Job ID = 9032635 sra ファイルのダウンロード中... Completed: 195487K bytes transferred in 5 seconds (302072K 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 22318 0 22318 0 0 2895 0 --:--:-- 0:00:07 --:--:-- 17797 100 31778 0 31778 0 0 3952 0 --:--:-- 0:00:08 --:--:-- 20036 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 10963496 spots for /home/okishinya/chipatlas/results/dm3/SRX859013/SRR1779569.sra Written 10963496 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: 00:03:02 10963496 reads; of these: 10963496 (100.00%) were unpaired; of these: 47665 (0.43%) aligned 0 times 10490335 (95.68%) aligned exactly 1 time 425496 (3.88%) aligned >1 times 99.57% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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] 509 / 10915831 = 0.0000 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 23:56:46: # Command line: callpeak -t SRX859013.bam -f BAM -g dm -n SRX859013.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX859013.20 # format = BAM # ChIP-seq file = ['SRX859013.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 23:56:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:56:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:56:46: # Command line: callpeak -t SRX859013.bam -f BAM -g dm -n SRX859013.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX859013.05 # format = BAM # ChIP-seq file = ['SRX859013.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 23:56:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:56:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:56:46: # Command line: callpeak -t SRX859013.bam -f BAM -g dm -n SRX859013.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX859013.10 # format = BAM # ChIP-seq file = ['SRX859013.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 23:56:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 23:56:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 23:56:52: 1000000 INFO @ Sat, 03 Jun 2017 23:56:52: 1000000 INFO @ Sat, 03 Jun 2017 23:56:52: 1000000 INFO @ Sat, 03 Jun 2017 23:56:58: 2000000 INFO @ Sat, 03 Jun 2017 23:56:58: 2000000 INFO @ Sat, 03 Jun 2017 23:56:58: 2000000 INFO @ Sat, 03 Jun 2017 23:57:03: 3000000 INFO @ Sat, 03 Jun 2017 23:57:04: 3000000 INFO @ Sat, 03 Jun 2017 23:57:04: 3000000 INFO @ Sat, 03 Jun 2017 23:57:09: 4000000 INFO @ Sat, 03 Jun 2017 23:57:10: 4000000 INFO @ Sat, 03 Jun 2017 23:57:10: 4000000 INFO @ Sat, 03 Jun 2017 23:57:14: 5000000 INFO @ Sat, 03 Jun 2017 23:57:15: 5000000 INFO @ Sat, 03 Jun 2017 23:57:16: 5000000 INFO @ Sat, 03 Jun 2017 23:57:19: 6000000 INFO @ Sat, 03 Jun 2017 23:57:21: 6000000 INFO @ Sat, 03 Jun 2017 23:57:23: 6000000 INFO @ Sat, 03 Jun 2017 23:57:25: 7000000 INFO @ Sat, 03 Jun 2017 23:57:27: 7000000 INFO @ Sat, 03 Jun 2017 23:57:29: 7000000 INFO @ Sat, 03 Jun 2017 23:57:30: 8000000 INFO @ Sat, 03 Jun 2017 23:57:33: 8000000 INFO @ Sat, 03 Jun 2017 23:57:35: 8000000 INFO @ Sat, 03 Jun 2017 23:57:36: 9000000 INFO @ Sat, 03 Jun 2017 23:57:39: 9000000 INFO @ Sat, 03 Jun 2017 23:57:41: 9000000 INFO @ Sat, 03 Jun 2017 23:57:41: 10000000 INFO @ Sat, 03 Jun 2017 23:57:45: 10000000 INFO @ Sat, 03 Jun 2017 23:57:46: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 23:57:46: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 23:57:46: #1 total tags in treatment: 10915322 INFO @ Sat, 03 Jun 2017 23:57:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:57:46: #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 23:57:47: 10000000 INFO @ Sat, 03 Jun 2017 23:57:49: #1 tags after filtering in treatment: 10915227 INFO @ Sat, 03 Jun 2017 23:57:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:57:49: #1 finished! INFO @ Sat, 03 Jun 2017 23:57:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:57:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 23:57:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 23:57:51: #1 total tags in treatment: 10915322 INFO @ Sat, 03 Jun 2017 23:57:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:57:51: #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 