Job ID = 2161279 sra ファイルのダウンロード中... Completed: 635643K bytes transferred in 8 seconds (582010K 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 15665 0 15665 0 0 16346 0 --:--:-- --:--:-- --:--:-- 20397 100 34375 0 34375 0 0 35839 0 --:--:-- --:--:-- --:--:-- 44759 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 12932448 spots for /home/okishinya/chipatlas/results/dm3/SRX016145/SRR034699.sra Written 12932448 spots total Written 14232213 spots for /home/okishinya/chipatlas/results/dm3/SRX016145/SRR034698.sra Written 14232213 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: 00:07:09 27164661 reads; of these: 27164661 (100.00%) were unpaired; of these: 495994 (1.83%) aligned 0 times 22697553 (83.56%) aligned exactly 1 time 3971114 (14.62%) aligned >1 times 98.17% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 11990055 / 26668667 = 0.4496 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 @ Tue, 21 Apr 2015 12:25:09: # Command line: callpeak -t SRX016145.bam -f BAM -g dm -n SRX016145.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016145.05 # format = BAM # ChIP-seq file = ['SRX016145.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:25:09: # Command line: callpeak -t SRX016145.bam -f BAM -g dm -n SRX016145.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016145.20 # format = BAM # ChIP-seq file = ['SRX016145.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:25:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:25:09: # Command line: callpeak -t SRX016145.bam -f BAM -g dm -n SRX016145.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016145.10 # format = BAM # ChIP-seq file = ['SRX016145.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:25:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:25:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:25:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:25:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:25:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:25:15: 1000000 INFO @ Tue, 21 Apr 2015 12:25:15: 1000000 INFO @ Tue, 21 Apr 2015 12:25:15: 1000000 INFO @ Tue, 21 Apr 2015 12:25:20: 2000000 INFO @ Tue, 21 Apr 2015 12:25:22: 2000000 INFO @ Tue, 21 Apr 2015 12:25:22: 2000000 INFO @ Tue, 21 Apr 2015 12:25:26: 3000000 INFO @ Tue, 21 Apr 2015 12:25:28: 3000000 INFO @ Tue, 21 Apr 2015 12:25:28: 3000000 INFO @ Tue, 21 Apr 2015 12:25:31: 4000000 INFO @ Tue, 21 Apr 2015 12:25:34: 4000000 INFO @ Tue, 21 Apr 2015 12:25:34: 4000000 INFO @ Tue, 21 Apr 2015 12:25:37: 5000000 INFO @ Tue, 21 Apr 2015 12:25:40: 5000000 INFO @ Tue, 21 Apr 2015 12:25:40: 5000000 INFO @ Tue, 21 Apr 2015 12:25:43: 6000000 INFO @ Tue, 21 Apr 2015 12:25:46: 6000000 INFO @ Tue, 21 Apr 2015 12:25:46: 6000000 INFO @ Tue, 21 Apr 2015 12:25:48: 7000000 INFO @ Tue, 21 Apr 2015 12:25:52: 7000000 INFO @ Tue, 21 Apr 2015 12:25:53: 7000000 INFO @ Tue, 21 Apr 2015 12:25:54: 8000000 INFO @ Tue, 21 Apr 2015 12:25:58: 8000000 INFO @ Tue, 21 Apr 2015 12:25:59: 8000000 INFO @ Tue, 21 Apr 2015 12:25:59: 9000000 INFO @ Tue, 21 Apr 2015 12:26:04: 9000000 INFO @ Tue, 21 Apr 2015 12:26:05: 10000000 INFO @ Tue, 21 Apr 2015 12:26:05: 9000000 INFO @ Tue, 21 Apr 2015 12:26:10: 10000000 INFO @ Tue, 21 Apr 2015 12:26:10: 11000000 INFO @ Tue, 21 Apr 2015 12:26:11: 10000000 INFO @ Tue, 21 Apr 2015 12:26:16: 11000000 INFO @ Tue, 21 Apr 2015 12:26:16: 12000000 INFO @ Tue, 21 Apr 2015 12:26:18: 11000000 INFO @ Tue, 21 Apr 2015 12:26:22: 13000000 INFO @ Tue, 21 Apr 2015 12:26:22: 12000000 INFO @ Tue, 21 Apr 2015 12:26:24: 12000000 INFO @ Tue, 21 Apr 2015 12:26:27: 14000000 INFO @ Tue, 21 Apr 2015 12:26:29: 13000000 INFO @ Tue, 21 Apr 2015 12:26:30: 13000000 INFO @ Tue, 21 Apr 2015 12:26:31: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:26:31: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:26:31: #1 total tags in treatment: 14678612 INFO @ Tue, 21 Apr 2015 12:26:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:26:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:26:34: #1 tags after filtering in treatment: 14677095 INFO @ Tue, 21 Apr 2015 12:26:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:26:34: #1 finished! INFO @ Tue, 21 Apr 2015 12:26:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:26:35: 14000000 INFO @ Tue, 21 Apr 2015 12:26:36: #2 number of paired peaks: 340 WARNING @ Tue, 21 Apr 2015 12:26:36: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Tue, 21 Apr 2015 12:26:36: start model_add_line... INFO @ Tue, 21 Apr 2015 12:26:36: 14000000 INFO @ Tue, 21 Apr 2015 12:26:39: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:26:39: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:26:39: #1 total tags in treatment: 14678612 INFO @ Tue, 21 Apr 2015 12:26:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:26:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:26:39: start X-correlation... INFO @ Tue, 21 Apr 2015 12:26:39: end of X-cor INFO @ Tue, 21 Apr 2015 12:26:39: #2 finished! INFO @ Tue, 21 Apr 2015 12:26:39: #2 predicted fragment length is 193 bps INFO @ Tue, 21 Apr 2015 12:26:39: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 21 Apr 2015 12:26:39: #2.2 Generate R script for model : SRX016145.05_model.r INFO @ Tue, 21 Apr 2015 12:26:39: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:26:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:26:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:26:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:26:41: #1 total tags in treatment: 14678612 INFO @ Tue, 21 Apr 2015 12:26:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:26:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:26:42: #1 tags after filtering in treatment: 14677095 INFO @ Tue, 21 Apr 2015 12:26:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:26:42: #1 finished! INFO @ Tue, 21 Apr 2015 12:26:42: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:26:43: #1 tags after filtering in treatment: 14677095 INFO @ Tue, 21 Apr 2015 12:26:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:26:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:26:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:26:44: #2 number of paired peaks: 340 WARNING @ Tue, 21 Apr 2015 12:26:44: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Tue, 21 Apr 2015 12:26:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:26:46: #2 number of paired peaks: 340 WARNING @ Tue, 21 Apr 2015 12:26:46: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Tue, 21 Apr 2015 12:26:46: start model_add_line... INFO @ Tue, 21 Apr 2015 12:26:48: start X-correlation... INFO @ Tue, 21 Apr 2015 12:26:48: end of X-cor INFO @ Tue, 21 Apr 2015 12:26:48: #2 finished! INFO @ Tue, 21 Apr 2015 12:26:48: #2 predicted fragment length is 193 bps INFO @ Tue, 21 Apr 2015 12:26:48: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 21 Apr 2015 12:26:48: #2.2 Generate R script for model : SRX016145.10_model.r INFO @ Tue, 21 Apr 2015 12:26:48: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:26:49: start X-correlation... INFO @ Tue, 21 Apr 2015 12:26:49: end of X-cor INFO @ Tue, 21 Apr 2015 12:26:49: #2 finished! INFO @ Tue, 21 Apr 2015 12:26:49: #2 predicted fragment length is 193 bps INFO @ Tue, 21 Apr 2015 12:26:49: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 21 Apr 2015 12:26:49: #2.2 Generate R script for model : SRX016145.20_model.r INFO @ Tue, 21 Apr 2015 12:26:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:26:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:27:58: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:28:09: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:28:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:29:05: #4 Write output xls file... SRX016145.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:29:05: #4 Write output xls file... SRX016145.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:29:06: #4 Write peak in narrowPeak format file... SRX016145.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:29:06: #4 Write summits bed file... SRX016145.20_summits.bed INFO @ Tue, 21 Apr 2015 12:29:06: Done! INFO @ Tue, 21 Apr 2015 12:29:06: #4 Write peak in narrowPeak format file... SRX016145.05_peaks.narrowPeak pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1264 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:29:06: #4 Write summits bed file... SRX016145.05_summits.bed INFO @ Tue, 21 Apr 2015 12:29:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6198 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:29:11: #4 Write output xls file... SRX016145.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:29:11: #4 Write peak in narrowPeak format file... SRX016145.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:29:11: #4 Write summits bed file... SRX016145.10_summits.bed INFO @ Tue, 21 Apr 2015 12:29:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2769 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。