Job ID = 2162433 sra ファイルのダウンロード中... Completed: 461550K bytes transferred in 6 seconds (602200K bits/sec), in 1 file, 2 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 16338 0 16338 0 0 22869 0 --:--:-- --:--:-- --:--:-- 31179 100 38285 0 38285 0 0 53525 0 --:--:-- --:--:-- --:--:-- 72923 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 11889914 spots for /home/okishinya/chipatlas/results/dm3/SRX099637/SRR350627.sra Written 11889914 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:03:29 11889914 reads; of these: 11889914 (100.00%) were unpaired; of these: 6643994 (55.88%) aligned 0 times 3096055 (26.04%) aligned exactly 1 time 2149865 (18.08%) aligned >1 times 44.12% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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_rmdupse_core] 2380052 / 5245920 = 0.4537 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 14:01:41: # Command line: callpeak -t SRX099637.bam -f BAM -g dm -n SRX099637.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX099637.05 # format = BAM # ChIP-seq file = ['SRX099637.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 14:01:41: # Command line: callpeak -t SRX099637.bam -f BAM -g dm -n SRX099637.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX099637.10 # format = BAM # ChIP-seq file = ['SRX099637.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 14:01:41: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:41: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:41: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:41: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:41: # Command line: callpeak -t SRX099637.bam -f BAM -g dm -n SRX099637.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX099637.20 # format = BAM # ChIP-seq file = ['SRX099637.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 14:01:41: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:01:41: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:01:48: 1000000 INFO @ Tue, 21 Apr 2015 14:01:48: 1000000 INFO @ Tue, 21 Apr 2015 14:01:49: 1000000 INFO @ Tue, 21 Apr 2015 14:01:54: 2000000 INFO @ Tue, 21 Apr 2015 14:01:54: 2000000 INFO @ Tue, 21 Apr 2015 14:01:56: 2000000 INFO @ Tue, 21 Apr 2015 14:01:59: #1 tag size is determined as 55 bps INFO @ Tue, 21 Apr 2015 14:01:59: #1 tag size = 55 INFO @ Tue, 21 Apr 2015 14:01:59: #1 total tags in treatment: 2865868 INFO @ Tue, 21 Apr 2015 14:01:59: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:01:59: #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 14:02:00: #1 tag size is determined as 55 bps INFO @ Tue, 21 Apr 2015 14:02:00: #1 tag size = 55 INFO @ Tue, 21 Apr 2015 14:02:00: #1 total tags in treatment: 2865868 INFO @ Tue, 21 Apr 2015 14:02:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:02:00: #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 14:02:00: #1 tags after filtering in treatment: 2864676 INFO @ Tue, 21 Apr 2015 14:02:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:02:00: #1 finished! INFO @ Tue, 21 Apr 2015 14:02:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:02:00: #1 tags after filtering in treatment: 2864676 INFO @ Tue, 21 Apr 2015 14:02:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:02:00: #1 finished! INFO @ Tue, 21 Apr 2015 14:02:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:02:01: #2 number of paired peaks: 2740 INFO @ Tue, 21 Apr 2015 14:02:01: start model_add_line... INFO @ Tue, 21 Apr 2015 14:02:01: #2 number of paired peaks: 2740 INFO @ Tue, 21 Apr 2015 14:02:01: start model_add_line... INFO @ Tue, 21 Apr 2015 14:02:01: #1 tag size is determined as 55 bps INFO @ Tue, 21 Apr 2015 14:02:01: #1 tag size = 55 INFO @ Tue, 21 Apr 2015 14:02:01: #1 total tags in treatment: 2865868 INFO @ Tue, 21 Apr 2015 14:02:01: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:02:01: #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 14:02:02: #1 tags after filtering in treatment: 2864676 INFO @ Tue, 21 Apr 2015 14:02:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:02:02: #1 finished! INFO @ Tue, 21 Apr 2015 14:02:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:02:03: #2 number of paired peaks: 2740 INFO @ Tue, 21 Apr 2015 14:02:03: start model_add_line... INFO @ Tue, 21 Apr 2015 14:02:08: start X-correlation... INFO @ Tue, 21 Apr 2015 14:02:08: end of X-cor INFO @ Tue, 21 Apr 2015 14:02:08: #2 finished! INFO @ Tue, 21 Apr 2015 14:02:08: #2 predicted fragment length is 65 bps INFO @ Tue, 21 Apr 2015 14:02:08: #2 alternative fragment length(s) may be 65 bps INFO @ Tue, 21 Apr 2015 14:02:08: #2.2 Generate R script for model : SRX099637.05_model.r WARNING @ Tue, 21 Apr 2015 14:02:08: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:02:08: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Tue, 21 Apr 2015 14:02:08: #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 14:02:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:02:08: start X-correlation... INFO @ Tue, 21 Apr 2015 14:02:08: end of X-cor INFO @ Tue, 21 Apr 2015 14:02:08: #2 finished! INFO @ Tue, 21 Apr 2015 14:02:08: #2 predicted fragment length is 65 bps INFO @ Tue, 21 Apr 2015 14:02:08: #2 alternative fragment length(s) may be 65 bps INFO @ Tue, 21 Apr 2015 14:02:08: #2.2 Generate R script for model : SRX099637.10_model.r WARNING @ Tue, 21 Apr 2015 14:02:08: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:02:08: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Tue, 21 Apr 2015 14:02:08: #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 14:02:08: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:02:09: start X-correlation... INFO @ Tue, 21 Apr 2015 14:02:09: end of X-cor INFO @ Tue, 21 Apr 2015 14:02:09: #2 finished! INFO @ Tue, 21 Apr 2015 14:02:09: #2 predicted fragment length is 65 bps INFO @ Tue, 21 Apr 2015 14:02:09: #2 alternative fragment length(s) may be 65 bps INFO @ Tue, 21 Apr 2015 14:02:09: #2.2 Generate R script for model : SRX099637.20_model.r WARNING @ Tue, 21 Apr 2015 14:02:09: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:02:09: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Tue, 21 Apr 2015 14:02:09: #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 14:02:09: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:02:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:02:24: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:02:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:02:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:02:37: #4 Write output xls file... SRX099637.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:02:37: #4 Write peak in narrowPeak format file... SRX099637.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:02:37: #4 Write summits bed file... SRX099637.10_summits.bed INFO @ Tue, 21 Apr 2015 14:02:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2051 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:02:38: #4 Write output xls file... SRX099637.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:02:38: #4 Write peak in narrowPeak format file... SRX099637.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:02:38: #4 Write summits bed file... SRX099637.20_summits.bed INFO @ Tue, 21 Apr 2015 14:02:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (974 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:02:38: #4 Write output xls file... SRX099637.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:02:38: #4 Write peak in narrowPeak format file... SRX099637.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:02:38: #4 Write summits bed file... SRX099637.05_summits.bed INFO @ Tue, 21 Apr 2015 14:02:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3714 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。