Job ID = 9030084 sra ファイルのダウンロード中... Completed: 280354K bytes transferred in 5 seconds (410377K 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 14323 0 14323 0 0 1912 0 --:--:-- 0:00:07 --:--:-- 13987 100 38317 0 38317 0 0 4515 0 --:--:-- 0:00:08 --:--:-- 18978 100 51356 0 51356 0 0 5823 0 --:--:-- 0:00:08 --:--:-- 21835 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 8645377 spots for /home/okishinya/chipatlas/results/dm3/SRX287760/SRR869949.sra Written 8645377 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: 00:02:51 8645377 reads; of these: 8645377 (100.00%) were unpaired; of these: 520973 (6.03%) aligned 0 times 6385802 (73.86%) aligned exactly 1 time 1738602 (20.11%) aligned >1 times 93.97% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 718853 / 8124404 = 0.0885 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 16:39:49: # Command line: callpeak -t SRX287760.bam -f BAM -g dm -n SRX287760.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX287760.20 # format = BAM # ChIP-seq file = ['SRX287760.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 16:39:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 16:39:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 16:39:49: # Command line: callpeak -t SRX287760.bam -f BAM -g dm -n SRX287760.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX287760.05 # format = BAM # ChIP-seq file = ['SRX287760.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 16:39:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 16:39:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 16:39:49: # Command line: callpeak -t SRX287760.bam -f BAM -g dm -n SRX287760.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX287760.10 # format = BAM # ChIP-seq file = ['SRX287760.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 16:39:49: #1 read tag files... INFO @ Sat, 03 Jun 2017 16:39:49: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 16:39:55: 1000000 INFO @ Sat, 03 Jun 2017 16:39:55: 1000000 INFO @ Sat, 03 Jun 2017 16:39:56: 1000000 INFO @ Sat, 03 Jun 2017 16:40:02: 2000000 INFO @ Sat, 03 Jun 2017 16:40:02: 2000000 INFO @ Sat, 03 Jun 2017 16:40:04: 2000000 INFO @ Sat, 03 Jun 2017 16:40:09: 3000000 INFO @ Sat, 03 Jun 2017 16:40:11: 3000000 INFO @ Sat, 03 Jun 2017 16:40:12: 3000000 INFO @ Sat, 03 Jun 2017 16:40:15: 4000000 INFO @ Sat, 03 Jun 2017 16:40:18: 4000000 INFO @ Sat, 03 Jun 2017 16:40:19: 4000000 INFO @ Sat, 03 Jun 2017 16:40:21: 5000000 INFO @ Sat, 03 Jun 2017 16:40:26: 5000000 INFO @ Sat, 03 Jun 2017 16:40:28: 5000000 INFO @ Sat, 03 Jun 2017 16:40:28: 6000000 INFO @ Sat, 03 Jun 2017 16:40:34: 6000000 INFO @ Sat, 03 Jun 2017 16:40:35: 7000000 INFO @ Sat, 03 Jun 2017 16:40:35: 6000000 INFO @ Sat, 03 Jun 2017 16:40:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 16:40:37: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 16:40:37: #1 total tags in treatment: 7405551 INFO @ Sat, 03 Jun 2017 16:40:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 16:40:37: #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 16:40:39: #1 tags after filtering in treatment: 7404745 INFO @ Sat, 03 Jun 2017 16:40:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 16:40:39: #1 finished! INFO @ Sat, 03 Jun 2017 16:40:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 16:40:40: #2 number of paired peaks: 589 WARNING @ Sat, 03 Jun 2017 16:40:40: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Sat, 03 Jun 2017 16:40:40: start model_add_line... INFO @ Sat, 03 Jun 2017 16:40:42: 7000000 INFO @ Sat, 03 Jun 2017 16:40:43: start X-correlation... INFO @ Sat, 03 Jun 2017 16:40:43: end of X-cor INFO @ Sat, 03 Jun 2017 16:40:43: #2 finished! INFO @ Sat, 03 Jun 2017 16:40:43: #2 predicted fragment length is 180 bps INFO @ Sat, 03 Jun 2017 16:40:43: #2 alternative fragment length(s) may be 180,195 bps INFO @ Sat, 03 Jun 2017 16:40:43: #2.2 Generate R script for model : SRX287760.20_model.r INFO @ Sat, 03 Jun 2017 16:40:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 16:40:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 