Job ID = 9025451 sra ファイルのダウンロード中... Completed: 1080871K bytes transferred in 12 seconds (711601K 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 --:--:-- 0:00:07 --:--:-- 0 100 14324 0 14324 0 0 1674 0 --:--:-- 0:00:08 --:--:-- 6659 100 40382 0 40382 0 0 4228 0 --:--:-- 0:00:09 --:--:-- 12835 100 64797 0 64797 0 0 6556 0 --:--:-- 0:00:09 --:--:-- 18630 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 34711485 spots for /home/okishinya/chipatlas/results/ce10/SRX1007136/SRR1993096.sra Written 34711485 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: 00:07:15 34711485 reads; of these: 34711485 (100.00%) were unpaired; of these: 7208373 (20.77%) aligned 0 times 23777589 (68.50%) aligned exactly 1 time 3725523 (10.73%) aligned >1 times 79.23% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6834698 / 27503112 = 0.2485 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 04:04:59: # Command line: callpeak -t SRX1007136.bam -f BAM -g ce -n SRX1007136.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1007136.20 # format = BAM # ChIP-seq file = ['SRX1007136.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:04:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:04:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:04:59: # Command line: callpeak -t SRX1007136.bam -f BAM -g ce -n SRX1007136.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1007136.10 # format = BAM # ChIP-seq file = ['SRX1007136.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:04:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:04:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:04:59: # Command line: callpeak -t SRX1007136.bam -f BAM -g ce -n SRX1007136.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1007136.05 # format = BAM # ChIP-seq file = ['SRX1007136.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:04:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:04:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:05:05: 1000000 INFO @ Sat, 03 Jun 2017 04:05:06: 1000000 INFO @ Sat, 03 Jun 2017 04:05:06: 1000000 INFO @ Sat, 03 Jun 2017 04:05:11: 2000000 INFO @ Sat, 03 Jun 2017 04:05:13: 2000000 INFO @ Sat, 03 Jun 2017 04:05:14: 2000000 INFO @ Sat, 03 Jun 2017 04:05:17: 3000000 INFO @ Sat, 03 Jun 2017 04:05:21: 3000000 INFO @ Sat, 03 Jun 2017 04:05:21: 3000000 INFO @ Sat, 03 Jun 2017 04:05:23: 4000000 INFO @ Sat, 03 Jun 2017 04:05:28: 4000000 INFO @ Sat, 03 Jun 2017 04:05:29: 4000000 INFO @ Sat, 03 Jun 2017 04:05:29: 5000000 INFO @ Sat, 03 Jun 2017 04:05:34: 6000000 INFO @ Sat, 03 Jun 2017 04:05:35: 5000000 INFO @ Sat, 03 Jun 2017 04:05:36: 5000000 INFO @ Sat, 03 Jun 2017 04:05:40: 7000000 INFO @ Sat, 03 Jun 2017 04:05:42: 6000000 INFO @ Sat, 03 Jun 2017 04:05:43: 6000000 INFO @ Sat, 03 Jun 2017 04:05:46: 8000000 INFO @ Sat, 03 Jun 2017 04:05:50: 7000000 INFO @ Sat, 03 Jun 2017 04:05:50: 7000000 INFO @ Sat, 03 Jun 2017 04:05:52: 9000000 INFO @ Sat, 03 Jun 2017 04:05:57: 8000000 INFO @ Sat, 03 Jun 2017 04:05:57: 10000000 INFO @ Sat, 03 Jun 2017 04:05:57: 8000000 INFO @ Sat, 03 Jun 2017 04:06:04: 9000000 INFO @ Sat, 03 Jun 2017 04:06:05: 9000000 INFO @ Sat, 03 Jun 2017 04:06:05: 11000000 INFO @ Sat, 03 Jun 2017 04:06:12: 10000000 INFO @ Sat, 03 Jun 2017 04:06:12: 10000000 INFO @ Sat, 03 Jun 2017 04:06:13: 12000000 INFO @ Sat, 03 Jun 2017 04:06:19: 11000000 INFO @ Sat, 03 Jun 2017 04:06:20: 11000000 INFO @ Sat, 03 Jun 2017 04:06:21: 13000000 INFO @ Sat, 03 Jun 2017 04:06:27: 12000000 INFO @ Sat, 03 Jun 2017 04:06:27: 12000000 INFO @ Sat, 03 Jun 2017 04:06:29: 14000000 INFO @ Sat, 03 Jun 2017 04:06:34: 13000000 INFO @ Sat, 03 Jun 2017 04:06:35: 13000000 INFO @ Sat, 03 Jun 2017 04:06:35: 15000000 INFO @ Sat, 03 Jun 2017 04:06:41: 16000000 INFO @ Sat, 03 Jun 2017 04:06:41: 14000000 INFO @ Sat, 03 Jun 2017 04:06:42: 14000000 INFO @ Sat, 03 Jun 2017 04:06:46: 17000000 INFO @ Sat, 03 Jun 2017 04:06:49: 15000000 INFO @ Sat, 03 Jun 2017 04:06:49: 15000000 INFO @ Sat, 03 Jun 2017 04:06:52: 18000000 INFO @ Sat, 03 Jun 2017 04:06:56: 16000000 INFO @ Sat, 03 Jun 2017 04:06:57: 16000000 INFO @ Sat, 03 Jun 2017 04:06:57: 19000000 INFO @ Sat, 03 Jun 2017 04:07:03: 20000000 INFO @ Sat, 03 Jun 2017 04:07:03: 17000000 INFO @ Sat, 03 Jun 2017 04:07:04: 17000000 INFO @ Sat, 03 Jun 2017 04:07:07: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:07:07: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:07:07: #1 total tags in treatment: 20668414 INFO @ Sat, 03 Jun 2017 04:07:07: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:07:07: #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 04:07:10: 18000000 INFO @ Sat, 03 Jun 2017 04:07:11: #1 tags after filtering in treatment: 20660777 INFO @ Sat, 03 Jun 2017 04:07:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:07:11: #1 finished! INFO @ Sat, 03 Jun 2017 04:07:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:07:11: 18000000 INFO @ Sat, 03 Jun 2017 04:07:15: #2 number of paired peaks: 896 WARNING @ Sat, 03 Jun 2017 04:07:15: Fewer paired peaks (896) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 896 pairs to build model! INFO @ Sat, 03 Jun 2017 04:07:15: start model_add_line... INFO @ Sat, 03 Jun 2017 04:07:18: 19000000 INFO @ Sat, 03 Jun 2017 04:07:18: 19000000 INFO @ Sat, 03 Jun 2017 04:07:25: 20000000 INFO @ Sat, 03 Jun 2017 04:07:26: 20000000 INFO @ Sat, 03 Jun 2017 04:07:30: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:07:30: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:07:30: #1 total tags in treatment: 20668414 INFO @ Sat, 03 Jun 2017 04:07:30: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:07:30: #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 04:07:31: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:07:31: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:07:31: #1 total tags in treatment: 20668414 INFO @ Sat, 03 Jun 2017 04:07:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:07:31: #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 04:07:31: start X-correlation... INFO @ Sat, 03 Jun 2017 04:07:31: end of X-cor INFO @ Sat, 03 Jun 2017 04:07:31: #2 finished! INFO @ Sat, 03 Jun 2017 04:07:31: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 04:07:31: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sat, 03 Jun 2017 04:07:31: #2.2 Generate R script for model : SRX1007136.10_model.r WARNING @ Sat, 03 Jun 2017 04:07:31: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:07:31: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sat, 03 Jun 2017 04:07:31: #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 04:07:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:07:34: #1 tags after filtering in treatment: 20660777 INFO @ Sat, 03 Jun 2017 04:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:07:34: #1 finished! INFO @ Sat, 03 Jun 2017 04:07:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:07:34: #1 tags after filtering in treatment: 20660777 INFO @ Sat, 03 Jun 2017 04:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:07:34: #1 finished! INFO @ Sat, 03 Jun 2017 04:07:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:07:37: #2 number of paired peaks: 896 WARNING @ Sat, 03 Jun 2017 04:07:37: Fewer paired peaks (896) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 896 pairs to build model! INFO @ Sat, 03 Jun 2017 04:07:37: start model_add_line... INFO @ Sat, 03 Jun 2017 04:07:38: #2 number of paired peaks: 896 WARNING @ Sat, 03 Jun 2017 04:07:38: Fewer paired peaks (896) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 896 pairs to build model! INFO @ Sat, 03 Jun 2017 04:07:38: start model_add_line... INFO @ Sat, 03 Jun 2017 04:07:53: start X-correlation... INFO @ Sat, 03 Jun 2017 04:07:53: end of X-cor INFO @ Sat, 03 Jun 2017 04:07:53: #2 finished! INFO @ Sat, 03 Jun 2017 04:07:53: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 04:07:53: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sat, 03 Jun 2017 04:07:53: #2.2 Generate R script for model : SRX1007136.20_model.r WARNING @ Sat, 03 Jun 2017 04:07:53: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:07:53: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sat, 03 Jun 2017 04:07:53: #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 04:07:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:07:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:07:54: start X-correlation... INFO @ Sat, 03 Jun 2017 04:07:54: end of X-cor INFO @ Sat, 03 Jun 2017 04:07:54: #2 finished! INFO @ Sat, 03 Jun 2017 04:07:54: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 04:07:54: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sat, 03 Jun 2017 04:07:54: #2.2 Generate R script for model : SRX1007136.05_model.r WARNING @ Sat, 03 Jun 2017 04:07:54: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:07:54: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sat, 03 Jun 2017 04:07:54: #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 04:07:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:07:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:09:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:09:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:09:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:10:18: #4 Write output xls file... SRX1007136.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:10:18: #4 Write peak in narrowPeak format file... SRX1007136.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:10:18: #4 Write summits bed file... SRX1007136.10_summits.bed INFO @ Sat, 03 Jun 2017 04:10:18: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8517 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:10:41: #4 Write output xls file... SRX1007136.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:10:41: #4 Write peak in narrowPeak format file... SRX1007136.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:10:41: #4 Write summits bed file... SRX1007136.20_summits.bed INFO @ Sat, 03 Jun 2017 04:10:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3910 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:10:57: #4 Write output xls file... SRX1007136.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:10:57: #4 Write peak in narrowPeak format file... SRX1007136.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:10:57: #4 Write summits bed file... SRX1007136.05_summits.bed INFO @ Sat, 03 Jun 2017 04:10:57: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (15687 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。