Job ID = 9025599 sra ファイルのダウンロード中... Completed: 586856K bytes transferred in 156 seconds (30734K 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 1848 0 --:--:-- 0:00:07 --:--:-- 10571 100 38318 0 38318 0 0 4382 0 --:--:-- 0:00:08 --:--:-- 16305 100 60000 0 60000 0 0 6491 0 --:--:-- 0:00:09 --:--:-- 21060 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 21274743 spots for /home/okishinya/chipatlas/results/ce10/SRX1936244/SRR3879851.sra Written 21274743 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: 00:05:10 21274743 reads; of these: 21274743 (100.00%) were unpaired; of these: 3317001 (15.59%) aligned 0 times 14918877 (70.12%) aligned exactly 1 time 3038865 (14.28%) aligned >1 times 84.41% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 2354606 / 17957742 = 0.1311 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 04:40:20: # Command line: callpeak -t SRX1936244.bam -f BAM -g ce -n SRX1936244.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1936244.10 # format = BAM # ChIP-seq file = ['SRX1936244.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 04:40:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:20: # Command line: callpeak -t SRX1936244.bam -f BAM -g ce -n SRX1936244.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1936244.20 # format = BAM # ChIP-seq file = ['SRX1936244.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 04:40:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:20: # Command line: callpeak -t SRX1936244.bam -f BAM -g ce -n SRX1936244.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1936244.05 # format = BAM # ChIP-seq file = ['SRX1936244.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 04:40:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:40:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:40:27: 1000000 INFO @ Sat, 03 Jun 2017 04:40:27: 1000000 INFO @ Sat, 03 Jun 2017 04:40:27: 1000000 INFO @ Sat, 03 Jun 2017 04:40:34: 2000000 INFO @ Sat, 03 Jun 2017 04:40:34: 2000000 INFO @ Sat, 03 Jun 2017 04:40:34: 2000000 INFO @ Sat, 03 Jun 2017 04:40:40: 3000000 INFO @ Sat, 03 Jun 2017 04:40:41: 3000000 INFO @ Sat, 03 Jun 2017 04:40:41: 3000000 INFO @ Sat, 03 Jun 2017 04:40:47: 4000000 INFO @ Sat, 03 Jun 2017 04:40:48: 4000000 INFO @ Sat, 03 Jun 2017 04:40:48: 4000000 INFO @ Sat, 03 Jun 2017 04:40:54: 5000000 INFO @ Sat, 03 Jun 2017 04:40:55: 5000000 INFO @ Sat, 03 Jun 2017 04:40:55: 5000000 INFO @ Sat, 03 Jun 2017 04:41:00: 6000000 INFO @ Sat, 03 Jun 2017 04:41:01: 6000000 INFO @ Sat, 03 Jun 2017 04:41:01: 6000000 INFO @ Sat, 03 Jun 2017 04:41:07: 7000000 INFO @ Sat, 03 Jun 2017 04:41:08: 7000000 INFO @ Sat, 03 Jun 2017 04:41:08: 7000000 INFO @ Sat, 03 Jun 2017 04:41:14: 8000000 INFO @ Sat, 03 Jun 2017 04:41:17: 8000000 INFO @ Sat, 03 Jun 2017 04:41:17: 8000000 INFO @ Sat, 03 Jun 2017 04:41:22: 9000000 INFO @ Sat, 03 Jun 2017 04:41:26: 9000000 INFO @ Sat, 03 Jun 2017 04:41:26: 9000000 INFO @ Sat, 03 Jun 2017 04:41:31: 10000000 INFO @ Sat, 03 Jun 2017 04:41:35: 10000000 INFO @ Sat, 03 Jun 2017 04:41:35: 10000000 INFO @ Sat, 03 Jun 2017 04:41:39: 11000000 INFO @ Sat, 03 Jun 2017 04:41:44: 11000000 INFO @ Sat, 03 Jun 2017 04:41:44: 11000000 INFO @ Sat, 03 Jun 2017 04:41:47: 12000000 INFO @ Sat, 03 Jun 2017 04:41:53: 12000000 INFO @ Sat, 03 Jun 2017 04:41:53: 12000000 INFO @ Sat, 03 Jun 2017 04:41:55: 13000000 INFO @ Sat, 03 Jun 2017 04:42:01: 13000000 INFO @ Sat, 03 Jun 2017 04:42:01: 13000000 INFO @ Sat, 03 Jun 2017 04:42:03: 14000000 INFO @ Sat, 03 Jun 2017 04:42:10: 14000000 INFO @ Sat, 03 Jun 2017 04:42:10: 14000000 INFO @ Sat, 03 Jun 2017 04:42:11: 15000000 INFO @ Sat, 03 Jun 2017 04:42:16: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:42:16: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:42:16: #1 total tags in treatment: 15603136 INFO @ Sat, 03 Jun 2017 04:42:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:16: #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 04:42:18: 15000000 INFO @ Sat, 03 Jun 2017 04:42:19: #1 tags after filtering in treatment: 15599972 INFO @ Sat, 03 Jun 2017 04:42:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:19: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:42:19: 15000000 INFO @ Sat, 03 Jun 2017 04:42:22: #2 number of paired peaks: 252 WARNING @ Sat, 03 Jun 2017 04:42:22: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 03 Jun 2017 04:42:22: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:23: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:42:23: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:42:23: #1 total tags in treatment: 15603136 INFO @ Sat, 03 Jun 2017 04:42:23: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:23: #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 04:42:24: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:42:24: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:42:24: #1 total tags in treatment: 15603136 INFO @ Sat, 03 Jun 2017 04:42:24: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:42:24: #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 04:42:26: #1 tags after filtering in treatment: 15599972 INFO @ Sat, 03 Jun 2017 04:42:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:26: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:42:27: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:27: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:27: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:27: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 04:42:27: #2 alternative fragment length(s) may be 1,46,505,530 bps INFO @ Sat, 03 Jun 2017 04:42:27: #2.2 Generate R script for model : SRX1936244.10_model.r WARNING @ Sat, 03 Jun 2017 04:42:27: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:42:27: #2 You may need to consider one of the other alternative d(s): 1,46,505,530 WARNING @ Sat, 03 Jun 2017 04:42:27: #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 04:42:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:42:27: #1 tags after filtering in treatment: 15599972 INFO @ Sat, 03 Jun 2017 04:42:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:42:27: #1 finished! INFO @ Sat, 03 Jun 2017 04:42:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:42:29: #2 number of paired peaks: 252 WARNING @ Sat, 03 Jun 2017 04:42:29: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 03 Jun 2017 04:42:29: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:29: #2 number of paired peaks: 252 WARNING @ Sat, 03 Jun 2017 04:42:29: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 03 Jun 2017 04:42:29: start model_add_line... INFO @ Sat, 03 Jun 2017 04:42:34: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:34: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:34: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:34: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 04:42:34: #2 alternative fragment length(s) may be 1,46,505,530 bps INFO @ Sat, 03 Jun 2017 04:42:34: #2.2 Generate R script for model : SRX1936244.05_model.r WARNING @ Sat, 03 Jun 2017 04:42:34: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:42:34: #2 You may need to consider one of the other alternative d(s): 1,46,505,530 WARNING @ Sat, 03 Jun 2017 04:42:34: #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 04:42:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:42:34: start X-correlation... INFO @ Sat, 03 Jun 2017 04:42:34: end of X-cor INFO @ Sat, 03 Jun 2017 04:42:34: #2 finished! INFO @ Sat, 03 Jun 2017 04:42:34: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 04:42:34: #2 alternative fragment length(s) may be 1,46,505,530 bps INFO @ Sat, 03 Jun 2017 04:42:34: #2.2 Generate R script for model : SRX1936244.20_model.r WARNING @ Sat, 03 Jun 2017 04:42:34: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:42:34: #2 You may need to consider one of the other alternative d(s): 1,46,505,530 WARNING @ Sat, 03 Jun 2017 04:42:34: #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 04:42:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:42:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:43:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:44:34: #4 Write output xls file... SRX1936244.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:34: #4 Write peak in narrowPeak format file... SRX1936244.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:34: #4 Write summits bed file... SRX1936244.10_summits.bed INFO @ Sat, 03 Jun 2017 04:44:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (428 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:44:50: #4 Write output xls file... SRX1936244.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:50: #4 Write peak in narrowPeak format file... SRX1936244.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:50: #4 Write summits bed file... SRX1936244.20_summits.bed INFO @ Sat, 03 Jun 2017 04:44:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:44:57: #4 Write output xls file... SRX1936244.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:57: #4 Write peak in narrowPeak format file... SRX1936244.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:57: #4 Write summits bed file... SRX1936244.05_summits.bed INFO @ Sat, 03 Jun 2017 04:44:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (674 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。