Job ID = 9029465 sra ファイルのダウンロード中... Completed: 223371K bytes transferred in 4 seconds (366793K 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 7663 0 7663 0 0 1082 0 --:--:-- 0:00:07 --:--:-- 11203 100 30318 0 30318 0 0 3755 0 --:--:-- 0:00:08 --:--:-- 18046 100 53410 0 53410 0 0 6230 0 --:--:-- 0:00:08 --:--:-- 24533 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 8694064 spots for /home/okishinya/chipatlas/results/dm3/SRX1794217/SRR3575249.sra Written 8694064 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: 00:02:58 8694064 reads; of these: 8694064 (100.00%) were unpaired; of these: 288117 (3.31%) aligned 0 times 6357384 (73.12%) aligned exactly 1 time 2048563 (23.56%) aligned >1 times 96.69% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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_rmdupse_core] 263105 / 8405947 = 0.0313 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 13:55:16: # Command line: callpeak -t SRX1794217.bam -f BAM -g dm -n SRX1794217.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794217.10 # format = BAM # ChIP-seq file = ['SRX1794217.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 13:55:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:16: # Command line: callpeak -t SRX1794217.bam -f BAM -g dm -n SRX1794217.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794217.20 # format = BAM # ChIP-seq file = ['SRX1794217.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 13:55:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:16: # Command line: callpeak -t SRX1794217.bam -f BAM -g dm -n SRX1794217.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794217.05 # format = BAM # ChIP-seq file = ['SRX1794217.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 13:55:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:21: 1000000 INFO @ Sat, 03 Jun 2017 13:55:22: 1000000 INFO @ Sat, 03 Jun 2017 13:55:22: 1000000 INFO @ Sat, 03 Jun 2017 13:55:27: 2000000 INFO @ Sat, 03 Jun 2017 13:55:28: 2000000 INFO @ Sat, 03 Jun 2017 13:55:28: 2000000 INFO @ Sat, 03 Jun 2017 13:55:33: 3000000 INFO @ Sat, 03 Jun 2017 13:55:34: 3000000 INFO @ Sat, 03 Jun 2017 13:55:34: 3000000 INFO @ Sat, 03 Jun 2017 13:55:39: 4000000 INFO @ Sat, 03 Jun 2017 13:55:41: 4000000 INFO @ Sat, 03 Jun 2017 13:55:41: 4000000 INFO @ Sat, 03 Jun 2017 13:55:45: 5000000 INFO @ Sat, 03 Jun 2017 13:55:47: 5000000 INFO @ Sat, 03 Jun 2017 13:55:48: 5000000 INFO @ Sat, 03 Jun 2017 13:55:51: 6000000 INFO @ Sat, 03 Jun 2017 13:55:54: 6000000 INFO @ Sat, 03 Jun 2017 13:55:55: 6000000 INFO @ Sat, 03 Jun 2017 13:55:57: 7000000 INFO @ Sat, 03 Jun 2017 13:56:00: 7000000 INFO @ Sat, 03 Jun 2017 13:56:01: 7000000 INFO @ Sat, 03 Jun 2017 13:56:03: 8000000 INFO @ Sat, 03 Jun 2017 13:56:04: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:04: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:04: #1 total tags in treatment: 8142842 INFO @ Sat, 03 Jun 2017 13:56:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:04: #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 13:56:05: #1 tags after filtering in treatment: 8142196 INFO @ Sat, 03 Jun 2017 13:56:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:05: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:05: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:07: #2 number of paired peaks: 266 WARNING @ Sat, 03 Jun 2017 13:56:07: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sat, 03 Jun 2017 13:56:07: start model_add_line... INFO @ Sat, 03 Jun 2017 13:56:07: 8000000 INFO @ Sat, 03 Jun 2017 13:56:08: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:08: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:08: #1 total tags in treatment: 8142842 INFO @ Sat, 03 Jun 2017 13:56:08: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:08: #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 13:56:08: 8000000 INFO @ Sat, 03 Jun 2017 13:56:09: start X-correlation... INFO @ Sat, 03 Jun 2017 13:56:09: end of X-cor INFO @ Sat, 03 Jun 2017 13:56:09: #2 finished! INFO @ Sat, 03 Jun 2017 13:56:09: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:56:09: #2 alternative fragment length(s) may be 4,55,558,577 bps INFO @ Sat, 03 Jun 2017 13:56:09: #2.2 Generate R script for model : SRX1794217.20_model.r WARNING @ Sat, 03 Jun 2017 