23:57:51: #2 number of paired peaks: 1998 INFO @ Sat, 03 Jun 2017 23:57:51: start model_add_line... INFO @ Sat, 03 Jun 2017 23:57:53: #1 tags after filtering in treatment: 10915227 INFO @ Sat, 03 Jun 2017 23:57:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:57:53: #1 finished! INFO @ Sat, 03 Jun 2017 23:57:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:57:53: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 23:57:53: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 23:57:53: #1 total tags in treatment: 10915322 INFO @ Sat, 03 Jun 2017 23:57:53: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 23:57:53: #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 23:57:55: #2 number of paired peaks: 1998 INFO @ Sat, 03 Jun 2017 23:57:55: start model_add_line... INFO @ Sat, 03 Jun 2017 23:57:55: #1 tags after filtering in treatment: 10915227 INFO @ Sat, 03 Jun 2017 23:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 23:57:55: #1 finished! INFO @ Sat, 03 Jun 2017 23:57:55: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 23:57:57: #2 number of paired peaks: 1998 INFO @ Sat, 03 Jun 2017 23:57:57: start model_add_line... INFO @ Sat, 03 Jun 2017 23:58:05: start X-correlation... INFO @ Sat, 03 Jun 2017 23:58:05: end of X-cor INFO @ Sat, 03 Jun 2017 23:58:05: #2 finished! INFO @ Sat, 03 Jun 2017 23:58:05: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Jun 2017 23:58:05: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 03 Jun 2017 23:58:05: #2.2 Generate R script for model : SRX859013.05_model.r INFO @ Sat, 03 Jun 2017 23:58:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:58:09: start X-correlation... INFO @ Sat, 03 Jun 2017 23:58:09: end of X-cor INFO @ Sat, 03 Jun 2017 23:58:09: #2 finished! INFO @ Sat, 03 Jun 2017 23:58:09: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Jun 2017 23:58:09: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 03 Jun 2017 23:58:09: #2.2 Generate R script for model : SRX859013.20_model.r INFO @ Sat, 03 Jun 2017 23:58:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:58:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:58:12: start X-correlation... INFO @ Sat, 03 Jun 2017 23:58:12: end of X-cor INFO @ Sat, 03 Jun 2017 23:58:12: #2 finished! INFO @ Sat, 03 Jun 2017 23:58:12: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Jun 2017 23:58:12: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 03 Jun 2017 23:58:12: #2.2 Generate R script for model : SRX859013.10_model.r INFO @ Sat, 03 Jun 2017 23:58:12: #3 Call peaks... INFO @ Sat, 03 Jun 2017 23:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 23:59:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:59:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:59:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 23:59:55: #4 Write output xls file... SRX859013.05_peaks.xls INFO @ Sat, 03 Jun 2017 23:59:56: #4 Write peak in narrowPeak format file... SRX859013.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:59:56: #4 Write summits bed file... SRX859013.05_summits.bed INFO @ Sat, 03 Jun 2017 23:59:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5174 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 23:59:57: #4 Write output xls file... SRX859013.20_peaks.xls INFO @ Sat, 03 Jun 2017 23:59:57: #4 Write peak in narrowPeak format file... SRX859013.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:59:57: #4 Write summits bed file... SRX859013.20_summits.bed INFO @ Sat, 03 Jun 2017 23:59:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2071 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 23:59:58: #4 Write output xls file... SRX859013.10_peaks.xls INFO @ Sat, 03 Jun 2017 23:59:58: #4 Write peak in narrowPeak format file... SRX859013.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 23:59:58: #4 Write summits bed file... SRX859013.10_summits.bed INFO @ Sat, 03 Jun 2017 23:59:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3434 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。