Job ID = 9029296 sra ファイルのダウンロード中... Completed: 381098K bytes transferred in 6 seconds (478936K 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 1055 0 --:--:-- 0:00:07 --:--:-- 9111 100 28797 0 28797 0 0 3486 0 --:--:-- 0:00:08 --:--:-- 15667 100 54861 0 54861 0 0 6036 0 --:--:-- 0:00:09 --:--:-- 20562 100 98k 0 98k 0 0 10330 0 --:--:-- 0:00:09 --:--:-- 30239 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 11450650 spots for /home/okishinya/chipatlas/results/dm3/SRX1537617/SRR3109312.sra Written 11450650 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: 00:05:20 11450650 reads; of these: 11450650 (100.00%) were unpaired; of these: 1418200 (12.39%) aligned 0 times 6699289 (58.51%) aligned exactly 1 time 3333161 (29.11%) aligned >1 times 87.61% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 2294428 / 10032450 = 0.2287 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 13:12:50: # Command line: callpeak -t SRX1537617.bam -f BAM -g dm -n SRX1537617.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1537617.05 # format = BAM # ChIP-seq file = ['SRX1537617.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 13:12:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:50: # Command line: callpeak -t SRX1537617.bam -f BAM -g dm -n SRX1537617.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1537617.20 # format = BAM # ChIP-seq file = ['SRX1537617.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 13:12:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:50: # Command line: callpeak -t SRX1537617.bam -f BAM -g dm -n SRX1537617.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1537617.10 # format = BAM # ChIP-seq file = ['SRX1537617.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 13:12:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:57: 1000000 INFO @ Sat, 03 Jun 2017 13:12:57: 1000000 INFO @ Sat, 03 Jun 2017 13:12:57: 1000000 INFO @ Sat, 03 Jun 2017 13:13:04: 2000000 INFO @ Sat, 03 Jun 2017 13:13:05: 2000000 INFO @ Sat, 03 Jun 2017 13:13:05: 2000000 INFO @ Sat, 03 Jun 2017 13:13:10: 3000000 INFO @ Sat, 03 Jun 2017 13:13:12: 3000000 INFO @ Sat, 03 Jun 2017 13:13:12: 3000000 INFO @ Sat, 03 Jun 2017 13:13:17: 4000000 INFO @ Sat, 03 Jun 2017 13:13:20: 4000000 INFO @ Sat, 03 Jun 2017 13:13:20: 4000000 INFO @ Sat, 03 Jun 2017 13:13:24: 5000000 INFO @ Sat, 03 Jun 2017 13:13:28: 5000000 INFO @ Sat, 03 Jun 2017 13:13:28: 5000000 INFO @ Sat, 03 Jun 2017 13:13:31: 6000000 INFO @ Sat, 03 Jun 2017 13:13:35: 6000000 INFO @ Sat, 03 Jun 2017 13:13:36: 6000000 INFO @ Sat, 03 Jun 2017 13:13:38: 7000000 INFO @ Sat, 03 Jun 2017 13:13:43: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:13:43: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:13:43: #1 total tags in treatment: 7738022 INFO @ Sat, 03 Jun 2017 13:13:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:43: #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 13:13:43: 7000000 INFO @ Sat, 03 Jun 2017 13:13:44: 7000000 INFO @ Sat, 03 Jun 2017 13:13:44: #1 tags after filtering in treatment: 7736201 INFO @ Sat, 03 Jun 2017 13:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:44: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:45: #2 number of paired peaks: 675 WARNING @ Sat, 03 Jun 2017 13:13:45: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Sat, 03 Jun 2017 13:13:45: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:49: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:13:49: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:13:49: #1 total tags in treatment: 7738022 INFO @ Sat, 03 Jun 2017 13:13:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:49: #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 13:13:49: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:13:49: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:13:49: #1 total tags in treatment: 7738022 INFO @ Sat, 03 Jun 2017 13:13:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:49: #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 13:13:49: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:49: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:49: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:49: #2 predicted fragment length is 137 bps INFO @ Sat, 03 Jun 2017 13:13:49: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 03 Jun 2017 13:13:49: #2.2 Generate R script for model : SRX1537617.05_model.r INFO @ Sat, 03 Jun 2017 13:13:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:50: #1 tags after filtering in treatment: 7736201 INFO @ Sat, 03 Jun 2017 13:13:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:50: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:51: #1 tags after filtering in treatment: 7736201 INFO @ Sat, 03 Jun 2017 13:13:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:51: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:52: #2 number of paired peaks: 675 WARNING @ Sat, 03 Jun 2017 13:13:52: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Sat, 03 Jun 2017 13:13:52: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:53: #2 number of paired peaks: 675 WARNING @ Sat, 03 Jun 2017 13:13:53: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Sat, 03 Jun 2017 13:13:53: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:56: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:56: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:56: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:56: #2 predicted fragment length is 137 bps INFO @ Sat, 03 Jun 2017 13:13:56: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 03 Jun 2017 13:13:56: #2.2 Generate R script for model : SRX1537617.20_model.r INFO @ Sat, 03 Jun 2017 13:13:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:57: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:57: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:57: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:57: #2 predicted fragment length is 137 bps INFO @ Sat, 03 Jun 2017 13:13:57: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 03 Jun 2017 13:13:57: #2.2 Generate R script for model : SRX1537617.10_model.r INFO @ Sat, 03 Jun 2017 13:13:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:14:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:15:07: #4 Write output xls file... SRX1537617.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:07: #4 Write peak in narrowPeak format file... SRX1537617.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:07: #4 Write summits bed file... SRX1537617.05_summits.bed INFO @ Sat, 03 Jun 2017 13:15:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1815 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:15:15: #4 Write output xls file... SRX1537617.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:15: #4 Write peak in narrowPeak format file... SRX1537617.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:15: #4 Write summits bed file... SRX1537617.20_summits.bed INFO @ Sat, 03 Jun 2017 13:15:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1056 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:15:18: #4 Write output xls file... SRX1537617.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:15:18: #4 Write peak in narrowPeak format file... SRX1537617.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:15:18: #4 Write summits bed file... SRX1537617.10_summits.bed INFO @ Sat, 03 Jun 2017 13:15:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1424 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。