sat, 03 Jun 2017 15:28:25: 2000000 INFO @ Sat, 03 Jun 2017 15:28:29: 3000000 INFO @ Sat, 03 Jun 2017 15:28:32: 3000000 INFO @ Sat, 03 Jun 2017 15:28:32: 3000000 INFO @ Sat, 03 Jun 2017 15:28:35: 4000000 INFO @ Sat, 03 Jun 2017 15:28:38: 4000000 INFO @ Sat, 03 Jun 2017 15:28:38: 4000000 INFO @ Sat, 03 Jun 2017 15:28:41: 5000000 INFO @ Sat, 03 Jun 2017 15:28:44: 5000000 INFO @ Sat, 03 Jun 2017 15:28:44: 5000000 INFO @ Sat, 03 Jun 2017 15:28:46: 6000000 INFO @ Sat, 03 Jun 2017 15:28:51: 6000000 INFO @ Sat, 03 Jun 2017 15:28:51: 6000000 INFO @ Sat, 03 Jun 2017 15:28:52: 7000000 INFO @ Sat, 03 Jun 2017 15:28:57: 7000000 INFO @ Sat, 03 Jun 2017 15:28:57: 7000000 INFO @ Sat, 03 Jun 2017 15:28:57: 8000000 INFO @ Sat, 03 Jun 2017 15:29:03: 9000000 INFO @ Sat, 03 Jun 2017 15:29:04: 8000000 INFO @ Sat, 03 Jun 2017 15:29:04: 8000000 INFO @ Sat, 03 Jun 2017 15:29:09: 10000000 INFO @ Sat, 03 Jun 2017 15:29:10: 9000000 INFO @ Sat, 03 Jun 2017 15:29:10: 9000000 INFO @ Sat, 03 Jun 2017 15:29:14: 11000000 INFO @ Sat, 03 Jun 2017 15:29:16: 10000000 INFO @ Sat, 03 Jun 2017 15:29:16: 10000000 INFO @ Sat, 03 Jun 2017 15:29:18: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:29:18: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:29:18: #1 total tags in treatment: 11652302 INFO @ Sat, 03 Jun 2017 15:29:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:29:18: #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 15:29:20: #1 tags after filtering in treatment: 11648759 INFO @ Sat, 03 Jun 2017 15:29:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:29:20: #1 finished! INFO @ Sat, 03 Jun 2017 15:29:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:29:23: 11000000 INFO @ Sat, 03 Jun 2017 15:29:23: 11000000 INFO @ Sat, 03 Jun 2017 15:29:23: #2 number of paired peaks: 2646 INFO @ Sat, 03 Jun 2017 15:29:23: start model_add_line... INFO @ Sat, 03 Jun 2017 15:29:27: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:29:27: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:29:27: #1 total tags in treatment: 11652302 INFO @ Sat, 03 Jun 2017 15:29:27: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:29:27: #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 15:29:27: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:29:27: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:29:27: #1 total tags in treatment: 11652302 INFO @ Sat, 03 Jun 2017 15:29:27: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:29:27: #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 15:29:29: #1 tags after filtering in treatment: 11648759 INFO @ Sat, 03 Jun 2017 15:29:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:29:29: #1 finished! INFO @ Sat, 03 Jun 2017 15:29:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:29:30: #1 tags after filtering in treatment: 11648759 INFO @ Sat, 03 Jun 2017 15:29:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:29:30: #1 finished! INFO @ Sat, 03 Jun 2017 15:29:30: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:29:31: #2 number of paired peaks: 2646 INFO @ Sat, 03 Jun 2017 15:29:31: start model_add_line... INFO @ Sat, 03 Jun 2017 15:29:32: #2 number of paired peaks: 2646 INFO @ Sat, 03 Jun 2017 15:29:32: start model_add_line... INFO @ Sat, 03 Jun 2017 15:29:46: start X-correlation... INFO @ Sat, 03 Jun 2017 15:29:46: end of X-cor INFO @ Sat, 03 Jun 2017 15:29:46: #2 finished! INFO @ Sat, 03 Jun 2017 15:29:46: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Jun 2017 15:29:46: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 03 Jun 2017 15:29:46: #2.2 Generate R script for model : SRX2055949.10_model.r WARNING @ Sat, 03 Jun 2017 15:29:46: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:29:46: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 03 Jun 2017 15:29:46: #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 15:29:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:29:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:29:54: start X-correlation... INFO @ Sat, 03 Jun 2017 15:29:54: end of X-cor INFO @ Sat, 03 Jun 2017 15:29:54: #2 finished! INFO @ Sat, 03 Jun 2017 15:29:54: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Jun 2017 15:29:54: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 03 Jun 2017 15:29:54: #2.2 Generate R script for model : SRX2055949.05_model.r WARNING @ Sat, 03 Jun 2017 15:29:54: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:29:54: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 03 Jun 2017 15:29:54: #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 15:29:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:29:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:29:56: start X-correlation... INFO @ Sat, 03 Jun 2017 15:29:56: end of X-cor INFO @ Sat, 03 Jun 2017 15:29:56: #2 finished! INFO @ Sat, 03 Jun 2017 15:29:56: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Jun 2017 15:29:56: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 03 Jun 2017 15:29:56: #2.2 Generate R script for model : SRX2055949.20_model.r WARNING @ Sat, 03 Jun 2017 15:29:56: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:29:56: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 03 Jun 2017 15:29:56: #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 15:29:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:29:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:30:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:31:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:31:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:31:46: #4 Write output xls file... SRX2055949.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:31:46: #4 Write peak in narrowPeak format file... SRX2055949.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:31:46: #4 Write summits bed file... SRX2055949.20_summits.bed INFO @ Sat, 03 Jun 2017 15:31:46: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2138 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:31:47: #4 Write output xls file... SRX2055949.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:31:47: #4 Write peak in narrowPeak format file... SRX2055949.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:31:47: #4 Write summits bed file... SRX2055949.10_summits.bed INFO @ Sat, 03 Jun 2017 15:31:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3615 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:31:56: #4 Write output xls file... SRX2055949.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:31:56: #4 Write peak in narrowPeak format file... SRX2055949.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:31:56: #4 Write summits bed file... SRX2055949.05_summits.bed INFO @ Sat, 03 Jun 2017 15:31:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7290 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。