Job ID = 9025988 sra ファイルのダウンロード中... Completed: 703571K bytes transferred in 8 seconds (658701K 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 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 100 22317 0 22317 0 0 2435 0 --:--:-- 0:00:09 --:--:-- 8153 100 44725 0 44725 0 0 4457 0 --:--:-- 0:00:10 --:--:-- 12396 100 71475 0 71475 0 0 6786 0 --:--:-- 0:00:10 --:--:-- 17411 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 20024866 spots for /home/okishinya/chipatlas/results/ce10/SRX330983/SRR947188.sra Written 20024866 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: 00:05:48 20024866 reads; of these: 20024866 (100.00%) were unpaired; of these: 1642855 (8.20%) aligned 0 times 13197426 (65.91%) aligned exactly 1 time 5184585 (25.89%) aligned >1 times 91.80% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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_sort_core] merging from 8 files... [bam_rmdupse_core] 12053123 / 18382011 = 0.6557 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 05:29:20: # Command line: callpeak -t SRX330983.bam -f BAM -g ce -n SRX330983.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX330983.10 # format = BAM # ChIP-seq file = ['SRX330983.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 05:29:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:29:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:29:20: # Command line: callpeak -t SRX330983.bam -f BAM -g ce -n SRX330983.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX330983.20 # format = BAM # ChIP-seq file = ['SRX330983.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 05:29:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:29:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:29:20: # Command line: callpeak -t SRX330983.bam -f BAM -g ce -n SRX330983.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX330983.05 # format = BAM # ChIP-seq file = ['SRX330983.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 05:29:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:29:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:29:27: 1000000 INFO @ Sat, 03 Jun 2017 05:29:28: 1000000 INFO @ Sat, 03 Jun 2017 05:29:28: 1000000 INFO @ Sat, 03 Jun 2017 05:29:34: 2000000 INFO @ Sat, 03 Jun 2017 05:29:35: 2000000 INFO @ Sat, 03 Jun 2017 05:29:35: 2000000 INFO @ Sat, 03 Jun 2017 05:29:42: 3000000 INFO @ Sat, 03 Jun 2017 05:29:42: 3000000 INFO @ Sat, 03 Jun 2017 05:29:42: 3000000 INFO @ Sat, 03 Jun 2017 05:29:49: 4000000 INFO @ Sat, 03 Jun 2017 05:29:49: 4000000 INFO @ Sat, 03 Jun 2017 05:29:49: 4000000 INFO @ Sat, 03 Jun 2017 05:29:55: 5000000 INFO @ Sat, 03 Jun 2017 05:29:56: 5000000 INFO @ Sat, 03 Jun 2017 05:29:56: 5000000 INFO @ Sat, 03 Jun 2017 05:30:02: 6000000 INFO @ Sat, 03 Jun 2017 05:30:04: 6000000 INFO @ Sat, 03 Jun 2017 05:30:04: 6000000 INFO @ Sat, 03 Jun 2017 05:30:04: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 05:30:04: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 05:30:04: #1 total tags in treatment: 6328888 INFO @ Sat, 03 Jun 2017 05:30:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:30:04: #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 05:30:06: #1 tags after filtering in treatment: 6325793 INFO @ Sat, 03 Jun 2017 05:30:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:30:06: #1 finished! INFO @ Sat, 03 Jun 2017 05:30:06: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:30:06: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 05:30:06: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 05:30:06: #1 total tags in treatment: 6328888 INFO @ Sat, 03 Jun 2017 05:30:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:30:06: #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 05:30:06: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 05:30:06: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 05:30:06: #1 total tags in treatment: 6328888 INFO @ Sat, 03 Jun 2017 05:30:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:30:06: #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 05:30:07: #2 number of paired peaks: 1958 INFO @ Sat, 03 Jun 2017 05:30:07: start model_add_line... INFO @ Sat, 03 Jun 2017 05:30:07: #1 tags after filtering in treatment: 6325793 INFO @ Sat, 03 Jun 2017 05:30:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:30:07: #1 finished! INFO @ Sat, 03 Jun 2017 05:30:07: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:30:08: #1 tags after filtering in treatment: 6325793 INFO @ Sat, 03 Jun 2017 05:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:30:08: #1 finished! INFO @ Sat, 03 Jun 2017 05:30:08: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:30:09: #2 number of paired peaks: 1958 INFO @ Sat, 03 Jun 2017 05:30:09: start model_add_line... INFO @ Sat, 03 Jun 2017 05:30:09: #2 number of paired peaks: 1958 INFO @ Sat, 03 Jun 2017 05:30:09: start model_add_line... INFO @ Sat, 03 Jun 2017 05:30:23: start X-correlation... INFO @ Sat, 03 Jun 2017 05:30:23: end of X-cor INFO @ Sat, 03 Jun 2017 05:30:23: #2 finished! INFO @ Sat, 03 Jun 2017 05:30:23: #2 predicted fragment length is 185 bps INFO @ Sat, 03 Jun 2017 05:30:23: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 03 Jun 2017 05:30:23: #2.2 Generate R script for model : SRX330983.20_model.r INFO @ Sat, 03 Jun 2017 05:30:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:30:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:30:24: start X-correlation... INFO @ Sat, 03 Jun 2017 05:30:24: end of X-cor INFO @ Sat, 03 Jun 2017 05:30:24: #2 finished! INFO @ Sat, 03 Jun 2017 05:30:24: #2 predicted fragment length is 185 bps INFO @ Sat, 03 Jun 2017 05:30:24: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 03 Jun 2017 05:30:24: #2.2 Generate R script for model : SRX330983.10_model.r INFO @ Sat, 03 Jun 2017 05:30:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:30:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:30:27: start X-correlation... INFO @ Sat, 03 Jun 2017 05:30:27: end of X-cor INFO @ Sat, 03 Jun 2017 05:30:27: #2 finished! INFO @ Sat, 03 Jun 2017 05:30:27: #2 predicted fragment length is 185 bps INFO @ Sat, 03 Jun 2017 05:30:27: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 03 Jun 2017 05:30:27: #2.2 Generate R script for model : SRX330983.05_model.r INFO @ Sat, 03 Jun 2017 05:30:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:30:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:31:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:31:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:31:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:31:35: #4 Write output xls file... SRX330983.20_peaks.xls INFO @ Sat, 03 Jun 2017 05:31:35: #4 Write peak in narrowPeak format file... SRX330983.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:31:35: #4 Write summits bed file... SRX330983.20_summits.bed INFO @ Sat, 03 Jun 2017 05:31:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1947 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 05:31:39: #4 Write output xls file... SRX330983.10_peaks.xls INFO @ Sat, 03 Jun 2017 05:31:39: #4 Write peak in narrowPeak format file... SRX330983.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:31:39: #4 Write summits bed file... SRX330983.10_summits.bed INFO @ Sat, 03 Jun 2017 05:31:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3491 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 05:31:40: #4 Write output xls file... SRX330983.05_peaks.xls INFO @ Sat, 03 Jun 2017 05:31:40: #4 Write peak in narrowPeak format file... SRX330983.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:31:40: #4 Write summits bed file... SRX330983.05_summits.bed INFO @ Sat, 03 Jun 2017 05:31:40: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5923 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。