Job ID = 9029498 sra ファイルのダウンロード中... Completed: 416039K bytes transferred in 6 seconds (560274K 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 --:--:-- 0:00:06 --:--:-- 0 100 30318 0 30318 0 0 3791 0 --:--:-- 0:00:07 --:--:-- 19055 100 55163 0 55163 0 0 6493 0 --:--:-- 0:00:08 --:--:-- 26419 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 11940468 spots for /home/okishinya/chipatlas/results/dm3/SRX1794252/SRR3575296.sra Written 11940468 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: 00:00:01 Multiseed full-index search: 00:03:39 11940468 reads; of these: 11940468 (100.00%) were unpaired; of these: 348181 (2.92%) aligned 0 times 9903892 (82.94%) aligned exactly 1 time 1688395 (14.14%) aligned >1 times 97.08% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 2677374 / 11592287 = 0.2310 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 14:02:55: # Command line: callpeak -t SRX1794252.bam -f BAM -g dm -n SRX1794252.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794252.10 # format = BAM # ChIP-seq file = ['SRX1794252.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 14:02:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:02:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:02:55: # Command line: callpeak -t SRX1794252.bam -f BAM -g dm -n SRX1794252.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794252.20 # format = BAM # ChIP-seq file = ['SRX1794252.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 14:02:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:02:55: # Command line: callpeak -t SRX1794252.bam -f BAM -g dm -n SRX1794252.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794252.05 # format = BAM # ChIP-seq file = ['SRX1794252.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 14:02:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:02:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:02:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:03:01: 1000000 INFO @ Sat, 03 Jun 2017 14:03:01: 1000000 INFO @ Sat, 03 Jun 2017 14:03:01: 1000000 INFO @ Sat, 03 Jun 2017 14:03:08: 2000000 INFO @ Sat, 03 Jun 2017 14:03:08: 2000000 INFO @ Sat, 03 Jun 2017 14:03:08: 2000000 INFO @ Sat, 03 Jun 2017 14:03:14: 3000000 INFO @ Sat, 03 Jun 2017 14:03:14: 3000000 INFO @ Sat, 03 Jun 2017 14:03:14: 3000000 INFO @ Sat, 03 Jun 2017 14:03:20: 4000000 INFO @ Sat, 03 Jun 2017 14:03:20: 4000000 INFO @ Sat, 03 Jun 2017 14:03:20: 4000000 INFO @ Sat, 03 Jun 2017 14:03:27: 5000000 INFO @ Sat, 03 Jun 2017 14:03:27: 5000000 INFO @ Sat, 03 Jun 2017 14:03:27: 5000000 INFO @ Sat, 03 Jun 2017 14:03:33: 6000000 INFO @ Sat, 03 Jun 2017 14:03:33: 6000000 INFO @ Sat, 03 Jun 2017 14:03:33: 6000000 INFO @ Sat, 03 Jun 2017 14:03:40: 7000000 INFO @ Sat, 03 Jun 2017 14:03:40: 7000000 INFO @ Sat, 03 Jun 2017 14:03:40: 7000000 INFO @ Sat, 03 Jun 2017 14:03:46: 8000000 INFO @ Sat, 03 Jun 2017 14:03:46: 8000000 INFO @ Sat, 03 Jun 2017 14:03:46: 8000000 INFO @ Sat, 03 Jun 2017 14:03:52: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:03:52: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:03:52: #1 total tags in treatment: 8914913 INFO @ Sat, 03 Jun 2017 14:03:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:03:52: #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 14:03:52: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:03:52: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:03:52: #1 total tags in treatment: 8914913 INFO @ Sat, 03 Jun 2017 14:03:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:03:52: #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 14:03:52: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:03:52: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:03:52: #1 total tags in treatment: 8914913 INFO @ Sat, 03 Jun 2017 14:03:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:03:52: #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 14:03:54: #1 tags after filtering in treatment: 8912185 INFO @ Sat, 03 Jun 2017 14:03:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:03:54: #1 finished! INFO @ Sat, 03 Jun 2017 14:03:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:03:54: #1 tags after filtering in treatment: 8912185 INFO @ Sat, 03 Jun 2017 14:03:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:03:54: #1 finished! INFO @ Sat, 03 Jun 2017 14:03:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:03:54: #1 tags after filtering in treatment: 8912185 INFO @ Sat, 03 Jun 2017 14:03:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:03:54: #1 finished! INFO @ Sat, 03 Jun 2017 14:03:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:03:57: #2 number of paired peaks: 11576 INFO @ Sat, 03 Jun 2017 14:03:57: start model_add_line... INFO @ Sat, 03 Jun 2017 14:03:57: #2 number of paired peaks: 11576 INFO @ Sat, 03 Jun 2017 14:03:57: start model_add_line... INFO @ Sat, 03 Jun 2017 14:03:57: #2 number of paired peaks: 11576 INFO @ Sat, 03 Jun 2017 14:03:57: start model_add_line... INFO @ Sat, 03 Jun 2017 14:05:21: start X-correlation... INFO @ Sat, 03 Jun 2017 14:05:21: end of X-cor INFO @ Sat, 03 Jun 2017 14:05:21: #2 finished! INFO @ Sat, 03 Jun 2017 14:05:21: #2 predicted fragment length is 179 bps INFO @ Sat, 03 Jun 2017 14:05:21: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 03 Jun 2017 14:05:21: #2.2 Generate R script for model : SRX1794252.20_model.r INFO @ Sat, 03 Jun 2017 14:05:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:05:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:05:23: start X-correlation... INFO @ Sat, 03 Jun 2017 14:05:23: end of X-cor INFO @ Sat, 03 Jun 2017 14:05:23: #2 finished! INFO @ Sat, 03 Jun 2017 14:05:23: #2 predicted fragment length is 179 bps INFO @ Sat, 03 Jun 2017 14:05:23: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 03 Jun 2017 14:05:23: #2.2 Generate R script for model : SRX1794252.10_model.r INFO @ Sat, 03 Jun 2017 14:05:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:05:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:05:23: start X-correlation... INFO @ Sat, 03 Jun 2017 14:05:23: end of X-cor INFO @ Sat, 03 Jun 2017 14:05:23: #2 finished! INFO @ Sat, 03 Jun 2017 14:05:23: #2 predicted fragment length is 179 bps INFO @ Sat, 03 Jun 2017 14:05:23: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 03 Jun 2017 14:05:23: #2.2 Generate R script for model : SRX1794252.05_model.r INFO @ Sat, 03 Jun 2017 14:05:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:05:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 14:06:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:06:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:06:20: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:07:03: #4 Write output xls file... SRX1794252.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:07:03: #4 Write peak in narrowPeak format file... SRX1794252.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:07:03: #4 Write summits bed file... SRX1794252.20_summits.bed INFO @ Sat, 03 Jun 2017 14:07:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7575 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:07:15: #4 Write output xls file... SRX1794252.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:07:15: #4 Write peak in narrowPeak format file... SRX1794252.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:07:15: #4 Write summits bed file... SRX1794252.10_summits.bed INFO @ Sat, 03 Jun 2017 14:07:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8600 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:07:15: #4 Write output xls file... SRX1794252.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:07:16: #4 Write peak in narrowPeak format file... SRX1794252.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:07:16: #4 Write summits bed file... SRX1794252.05_summits.bed INFO @ Sat, 03 Jun 2017 14:07:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9227 records, 4 fields): 13 millis CompletedMACS2peakCalling