Job ID = 2165960 sra ファイルのダウンロード中... Completed: 82823K bytes transferred in 4 seconds (157324K 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 --:--:-- --:--:-- --:--:-- 0 100 17834 0 17834 0 0 23585 0 --:--:-- --:--:-- --:--:-- 31564 100 36001 0 36001 0 0 47548 0 --:--:-- --:--:-- --:--:-- 63606 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 1262702 spots for /home/okishinya/chipatlas/results/sacCer3/SRX092435/SRR332230.sra Written 1262702 spots total Written 2197327 spots for /home/okishinya/chipatlas/results/sacCer3/SRX092435/SRR332229.sra Written 2197327 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: 00:00:28 3460029 reads; of these: 3460029 (100.00%) were unpaired; of these: 1472941 (42.57%) aligned 0 times 1716286 (49.60%) aligned exactly 1 time 270802 (7.83%) aligned >1 times 57.43% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 674817 / 1987088 = 0.3396 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 @ Wed, 22 Apr 2015 09:34:51: # Command line: callpeak -t SRX092435.bam -f BAM -g 12100000 -n SRX092435.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX092435.05 # format = BAM # ChIP-seq file = ['SRX092435.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Apr 2015 09:34:51: # Command line: callpeak -t SRX092435.bam -f BAM -g 12100000 -n SRX092435.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX092435.20 # format = BAM # ChIP-seq file = ['SRX092435.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Apr 2015 09:34:51: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:34:51: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:34:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:34:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:34:51: # Command line: callpeak -t SRX092435.bam -f BAM -g 12100000 -n SRX092435.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX092435.10 # format = BAM # ChIP-seq file = ['SRX092435.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Apr 2015 09:34:51: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:34:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:34:58: 1000000 INFO @ Wed, 22 Apr 2015 09:34:58: 1000000 INFO @ Wed, 22 Apr 2015 09:34:58: 1000000 INFO @ Wed, 22 Apr 2015 09:35:00: #1 tag size is determined as 34 bps INFO @ Wed, 22 Apr 2015 09:35:00: #1 tag size is determined as 34 bps INFO @ Wed, 22 Apr 2015 09:35:00: #1 tag size = 34 INFO @ Wed, 22 Apr 2015 09:35:00: #1 tag size = 34 INFO @ Wed, 22 Apr 2015 09:35:00: #1 total tags in treatment: 1312271 INFO @ Wed, 22 Apr 2015 09:35:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:35:00: #1 total tags in treatment: 1312271 INFO @ Wed, 22 Apr 2015 09:35:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2015 09:35:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:35:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2015 09:35:00: #1 tags after filtering in treatment: 1293459 INFO @ Wed, 22 Apr 2015 09:35:00: #1 Redundant rate of treatment: 0.01 INFO @ Wed, 22 Apr 2015 09:35:00: #1 finished! INFO @ Wed, 22 Apr 2015 09:35:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:35:00: #1 tags after filtering in treatment: 1293459 INFO @ Wed, 22 Apr 2015 09:35:00: #1 Redundant rate of treatment: 0.01 INFO @ Wed, 22 Apr 2015 09:35:00: #1 finished! INFO @ Wed, 22 Apr 2015 09:35:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:35:00: #2 number of paired peaks: 351 WARNING @ Wed, 22 Apr 2015 09:35:00: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Wed, 22 Apr 2015 09:35:00: start model_add_line... INFO @ Wed, 22 Apr 2015 09:35:00: #2 number of paired peaks: 351 WARNING @ Wed, 22 Apr 2015 09:35:00: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Wed, 22 Apr 2015 09:35:00: start model_add_line... INFO @ Wed, 22 Apr 2015 09:35:00: #1 tag size is determined as 34 bps INFO @ Wed, 22 Apr 2015 09:35:00: #1 tag size = 34 INFO @ Wed, 22 Apr 2015 09:35:00: #1 total tags in treatment: 1312271 INFO @ Wed, 22 Apr 2015 09:35:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:35:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2015 09:35:01: #1 tags after filtering in treatment: 1293459 INFO @ Wed, 22 Apr 2015 09:35:01: #1 Redundant rate of treatment: 0.01 INFO @ Wed, 22 Apr 2015 09:35:01: #1 finished! INFO @ Wed, 22 Apr 2015 09:35:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:35:01: #2 number of paired peaks: 351 WARNING @ Wed, 22 Apr 2015 09:35:01: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Wed, 22 Apr 2015 09:35:01: start model_add_line... INFO @ Wed, 22 Apr 2015 09:35:03: start X-correlation... INFO @ Wed, 22 Apr 2015 09:35:03: end of X-cor INFO @ Wed, 22 Apr 2015 09:35:03: #2 finished! INFO @ Wed, 22 Apr 2015 09:35:03: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2015 09:35:03: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2015 09:35:03: #2.2 Generate R script for model : SRX092435.05_model.r INFO @ Wed, 22 Apr 2015 09:35:03: start X-correlation... INFO @ Wed, 22 Apr 2015 09:35:03: end of X-cor INFO @ Wed, 22 Apr 2015 09:35:03: #2 finished! INFO @ Wed, 22 Apr 2015 09:35:03: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2015 09:35:03: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2015 09:35:03: #2.2 Generate R script for model : SRX092435.20_model.r INFO @ Wed, 22 Apr 2015 09:35:03: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:35:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:35:03: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:35:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:35:04: start X-correlation... INFO @ Wed, 22 Apr 2015 09:35:04: end of X-cor INFO @ Wed, 22 Apr 2015 09:35:04: #2 finished! INFO @ Wed, 22 Apr 2015 09:35:04: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2015 09:35:04: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2015 09:35:04: #2.2 Generate R script for model : SRX092435.10_model.r INFO @ Wed, 22 Apr 2015 09:35:04: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:35:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:35:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:35:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:35:14: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:35:19: #4 Write output xls file... SRX092435.20_peaks.xls INFO @ Wed, 22 Apr 2015 09:35:19: #4 Write peak in narrowPeak format file... SRX092435.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:35:19: #4 Write summits bed file... SRX092435.20_summits.bed INFO @ Wed, 22 Apr 2015 09:35:19: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (639 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2015 09:35:21: #4 Write output xls file... SRX092435.05_peaks.xls INFO @ Wed, 22 Apr 2015 09:35:21: #4 Write peak in narrowPeak format file... SRX092435.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:35:21: #4 Write summits bed file... SRX092435.05_summits.bed INFO @ Wed, 22 Apr 2015 09:35:21: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1908 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2015 09:35:21: #4 Write output xls file... SRX092435.10_peaks.xls INFO @ Wed, 22 Apr 2015 09:35:21: #4 Write peak in narrowPeak format file... SRX092435.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:35:21: #4 Write summits bed file... SRX092435.10_summits.bed INFO @ Wed, 22 Apr 2015 09:35:21: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1198 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。