16:40:43: 7000000 INFO @ Sat, 03 Jun 2017 16:40:45: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 16:40:45: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 16:40:45: #1 total tags in treatment: 7405551 INFO @ Sat, 03 Jun 2017 16:40:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 16:40:45: #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 16:40:46: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 16:40:46: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 16:40:46: #1 total tags in treatment: 7405551 INFO @ Sat, 03 Jun 2017 16:40:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 16:40:46: #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 16:40:47: #1 tags after filtering in treatment: 7404745 INFO @ Sat, 03 Jun 2017 16:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 16:40:47: #1 finished! INFO @ Sat, 03 Jun 2017 16:40:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 16:40:47: #1 tags after filtering in treatment: 7404745 INFO @ Sat, 03 Jun 2017 16:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 16:40:47: #1 finished! INFO @ Sat, 03 Jun 2017 16:40:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 16:40:48: #2 number of paired peaks: 589 WARNING @ Sat, 03 Jun 2017 16:40:48: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Sat, 03 Jun 2017 16:40:48: start model_add_line... INFO @ Sat, 03 Jun 2017 16:40:49: #2 number of paired peaks: 589 WARNING @ Sat, 03 Jun 2017 16:40:49: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Sat, 03 Jun 2017 16:40:49: start model_add_line... INFO @ Sat, 03 Jun 2017 16:40:51: start X-correlation... INFO @ Sat, 03 Jun 2017 16:40:51: end of X-cor INFO @ Sat, 03 Jun 2017 16:40:51: #2 finished! INFO @ Sat, 03 Jun 2017 16:40:51: #2 predicted fragment length is 180 bps INFO @ Sat, 03 Jun 2017 16:40:51: #2 alternative fragment length(s) may be 180,195 bps INFO @ Sat, 03 Jun 2017 16:40:51: #2.2 Generate R script for model : SRX287760.05_model.r INFO @ Sat, 03 Jun 2017 16:40:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 16:40:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 16:40:52: start X-correlation... INFO @ Sat, 03 Jun 2017 16:40:52: end of X-cor INFO @ Sat, 03 Jun 2017 16:40:52: #2 finished! INFO @ Sat, 03 Jun 2017 16:40:52: #2 predicted fragment length is 180 bps INFO @ Sat, 03 Jun 2017 16:40:52: #2 alternative fragment length(s) may be 180,195 bps INFO @ Sat, 03 Jun 2017 16:40:52: #2.2 Generate R script for model : SRX287760.10_model.r INFO @ Sat, 03 Jun 2017 16:40:52: #3 Call peaks... INFO @ Sat, 03 Jun 2017 16:40:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 16:41:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 16:41:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 16:41:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 16:41:56: #4 Write output xls file... SRX287760.20_peaks.xls INFO @ Sat, 03 Jun 2017 16:41:56: #4 Write peak in narrowPeak format file... SRX287760.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 16:41:56: #4 Write summits bed file... SRX287760.20_summits.bed INFO @ Sat, 03 Jun 2017 16:41:56: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (396 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 16:42:06: #4 Write output xls file... SRX287760.05_peaks.xls INFO @ Sat, 03 Jun 2017 16:42:07: #4 Write peak in narrowPeak format file... SRX287760.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 16:42:07: #4 Write summits bed file... SRX287760.05_summits.bed INFO @ Sat, 03 Jun 2017 16:42:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4264 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 16:42:10: #4 Write output xls file... SRX287760.10_peaks.xls INFO @ Sat, 03 Jun 2017 16:42:10: #4 Write peak in narrowPeak format file... SRX287760.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 16:42:10: #4 Write summits bed file... SRX287760.10_summits.bed INFO @ Sat, 03 Jun 2017 16:42:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1644 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。