Job ID = 9025464 sra ファイルのダウンロード中... Completed: 631449K bytes transferred in 8 seconds (613408K 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 --:--:-- 0 101 9799 0 9799 0 0 1299 0 --:--:-- 0:00:07 --:--:-- 9654 100 39694 0 39694 0 0 4651 0 --:--:-- 0:00:08 --:--:-- 19738 100 65196 0 65196 0 0 7353 0 --:--:-- 0:00:08 --:--:-- 27825 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 9026289 spots for /home/okishinya/chipatlas/results/ce10/SRX1099837/SRR2105906.sra Written 9026289 spots total Written 11017670 spots for /home/okishinya/chipatlas/results/ce10/SRX1099837/SRR2105907.sra Written 11017670 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: 00:05:02 20043959 reads; of these: 20043959 (100.00%) were unpaired; of these: 3941856 (19.67%) aligned 0 times 13825745 (68.98%) aligned exactly 1 time 2276358 (11.36%) aligned >1 times 80.33% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5838339 / 16102103 = 0.3626 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 04:05:32: # Command line: callpeak -t SRX1099837.bam -f BAM -g ce -n SRX1099837.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1099837.20 # format = BAM # ChIP-seq file = ['SRX1099837.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 04:05:32: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:05:32: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:05:32: # Command line: callpeak -t SRX1099837.bam -f BAM -g ce -n SRX1099837.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1099837.05 # format = BAM # ChIP-seq file = ['SRX1099837.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 04:05:32: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:05:32: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:05:32: # Command line: callpeak -t SRX1099837.bam -f BAM -g ce -n SRX1099837.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1099837.10 # format = BAM # ChIP-seq file = ['SRX1099837.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 04:05:32: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:05:32: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:05:40: 1000000 INFO @ Sat, 03 Jun 2017 04:05:40: 1000000 INFO @ Sat, 03 Jun 2017 04:05:40: 1000000 INFO @ Sat, 03 Jun 2017 04:05:47: 2000000 INFO @ Sat, 03 Jun 2017 04:05:47: 2000000 INFO @ Sat, 03 Jun 2017 04:05:48: 2000000 INFO @ Sat, 03 Jun 2017 04:05:54: 3000000 INFO @ Sat, 03 Jun 2017 04:05:55: 3000000 INFO @ Sat, 03 Jun 2017 04:05:55: 3000000 INFO @ Sat, 03 Jun 2017 04:06:02: 4000000 INFO @ Sat, 03 Jun 2017 04:06:02: 4000000 INFO @ Sat, 03 Jun 2017 04:06:03: 4000000 INFO @ Sat, 03 Jun 2017 04:06:09: 5000000 INFO @ Sat, 03 Jun 2017 04:06:10: 5000000 INFO @ Sat, 03 Jun 2017 04:06:10: 5000000 INFO @ Sat, 03 Jun 2017 04:06:16: 6000000 INFO @ Sat, 03 Jun 2017 04:06:17: 6000000 INFO @ Sat, 03 Jun 2017 04:06:17: 6000000 INFO @ Sat, 03 Jun 2017 04:06:24: 7000000 INFO @ Sat, 03 Jun 2017 04:06:25: 7000000 INFO @ Sat, 03 Jun 2017 04:06:25: 7000000 INFO @ Sat, 03 Jun 2017 04:06:31: 8000000 INFO @ Sat, 03 Jun 2017 04:06:32: 8000000 INFO @ Sat, 03 Jun 2017 04:06:33: 8000000 INFO @ Sat, 03 Jun 2017 04:06:38: 9000000 INFO @ Sat, 03 Jun 2017 04:06:40: 9000000 INFO @ Sat, 03 Jun 2017 04:06:40: 9000000 INFO @ Sat, 03 Jun 2017 04:06:45: 10000000 INFO @ Sat, 03 Jun 2017 04:06:47: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:06:47: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:06:47: #1 total tags in treatment: 10263764 INFO @ Sat, 03 Jun 2017 04:06:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:06:47: #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 04:06:47: 10000000 INFO @ Sat, 03 Jun 2017 04:06:48: 10000000 INFO @ Sat, 03 Jun 2017 04:06:49: #1 tags after filtering in treatment: 10261770 INFO @ Sat, 03 Jun 2017 04:06:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:06:49: #1 finished! INFO @ Sat, 03 Jun 2017 04:06:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:06:49: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:06:49: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:06:49: #1 total tags in treatment: 10263764 INFO @ Sat, 03 Jun 2017 04:06:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:06:49: #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 04:06:50: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:06:50: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:06:50: #1 total tags in treatment: 10263764 INFO @ Sat, 03 Jun 2017 04:06:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:06:50: #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 04:06:51: #2 number of paired peaks: 923 WARNING @ Sat, 03 Jun 2017 04:06:51: Fewer paired peaks (923) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 923 pairs to build model! INFO @ Sat, 03 Jun 2017 04:06:51: start model_add_line... INFO @ Sat, 03 Jun 2017 04:06:51: #1 tags after filtering in treatment: 10261770 INFO @ Sat, 03 Jun 2017 04:06:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:06:51: #1 finished! INFO @ Sat, 03 Jun 2017 04:06:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:06:52: #1 tags after filtering in treatment: 10261770 INFO @ Sat, 03 Jun 2017 04:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:06:52: #1 finished! INFO @ Sat, 03 Jun 2017 04:06:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:06:53: #2 number of paired peaks: 923 WARNING @ Sat, 03 Jun 2017 04:06:53: Fewer paired peaks (923) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 923 pairs to build model! INFO @ Sat, 03 Jun 2017 04:06:53: start model_add_line... INFO @ Sat, 03 Jun 2017 04:06:54: #2 number of paired peaks: 923 WARNING @ Sat, 03 Jun 2017 04:06:54: Fewer paired peaks (923) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 923 pairs to build model! INFO @ Sat, 03 Jun 2017 04:06:54: start model_add_line... INFO @ Sat, 03 Jun 2017 04:07:01: start X-correlation... INFO @ Sat, 03 Jun 2017 04:07:01: end of X-cor INFO @ Sat, 03 Jun 2017 04:07:01: #2 finished! INFO @ Sat, 03 Jun 2017 04:07:01: #2 predicted fragment length is 198 bps INFO @ Sat, 03 Jun 2017 04:07:01: #2 alternative fragment length(s) may be 198 bps INFO @ Sat, 03 Jun 2017 04:07:01: #2.2 Generate R script for model : SRX1099837.10_model.r INFO @ Sat, 03 Jun 2017 04:07:01: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:07:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:07:02: start X-correlation... INFO @ Sat, 03 Jun 2017 04:07:02: end of X-cor INFO @ Sat, 03 Jun 2017 04:07:02: #2 finished! INFO @ Sat, 03 Jun 2017 04:07:02: #2 predicted fragment length is 198 bps INFO @ Sat, 03 Jun 2017 04:07:02: #2 alternative fragment length(s) may be 198 bps INFO @ Sat, 03 Jun 2017 04:07:02: #2.2 Generate R script for model : SRX1099837.20_model.r INFO @ Sat, 03 Jun 2017 04:07:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:07:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:07:03: start X-correlation... INFO @ Sat, 03 Jun 2017 04:07:03: end of X-cor INFO @ Sat, 03 Jun 2017 04:07:03: #2 finished! INFO @ Sat, 03 Jun 2017 04:07:03: #2 predicted fragment length is 198 bps INFO @ Sat, 03 Jun 2017 04:07:03: #2 alternative fragment length(s) may be 198 bps INFO @ Sat, 03 Jun 2017 04:07:03: #2.2 Generate R script for model : SRX1099837.05_model.r INFO @ Sat, 03 Jun 2017 04:07:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:07:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:08:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:49: #4 Write output xls file... SRX1099837.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:08:49: #4 Write peak in narrowPeak format file... SRX1099837.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:08:49: #4 Write summits bed file... SRX1099837.10_summits.bed INFO @ Sat, 03 Jun 2017 04:08:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2436 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:08:49: #4 Write output xls file... SRX1099837.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:08:49: #4 Write peak in narrowPeak format file... SRX1099837.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:08:49: #4 Write summits bed file... SRX1099837.20_summits.bed INFO @ Sat, 03 Jun 2017 04:08:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1313 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:08:54: #4 Write output xls file... SRX1099837.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:08:54: #4 Write peak in narrowPeak format file... SRX1099837.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:08:54: #4 Write summits bed file... SRX1099837.05_summits.bed INFO @ Sat, 03 Jun 2017 04:08:54: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4138 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。