Job ID = 9028739 sra ファイルのダウンロード中... Completed: 1084131K bytes transferred in 11 seconds (748848K 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 2491 0 --:--:-- 0:00:08 --:--:-- 8639 100 72237 0 72237 0 0 7256 0 --:--:-- 0:00:09 --:--:-- 20172 100 127k 0 127k 0 0 12274 0 --:--:-- 0:00:10 --:--:-- 30518 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 34455150 spots for /home/okishinya/chipatlas/results/ce10/SRX707297/SRR1582080.sra Written 34455150 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: 00:07:06 34455150 reads; of these: 34455150 (100.00%) were unpaired; of these: 11913465 (34.58%) aligned 0 times 18177327 (52.76%) aligned exactly 1 time 4364358 (12.67%) aligned >1 times 65.42% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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 12 files... [bam_rmdupse_core] 14774640 / 22541685 = 0.6554 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 11:47:46: # Command line: callpeak -t SRX707297.bam -f BAM -g ce -n SRX707297.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX707297.05 # format = BAM # ChIP-seq file = ['SRX707297.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 11:47:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:47:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:47:46: # Command line: callpeak -t SRX707297.bam -f BAM -g ce -n SRX707297.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX707297.10 # format = BAM # ChIP-seq file = ['SRX707297.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 11:47:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:47:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:47:46: # Command line: callpeak -t SRX707297.bam -f BAM -g ce -n SRX707297.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX707297.20 # format = BAM # ChIP-seq file = ['SRX707297.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 11:47:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:47:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:47:55: 1000000 INFO @ Sat, 03 Jun 2017 11:47:56: 1000000 INFO @ Sat, 03 Jun 2017 11:47:56: 1000000 INFO @ Sat, 03 Jun 2017 11:48:02: 2000000 INFO @ Sat, 03 Jun 2017 11:48:05: 2000000 INFO @ Sat, 03 Jun 2017 11:48:05: 2000000 INFO @ Sat, 03 Jun 2017 11:48:09: 3000000 INFO @ Sat, 03 Jun 2017 11:48:14: 3000000 INFO @ Sat, 03 Jun 2017 11:48:14: 3000000 INFO @ Sat, 03 Jun 2017 11:48:16: 4000000 INFO @ Sat, 03 Jun 2017 11:48:22: 5000000 INFO @ Sat, 03 Jun 2017 11:48:23: 4000000 INFO @ Sat, 03 Jun 2017 11:48:23: 4000000 INFO @ Sat, 03 Jun 2017 11:48:30: 6000000 INFO @ Sat, 03 Jun 2017 11:48:32: 5000000 INFO @ Sat, 03 Jun 2017 11:48:32: 5000000 INFO @ Sat, 03 Jun 2017 11:48:37: 7000000 INFO @ Sat, 03 Jun 2017 11:48:39: 6000000 INFO @ Sat, 03 Jun 2017 11:48:39: 6000000 INFO @ Sat, 03 Jun 2017 11:48:42: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 11:48:42: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 11:48:42: #1 total tags in treatment: 7767045 INFO @ Sat, 03 Jun 2017 11:48:42: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:48:42: #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 11:48:43: #1 tags after filtering in treatment: 7764799 INFO @ Sat, 03 Jun 2017 11:48:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 11:48:43: #1 finished! INFO @ Sat, 03 Jun 2017 11:48:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 11:48:45: #2 number of paired peaks: 1131 INFO @ Sat, 03 Jun 2017 11:48:45: start model_add_line... INFO @ Sat, 03 Jun 2017 11:48:46: 7000000 INFO @ Sat, 03 Jun 2017 11:48:46: 7000000 INFO @ Sat, 03 Jun 2017 11:48:51: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 11:48:51: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 11:48:51: #1 total tags in treatment: 7767045 INFO @ Sat, 03 Jun 2017 11:48:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:48:51: #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 11:48:51: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 11:48:51: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 11:48:51: #1 total tags in treatment: 7767045 INFO @ Sat, 03 Jun 2017 11:48:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:48:51: #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 11:48:52: #1 tags after filtering in treatment: 7764799 INFO @ Sat, 03 Jun 2017 11:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 11:48:52: #1 finished! INFO @ Sat, 03 Jun 2017 11:48:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 11:48:52: #1 tags after filtering in treatment: 7764799 INFO @ Sat, 03 Jun 2017 11:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 11:48:52: #1 finished! INFO @ Sat, 03 Jun 2017 11:48:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 11:48:54: #2 number of paired peaks: 1131 INFO @ Sat, 03 Jun 2017 11:48:54: start model_add_line... INFO @ Sat, 03 Jun 2017 11:48:54: #2 number of paired peaks: 1131 INFO @ Sat, 03 Jun 2017 11:48:54: start model_add_line... INFO @ Sat, 03 Jun 2017 11:48:55: start X-correlation... INFO @ Sat, 03 Jun 2017 11:48:55: end of X-cor INFO @ Sat, 03 Jun 2017 11:48:55: #2 finished! INFO @ Sat, 03 Jun 2017 11:48:55: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Jun 2017 11:48:55: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 03 Jun 2017 11:48:55: #2.2 Generate R script for model : SRX707297.10_model.r INFO @ Sat, 03 Jun 2017 11:48:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 11:48:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 11:49:03: start X-correlation... INFO @ Sat, 03 Jun 2017 11:49:03: end of X-cor INFO @ Sat, 03 Jun 2017 11:49:03: #2 finished! INFO @ Sat, 03 Jun 2017 11:49:03: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Jun 2017 11:49:03: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 03 Jun 2017 11:49:03: #2.2 Generate R script for model : SRX707297.05_model.r INFO @ Sat, 03 Jun 2017 11:49:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 11:49:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 11:49:04: start X-correlation... INFO @ Sat, 03 Jun 2017 11:49:04: end of X-cor INFO @ Sat, 03 Jun 2017 11:49:04: #2 finished! INFO @ Sat, 03 Jun 2017 11:49:04: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Jun 2017 11:49:04: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 03 Jun 2017 11:49:04: #2.2 Generate R script for model : SRX707297.20_model.r INFO @ Sat, 03 Jun 2017 11:49:04: #3 Call peaks... INFO @ Sat, 03 Jun 2017 11:49:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 11:49:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 11:49:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 11:49:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 11:50:18: #4 Write output xls file... SRX707297.10_peaks.xls INFO @ Sat, 03 Jun 2017 11:50:18: #4 Write peak in narrowPeak format file... SRX707297.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 11:50:18: #4 Write summits bed file... SRX707297.10_summits.bed INFO @ Sat, 03 Jun 2017 11:50:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5044 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 11:50:27: #4 Write output xls file... SRX707297.20_peaks.xls INFO @ Sat, 03 Jun 2017 11:50:27: #4 Write peak in narrowPeak format file... SRX707297.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 11:50:27: #4 Write summits bed file... SRX707297.20_summits.bed INFO @ Sat, 03 Jun 2017 11:50:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1568 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 11:50:32: #4 Write output xls file... SRX707297.05_peaks.xls INFO @ Sat, 03 Jun 2017 11:50:32: #4 Write peak in narrowPeak format file... SRX707297.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 11:50:32: #4 Write summits bed file... SRX707297.05_summits.bed INFO @ Sat, 03 Jun 2017 11:50:32: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (13048 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。