Job ID = 9030318 sra ファイルのダウンロード中... Completed: 528926K bytes transferred in 7 seconds (583169K 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 1014 0 --:--:-- 0:00:07 --:--:-- 7763 100 30317 0 30317 0 0 3617 0 --:--:-- 0:00:08 --:--:-- 16694 100 58406 0 58406 0 0 6577 0 --:--:-- 0:00:08 --:--:-- 25251 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 17133552 spots for /home/okishinya/chipatlas/results/dm3/SRX287976/SRR870165.sra Written 17133552 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: 00:08:09 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 669317 (3.91%) aligned 0 times 11145605 (65.05%) aligned exactly 1 time 5318630 (31.04%) aligned >1 times 96.09% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 2377771 / 16464235 = 0.1444 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 17:48:45: # Command line: callpeak -t SRX287976.bam -f BAM -g dm -n SRX287976.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX287976.05 # format = BAM # ChIP-seq file = ['SRX287976.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 17:48:45: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:48:45: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:48:45: # Command line: callpeak -t SRX287976.bam -f BAM -g dm -n SRX287976.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX287976.10 # format = BAM # ChIP-seq file = ['SRX287976.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 17:48:45: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:48:45: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:48:45: # Command line: callpeak -t SRX287976.bam -f BAM -g dm -n SRX287976.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX287976.20 # format = BAM # ChIP-seq file = ['SRX287976.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 17:48:45: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:48:45: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:48:53: 1000000 INFO @ Sat, 03 Jun 2017 17:48:53: 1000000 INFO @ Sat, 03 Jun 2017 17:48:53: 1000000 INFO @ Sat, 03 Jun 2017 17:49:00: 2000000 INFO @ Sat, 03 Jun 2017 17:49:00: 2000000 INFO @ Sat, 03 Jun 2017 17:49:00: 2000000 INFO @ Sat, 03 Jun 2017 17:49:08: 3000000 INFO @ Sat, 03 Jun 2017 17:49:08: 3000000 INFO @ Sat, 03 Jun 2017 17:49:08: 3000000 INFO @ Sat, 03 Jun 2017 17:49:16: 4000000 INFO @ Sat, 03 Jun 2017 17:49:16: 4000000 INFO @ Sat, 03 Jun 2017 17:49:17: 4000000 INFO @ Sat, 03 Jun 2017 17:49:23: 5000000 INFO @ Sat, 03 Jun 2017 17:49:23: 5000000 INFO @ Sat, 03 Jun 2017 17:49:26: 5000000 INFO @ Sat, 03 Jun 2017 17:49:30: 6000000 INFO @ Sat, 03 Jun 2017 17:49:30: 6000000 INFO @ Sat, 03 Jun 2017 17:49:33: 6000000 INFO @ Sat, 03 Jun 2017 17:49:36: 7000000 INFO @ Sat, 03 Jun 2017 17:49:36: 7000000 INFO @ Sat, 03 Jun 2017 17:49:39: 7000000 INFO @ Sat, 03 Jun 2017 17:49:42: 8000000 INFO @ Sat, 03 Jun 2017 17:49:42: 8000000 INFO @ Sat, 03 Jun 2017 17:49:46: 8000000 INFO @ Sat, 03 Jun 2017 17:49:48: 9000000 INFO @ Sat, 03 Jun 2017 17:49:49: 9000000 INFO @ Sat, 03 Jun 2017 17:49:53: 9000000 INFO @ Sat, 03 Jun 2017 17:49:55: 10000000 INFO @ Sat, 03 Jun 2017 17:49:55: 10000000 INFO @ Sat, 03 Jun 2017 17:50:00: 10000000 INFO @ Sat, 03 Jun 2017 17:50:01: 11000000 INFO @ Sat, 03 Jun 2017 17:50:01: 11000000 INFO @ Sat, 03 Jun 2017 17:50:07: 12000000 INFO @ Sat, 03 Jun 2017 17:50:07: 11000000 INFO @ Sat, 03 Jun 2017 17:50:07: 12000000 INFO @ Sat, 03 Jun 2017 17:50:13: 13000000 INFO @ Sat, 03 Jun 2017 17:50:14: 13000000 INFO @ Sat, 03 Jun 2017 17:50:14: 12000000 INFO @ Sat, 03 Jun 2017 17:50:20: 14000000 INFO @ Sat, 03 Jun 2017 17:50:20: 14000000 INFO @ Sat, 03 Jun 2017 17:50:21: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:50:21: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:50:21: #1 total tags in treatment: 14086464 INFO @ Sat, 03 Jun 2017 17:50:21: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:50:21: #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 17:50:21: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:50:21: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:50:21: #1 total tags in treatment: 14086464 INFO @ Sat, 03 Jun 2017 17:50:21: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:50:21: #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 17:50:21: 13000000 INFO @ Sat, 03 Jun 2017 17:50:23: #1 tags after filtering in treatment: 14083587 INFO @ Sat, 03 Jun 2017 17:50:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:50:23: #1 finished! INFO @ Sat, 03 Jun 2017 17:50:23: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:50:24: #1 tags after filtering in treatment: 14083587 INFO @ Sat, 03 Jun 2017 17:50:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:50:24: #1 finished! INFO @ Sat, 03 Jun 2017 