Job ID = 9025647 sra ファイルのダウンロード中... Completed: 271080K bytes transferred in 6 seconds (352751K 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 14324 0 14324 0 0 1905 0 --:--:-- 0:00:07 --:--:-- 13165 100 50695 0 50695 0 0 6073 0 --:--:-- 0:00:08 --:--:-- 26431 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 9595716 spots for /home/okishinya/chipatlas/results/ce10/SRX2144173/SRR4188777.sra Written 9595716 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: 00:02:11 9595716 reads; of these: 9595716 (100.00%) were unpaired; of these: 2072998 (21.60%) aligned 0 times 6426443 (66.97%) aligned exactly 1 time 1096275 (11.42%) aligned >1 times 78.40% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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_rmdupse_core] 1596314 / 7522718 = 0.2122 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 04:51:00: # Command line: callpeak -t SRX2144173.bam -f BAM -g ce -n SRX2144173.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144173.10 # format = BAM # ChIP-seq file = ['SRX2144173.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 04:51:00: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:00: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:00: # Command line: callpeak -t SRX2144173.bam -f BAM -g ce -n SRX2144173.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144173.20 # format = BAM # ChIP-seq file = ['SRX2144173.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 04:51:00: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:00: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:00: # Command line: callpeak -t SRX2144173.bam -f BAM -g ce -n SRX2144173.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144173.05 # format = BAM # ChIP-seq file = ['SRX2144173.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 04:51:00: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:00: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:08: 1000000 INFO @ Sat, 03 Jun 2017 04:51:08: 1000000 INFO @ Sat, 03 Jun 2017 04:51:08: 1000000 INFO @ Sat, 03 Jun 2017 04:51:16: 2000000 INFO @ Sat, 03 Jun 2017 04:51:16: 2000000 INFO @ Sat, 03 Jun 2017 04:51:16: 2000000 INFO @ Sat, 03 Jun 2017 04:51:24: 3000000 INFO @ Sat, 03 Jun 2017 04:51:24: 3000000 INFO @ Sat, 03 Jun 2017 04:51:24: 3000000 INFO @ Sat, 03 Jun 2017 04:51:32: 4000000 INFO @ Sat, 03 Jun 2017 04:51:32: 4000000 INFO @ Sat, 03 Jun 2017 04:51:32: 4000000 INFO @ Sat, 03 Jun 2017 04:51:40: 5000000 INFO @ Sat, 03 Jun 2017 04:51:40: 5000000 INFO @ Sat, 03 Jun 2017 04:51:40: 5000000 INFO @ Sat, 03 Jun 2017 04:51:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:51:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:51:47: #1 total tags in treatment: 5926404 INFO @ Sat, 03 Jun 2017 04:51:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:47: #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 04:51:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:51:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:51:47: #1 total tags in treatment: 5926404 INFO @ Sat, 03 Jun 2017 04:51:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:47: #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 04:51:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:51:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:51:47: #1 total tags in treatment: 5926404 INFO @ Sat, 03 Jun 2017 04:51:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:47: #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 04:51:48: #1 tags after filtering in treatment: 5924987 INFO @ Sat, 03 Jun 2017 04:51:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:48: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:48: #1 tags after filtering in treatment: 5924987 INFO @ Sat, 03 Jun 2017 04:51:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:48: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:48: #1 tags after filtering in treatment: 5924987 INFO @ Sat, 03 Jun 2017 04:51:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:48: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:49: #2 number of paired peaks: 2002 INFO @ Sat, 03 Jun 2017 04:51:49: start model_add_line... INFO @ Sat, 03 Jun 2017 04:51:50: #2 number of paired peaks: 2002 INFO @ Sat, 03 Jun 2017 04:51:50: start model_add_line... INFO @ Sat, 03 Jun 2017 04:51:50: #2 number of paired peaks: 2002 INFO @ Sat, 03 Jun 2017 04:51:50: start model_add_line... INFO @ Sat, 03 Jun 2017 04:52:02: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:02: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:02: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:02: #2 predicted fragment length is 145 bps INFO @ Sat, 03 Jun 2017 04:52:02: #2 alternative fragment length(s) may be 4,145 bps INFO @ Sat, 03 Jun 2017 04:52:02: #2.2 Generate R script for model : SRX2144173.20_model.r INFO @ Sat, 03 Jun 2017 04:52:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:03: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:03: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:03: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:03: #2 predicted fragment length is 145 bps INFO @ Sat, 03 Jun 2017 04:52:03: #2 alternative fragment length(s) may be 4,145 bps INFO @ Sat, 03 Jun 2017 04:52:03: #2.2 Generate R script for model : SRX2144173.05_model.r INFO @ Sat, 03 Jun 2017 04:52:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:03: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:03: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:03: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:03: #2 predicted fragment length is 145 bps INFO @ Sat, 03 Jun 2017 04:52:03: #2 alternative fragment length(s) may be 4,145 bps INFO @ Sat, 03 Jun 2017 04:52:03: #2.2 Generate R script for model : SRX2144173.10_model.r INFO @ Sat, 03 Jun 2017 04:52:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:52:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:52:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:53:05: #4 Write output xls file... SRX2144173.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:53:05: #4 Write peak in narrowPeak format file... SRX2144173.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:53:05: #4 Write summits bed file... SRX2144173.20_summits.bed INFO @ Sat, 03 Jun 2017 04:53:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:53:05: #4 Write output xls file... SRX2144173.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:53:05: #4 Write peak in narrowPeak format file... SRX2144173.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:53:05: #4 Write summits bed file... SRX2144173.10_summits.bed INFO @ Sat, 03 Jun 2017 04:53:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1481 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:53:12: #4 Write output xls file... SRX2144173.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:53:12: #4 Write peak in narrowPeak format file... SRX2144173.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:53:12: #4 Write summits bed file... SRX2144173.05_summits.bed INFO @ Sat, 03 Jun 2017 04:53:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3059 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。