Job ID = 2161583 sra ファイルのダウンロード中... Completed: 671740K bytes transferred in 9 seconds (569539K 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 --:--:-- --:--:-- --:--:-- 0 108 1088 0 1088 0 0 1938 0 --:--:-- --:--:-- --:--:-- 2940 100 44460 0 44460 0 0 47276 0 --:--:-- --:--:-- --:--:-- 59359 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 10647855 spots for /home/okishinya/chipatlas/results/dm3/SRX032120/SRR073942.sra Written 10647855 spots total Written 16843352 spots for /home/okishinya/chipatlas/results/dm3/SRX032120/SRR073943.sra Written 16843352 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:22 27491207 reads; of these: 27491207 (100.00%) were unpaired; of these: 2188534 (7.96%) aligned 0 times 20359532 (74.06%) aligned exactly 1 time 4943141 (17.98%) aligned >1 times 92.04% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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] 15378799 / 25302673 = 0.6078 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 13:11:02: # Command line: callpeak -t SRX032120.bam -f BAM -g dm -n SRX032120.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX032120.05 # format = BAM # ChIP-seq file = ['SRX032120.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 13:11:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:11:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:11:02: # Command line: callpeak -t SRX032120.bam -f BAM -g dm -n SRX032120.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX032120.20 # format = BAM # ChIP-seq file = ['SRX032120.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 13:11:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:11:02: # Command line: callpeak -t SRX032120.bam -f BAM -g dm -n SRX032120.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX032120.10 # format = BAM # ChIP-seq file = ['SRX032120.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 13:11:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:11:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:11:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:11:08: 1000000 INFO @ Tue, 21 Apr 2015 13:11:08: 1000000 INFO @ Tue, 21 Apr 2015 13:11:08: 1000000 INFO @ Tue, 21 Apr 2015 13:11:14: 2000000 INFO @ Tue, 21 Apr 2015 13:11:14: 2000000 INFO @ Tue, 21 Apr 2015 13:11:14: 2000000 INFO @ Tue, 21 Apr 2015 13:11:20: 3000000 INFO @ Tue, 21 Apr 2015 13:11:20: 3000000 INFO @ Tue, 21 Apr 2015 13:11:20: 3000000 INFO @ Tue, 21 Apr 2015 13:11:26: 4000000 INFO @ Tue, 21 Apr 2015 13:11:26: 4000000 INFO @ Tue, 21 Apr 2015 13:11:26: 4000000 INFO @ Tue, 21 Apr 2015 13:11:32: 5000000 INFO @ Tue, 21 Apr 2015 13:11:32: 5000000 INFO @ Tue, 21 Apr 2015 13:11:32: 5000000 INFO @ Tue, 21 Apr 2015 13:11:38: 6000000 INFO @ Tue, 21 Apr 2015 13:11:38: 6000000 INFO @ Tue, 21 Apr 2015 13:11:38: 6000000 INFO @ Tue, 21 Apr 2015 13:11:44: 7000000 INFO @ Tue, 21 Apr 2015 13:11:44: 7000000 INFO @ Tue, 21 Apr 2015 13:11:44: 7000000 INFO @ Tue, 21 Apr 2015 13:11:50: 8000000 INFO @ Tue, 21 Apr 2015 13:11:50: 8000000 INFO @ Tue, 21 Apr 2015 13:11:50: 8000000 INFO @ Tue, 21 Apr 2015 13:11:56: 9000000 INFO @ Tue, 21 Apr 2015 13:11:56: 9000000 INFO @ Tue, 21 Apr 2015 13:11:56: 9000000 INFO @ Tue, 21 Apr 2015 13:12:02: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:12:02: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:12:02: #1 total tags in treatment: 9923874 INFO @ Tue, 21 Apr 2015 13:12:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:12:02: #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 13:12:02: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:12:02: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:12:02: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:12:02: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:12:02: #1 total tags in treatment: 9923874 INFO @ Tue, 21 Apr 2015 13:12:02: #1 total tags in treatment: 9923874 INFO @ Tue, 21 Apr 2015 13:12:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:12:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:12:02: #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 13:12:02: #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 13:12:04: #1 tags after filtering in treatment: 9923100 INFO @ Tue, 21 Apr 2015 13:12:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:12:04: #1 finished! INFO @ Tue, 21 Apr 2015 13:12:04: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:12:04: #1 tags after filtering in treatment: 9923100 INFO @ Tue, 21 