Job ID = 9025465 sra ファイルのダウンロード中... Completed: 423829K bytes transferred in 5 seconds (614259K bits/sec), in 2 files, 3 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 --:--:-- 0 100 14324 0 14324 0 0 1941 0 --:--:-- 0:00:07 --:--:-- 14210 100 40382 0 40382 0 0 4823 0 --:--:-- 0:00:08 --:--:-- 20160 100 50032 0 50032 0 0 5747 0 --:--:-- 0:00:08 --:--:-- 21426 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 5816551 spots for /home/okishinya/chipatlas/results/ce10/SRX1099838/SRR2105908.sra Written 5816551 spots total Written 7162624 spots for /home/okishinya/chipatlas/results/ce10/SRX1099838/SRR2105909.sra Written 7162624 spots total 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: 00:03:20 12979175 reads; of these: 12979175 (100.00%) were unpaired; of these: 742104 (5.72%) aligned 0 times 10331492 (79.60%) aligned exactly 1 time 1905579 (14.68%) aligned >1 times 94.28% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 8051904 / 12237071 = 0.6580 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 04:02:26: # Command line: callpeak -t SRX1099838.bam -f BAM -g ce -n SRX1099838.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1099838.05 # format = BAM # ChIP-seq file = ['SRX1099838.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 04:02:26: # Command line: callpeak -t SRX1099838.bam -f BAM -g ce -n SRX1099838.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1099838.10 # format = BAM # ChIP-seq file = ['SRX1099838.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 04:02:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:02:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:02:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:02:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:02:26: # Command line: callpeak -t SRX1099838.bam -f BAM -g ce -n SRX1099838.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1099838.20 # format = BAM # ChIP-seq file = ['SRX1099838.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 04:02:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:02:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:02:34: 1000000 INFO @ Sat, 03 Jun 2017 04:02:34: 1000000 INFO @ Sat, 03 Jun 2017 04:02:34: 1000000 INFO @ Sat, 03 Jun 2017 04:02:42: 2000000 INFO @ Sat, 03 Jun 2017 04:02:42: 2000000 INFO @ Sat, 03 Jun 2017 04:02:42: 2000000 INFO @ Sat, 03 Jun 2017 04:02:49: 3000000 INFO @ Sat, 03 Jun 2017 04:02:49: 3000000 INFO @ Sat, 03 Jun 2017 04:02:50: 3000000 INFO @ Sat, 03 Jun 2017 04:02:56: 4000000 INFO @ Sat, 03 Jun 2017 04:02:57: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:02:57: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:02:57: #1 total tags in treatment: 4185167 INFO @ Sat, 03 Jun 2017 04:02:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:02:57: #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 04:02:57: 4000000 INFO @ Sat, 03 Jun 2017 04:02:58: 4000000 INFO @ Sat, 03 Jun 2017 04:02:58: #1 tags after filtering in treatment: 4184392 INFO @ Sat, 03 Jun 2017 04:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:02:58: #1 finished! INFO @ Sat, 03 Jun 2017 04:02:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:02:59: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:02:59: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:02:59: #1 total tags in treatment: 4185167 INFO @ Sat, 03 Jun 2017 04:02:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:02:59: #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 04:02:59: #2 number of paired peaks: 1687 INFO @ Sat, 03 Jun 2017 04:02:59: start model_add_line... INFO @ Sat, 03 Jun 2017 04:02:59: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:02:59: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:02:59: #1 total tags in treatment: 4185167 INFO @ Sat, 03 Jun 2017 04:02:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:02:59: #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 04:03:00: #1 tags after filtering in treatment: 4184392 INFO @ Sat, 03 Jun 2017 04:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:03:00: #1 finished! INFO @ Sat, 03 Jun 2017 04:03:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:03:00: #1 tags after filtering in treatment: 4184392 INFO @ Sat, 03 Jun 2017 04:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:03:00: #1 finished! INFO @ Sat, 03 Jun 2017 04:03:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:03:01: #2 number of paired peaks: 1687 INFO @ Sat, 03 Jun 2017 04:03:01: start model_add_line... INFO @ Sat, 03 Jun 2017 04:03:01: #2 number of paired peaks: 1687 INFO @ Sat, 03 Jun 2017 04:03:01: start model_add_line... INFO @ Sat, 03 Jun 2017 04:03:07: start X-correlation... INFO @ Sat, 03 Jun 2017 04:03:07: end of X-cor INFO @ Sat, 03 Jun 2017 04:03:07: #2 finished! INFO @ Sat, 03 Jun 2017 04:03:07: #2 predicted fragment length is 230 bps INFO @ Sat, 03 Jun 2017 04:03:07: #2 alternative fragment length(s) may be 230 bps INFO @ Sat, 03 Jun 2017 04:03:07: #2.2 Generate R script for model : SRX1099838.05_model.r INFO @ Sat, 03 Jun 2017 04:03:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:03:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:03:09: start X-correlation... INFO @ Sat, 03 Jun 2017 04:03:09: end of X-cor INFO @ Sat, 03 Jun 2017 04:03:09: #2 finished! INFO @ Sat, 03 Jun 2017 04:03:09: #2 predicted fragment length is 230 bps INFO @ Sat, 03 Jun 2017 04:03:09: #2 alternative fragment length(s) may be 230 bps INFO @ Sat, 03 Jun 2017 04:03:09: #2.2 Generate R script for model : SRX1099838.10_model.r INFO @ Sat, 03 Jun 2017 04:03:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:03:09: start X-correlation... INFO @ Sat, 03 Jun 2017 04:03:09: end of X-cor INFO @ Sat, 03 Jun 2017 04:03:09: #2 finished! INFO @ Sat, 03 Jun 2017 04:03:09: #2 predicted fragment length is 230 bps INFO @ Sat, 03 Jun 2017 04:03:09: #2 alternative fragment length(s) may be 230 bps INFO @ Sat, 03 Jun 2017 04:03:09: #2.2 Generate R script for model : SRX1099838.20_model.r INFO @ Sat, 03 Jun 2017 04:03:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:03:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:03:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:03:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:03:54: #4 Write output xls file... SRX1099838.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:03:55: #4 Write peak in narrowPeak format file... SRX1099838.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:03:55: #4 Write summits bed file... SRX1099838.20_summits.bed INFO @ Sat, 03 Jun 2017 04:03:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:03:57: #4 Write output xls file... SRX1099838.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:03:57: #4 Write peak in narrowPeak format file... SRX1099838.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:03:57: #4 Write summits bed file... SRX1099838.05_summits.bed INFO @ Sat, 03 Jun 2017 04:03:57: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3274 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:03:59: #4 Write output xls file... SRX1099838.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:03:59: #4 Write peak in narrowPeak format file... SRX1099838.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:03:59: #4 Write summits bed file... SRX1099838.10_summits.bed INFO @ Sat, 03 Jun 2017 04:03:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1268 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。