13:56:09: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:56:09: #2 You may need to consider one of the other alternative d(s): 4,55,558,577 WARNING @ Sat, 03 Jun 2017 13:56:09: #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 13:56:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:56:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:09: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:09: #1 total tags in treatment: 8142842 INFO @ Sat, 03 Jun 2017 13:56:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:09: #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 13:56:10: #1 tags after filtering in treatment: 8142196 INFO @ Sat, 03 Jun 2017 13:56:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:10: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:10: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:11: #1 tags after filtering in treatment: 8142196 INFO @ Sat, 03 Jun 2017 13:56:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:11: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:12: #2 number of paired peaks: 266 WARNING @ Sat, 03 Jun 2017 13:56:12: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sat, 03 Jun 2017 13:56:12: start model_add_line... INFO @ Sat, 03 Jun 2017 13:56:12: #2 number of paired peaks: 266 WARNING @ Sat, 03 Jun 2017 13:56:12: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sat, 03 Jun 2017 13:56:12: start model_add_line... INFO @ Sat, 03 Jun 2017 13:56:14: start X-correlation... INFO @ Sat, 03 Jun 2017 13:56:14: end of X-cor INFO @ Sat, 03 Jun 2017 13:56:14: #2 finished! INFO @ Sat, 03 Jun 2017 13:56:14: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:56:14: #2 alternative fragment length(s) may be 4,55,558,577 bps INFO @ Sat, 03 Jun 2017 13:56:14: #2.2 Generate R script for model : SRX1794217.10_model.r WARNING @ Sat, 03 Jun 2017 13:56:14: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:56:14: #2 You may need to consider one of the other alternative d(s): 4,55,558,577 WARNING @ Sat, 03 Jun 2017 13:56:14: #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 13:56:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:56:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:56:14: start X-correlation... INFO @ Sat, 03 Jun 2017 13:56:14: end of X-cor INFO @ Sat, 03 Jun 2017 13:56:14: #2 finished! INFO @ Sat, 03 Jun 2017 13:56:14: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:56:14: #2 alternative fragment length(s) may be 4,55,558,577 bps INFO @ Sat, 03 Jun 2017 13:56:14: #2.2 Generate R script for model : SRX1794217.05_model.r WARNING @ Sat, 03 Jun 2017 13:56:14: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:56:14: #2 You may need to consider one of the other alternative d(s): 4,55,558,577 WARNING @ Sat, 03 Jun 2017 13:56:14: #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 13:56:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:56:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:56:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:56:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:57:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:57:30: #4 Write output xls file... SRX1794217.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:57:30: #4 Write peak in narrowPeak format file... SRX1794217.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:57:30: #4 Write summits bed file... SRX1794217.20_summits.bed INFO @ Sat, 03 Jun 2017 13:57:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:57:32: #4 Write output xls file... SRX1794217.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:57:32: #4 Write peak in narrowPeak format file... SRX1794217.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:57:32: #4 Write summits bed file... SRX1794217.05_summits.bed INFO @ Sat, 03 Jun 2017 13:57:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (956 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:57:38: #4 Write output xls file... SRX1794217.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:57:38: #4 Write peak in narrowPeak format file... SRX1794217.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:57:38: #4 Write summits bed file... SRX1794217.10_summits.bed INFO @ Sat, 03 Jun 2017 13:57:38: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (458 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。