Apr 2015 13:12:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:12:04: #1 finished! INFO @ Tue, 21 Apr 2015 13:12:04: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:12:04: #1 tags after filtering in treatment: 9923100 INFO @ Tue, 21 Apr 2015 13:12:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:12:04: #1 finished! INFO @ Tue, 21 Apr 2015 13:12:04: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:12:05: #2 number of paired peaks: 403 WARNING @ Tue, 21 Apr 2015 13:12:05: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 21 Apr 2015 13:12:05: start model_add_line... INFO @ Tue, 21 Apr 2015 13:12:05: #2 number of paired peaks: 403 WARNING @ Tue, 21 Apr 2015 13:12:05: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 21 Apr 2015 13:12:05: start model_add_line... INFO @ Tue, 21 Apr 2015 13:12:05: #2 number of paired peaks: 403 WARNING @ Tue, 21 Apr 2015 13:12:05: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Tue, 21 Apr 2015 13:12:05: start model_add_line... INFO @ Tue, 21 Apr 2015 13:12:08: start X-correlation... INFO @ Tue, 21 Apr 2015 13:12:08: end of X-cor INFO @ Tue, 21 Apr 2015 13:12:08: #2 finished! INFO @ Tue, 21 Apr 2015 13:12:08: #2 predicted fragment length is 53 bps INFO @ Tue, 21 Apr 2015 13:12:08: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 21 Apr 2015 13:12:08: #2.2 Generate R script for model : SRX032120.05_model.r INFO @ Tue, 21 Apr 2015 13:12:08: start X-correlation... INFO @ Tue, 21 Apr 2015 13:12:08: end of X-cor INFO @ Tue, 21 Apr 2015 13:12:08: #2 finished! INFO @ Tue, 21 Apr 2015 13:12:08: #2 predicted fragment length is 53 bps INFO @ Tue, 21 Apr 2015 13:12:08: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 21 Apr 2015 13:12:08: #2.2 Generate R script for model : SRX032120.20_model.r WARNING @ Tue, 21 Apr 2015 13:12:08: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:12:08: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 21 Apr 2015 13:12:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:12:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:12:08: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 21 Apr 2015 13:12:08: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:12:08: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 21 Apr 2015 13:12:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:12:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:12:08: start X-correlation... INFO @ Tue, 21 Apr 2015 13:12:08: end of X-cor INFO @ Tue, 21 Apr 2015 13:12:08: #2 finished! INFO @ Tue, 21 Apr 2015 13:12:08: #2 predicted fragment length is 53 bps INFO @ Tue, 21 Apr 2015 13:12:08: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 21 Apr 2015 13:12:08: #2.2 Generate R script for model : SRX032120.10_model.r WARNING @ Tue, 21 Apr 2015 13:12:08: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:12:08: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 21 Apr 2015 13:12:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:12:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:13:02: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:13:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:13:04: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:13:41: #4 Write output xls file... SRX032120.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:13:41: #4 Write peak in narrowPeak format file... SRX032120.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:13:41: #4 Write summits bed file... SRX032120.20_summits.bed INFO @ Tue, 21 Apr 2015 13:13:41: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (572 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:13:43: #4 Write output xls file... SRX032120.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:13:43: #4 Write peak in narrowPeak format file... SRX032120.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:13:43: #4 Write summits bed file... SRX032120.10_summits.bed INFO @ Tue, 21 Apr 2015 13:13:43: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (861 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:13:44: #4 Write output xls file... SRX032120.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:13:44: #4 Write peak in narrowPeak format file... SRX032120.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:13:44: #4 Write summits bed file... SRX032120.05_summits.bed INFO @ Tue, 21 Apr 2015 13:13:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1352 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。