17:50:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:50:26: #2 number of paired peaks: 345 WARNING @ Sat, 03 Jun 2017 17:50:26: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sat, 03 Jun 2017 17:50:26: start model_add_line... INFO @ Sat, 03 Jun 2017 17:50:26: #2 number of paired peaks: 345 WARNING @ Sat, 03 Jun 2017 17:50:26: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sat, 03 Jun 2017 17:50:26: start model_add_line... INFO @ Sat, 03 Jun 2017 17:50:28: 14000000 INFO @ Sat, 03 Jun 2017 17:50:28: start X-correlation... INFO @ Sat, 03 Jun 2017 17:50:28: end of X-cor INFO @ Sat, 03 Jun 2017 17:50:28: #2 finished! INFO @ Sat, 03 Jun 2017 17:50:28: #2 predicted fragment length is 42 bps INFO @ Sat, 03 Jun 2017 17:50:28: #2 alternative fragment length(s) may be 42 bps INFO @ Sat, 03 Jun 2017 17:50:28: #2.2 Generate R script for model : SRX287976.05_model.r WARNING @ Sat, 03 Jun 2017 17:50:28: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 17:50:28: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sat, 03 Jun 2017 17:50:28: #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 17:50:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:50:29: start X-correlation... INFO @ Sat, 03 Jun 2017 17:50:29: end of X-cor INFO @ Sat, 03 Jun 2017 17:50:29: #2 finished! INFO @ Sat, 03 Jun 2017 17:50:29: #2 predicted fragment length is 42 bps INFO @ Sat, 03 Jun 2017 17:50:29: #2 alternative fragment length(s) may be 42 bps INFO @ Sat, 03 Jun 2017 17:50:29: #2.2 Generate R script for model : SRX287976.20_model.r WARNING @ Sat, 03 Jun 2017 17:50:29: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 17:50:29: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sat, 03 Jun 2017 17:50:29: #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 17:50:29: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:50:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:50:29: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:50:29: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:50:29: #1 total tags in treatment: 14086464 INFO @ Sat, 03 Jun 2017 17:50:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:50:29: #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 17:50:31: #1 tags after filtering in treatment: 14083587 INFO @ Sat, 03 Jun 2017 17:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:50:31: #1 finished! INFO @ Sat, 03 Jun 2017 17:50:31: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:50:34: #2 number of paired peaks: 345 WARNING @ Sat, 03 Jun 2017 17:50:34: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sat, 03 Jun 2017 17:50:34: start model_add_line... INFO @ Sat, 03 Jun 2017 17:50:37: start X-correlation... INFO @ Sat, 03 Jun 2017 17:50:37: end of X-cor INFO @ Sat, 03 Jun 2017 17:50:37: #2 finished! INFO @ Sat, 03 Jun 2017 17:50:37: #2 predicted fragment length is 42 bps INFO @ Sat, 03 Jun 2017 17:50:37: #2 alternative fragment length(s) may be 42 bps INFO @ Sat, 03 Jun 2017 17:50:37: #2.2 Generate R script for model : SRX287976.10_model.r WARNING @ Sat, 03 Jun 2017 17:50:37: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 17:50:37: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sat, 03 Jun 2017 17:50:37: #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 17:50:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:51:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:51:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:51:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:52:33: #4 Write output xls file... SRX287976.20_peaks.xls INFO @ Sat, 03 Jun 2017 17:52:33: #4 Write peak in narrowPeak format file... SRX287976.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:52:33: #4 Write summits bed file... SRX287976.20_summits.bed INFO @ Sat, 03 Jun 2017 17:52:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1490 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 17:52:45: #4 Write output xls file... SRX287976.05_peaks.xls INFO @ Sat, 03 Jun 2017 17:52:45: #4 Write peak in narrowPeak format file... SRX287976.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:52:45: #4 Write summits bed file... SRX287976.05_summits.bed INFO @ Sat, 03 Jun 2017 17:52:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2193 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 17:52:59: #4 Write output xls file... SRX287976.10_peaks.xls INFO @ Sat, 03 Jun 2017 17:52:59: #4 Write peak in narrowPeak format file... SRX287976.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:52:59: #4 Write summits bed file... SRX287976.10_summits.bed INFO @ Sat, 03 Jun 2017 17:52:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1925 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。