Job ID = 2162400 sra ファイルのダウンロード中... Completed: 1107768K bytes transferred in 12 seconds (720866K 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 12759 0 12759 0 0 23232 0 --:--:-- --:--:-- --:--:-- 35540 100 36537 0 36537 0 0 49446 0 --:--:-- --:--:-- --:--:-- 66673 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 52414696 spots for /home/okishinya/chipatlas/results/dm3/SRX084582/SRR315122.sra Written 52414696 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: 00:12:44 52414696 reads; of these: 52414696 (100.00%) were unpaired; of these: 18520050 (35.33%) aligned 0 times 23824989 (45.45%) aligned exactly 1 time 10069657 (19.21%) aligned >1 times 64.67% overall alignment rate Time searching: 00:12:45 Overall time: 00:12:45 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 12 files... [bam_rmdupse_core] 21423825 / 33894646 = 0.6321 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 14:07:09: # Command line: callpeak -t SRX084582.bam -f BAM -g dm -n SRX084582.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX084582.10 # format = BAM # ChIP-seq file = ['SRX084582.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 14:07:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:07:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:07:09: # Command line: callpeak -t SRX084582.bam -f BAM -g dm -n SRX084582.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX084582.20 # format = BAM # ChIP-seq file = ['SRX084582.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 14:07:09: # Command line: callpeak -t SRX084582.bam -f BAM -g dm -n SRX084582.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX084582.05 # format = BAM # ChIP-seq file = ['SRX084582.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 14:07:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:07:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:07:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:07:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:07:15: 1000000 INFO @ Tue, 21 Apr 2015 14:07:15: 1000000 INFO @ Tue, 21 Apr 2015 14:07:15: 1000000 INFO @ Tue, 21 Apr 2015 14:07:21: 2000000 INFO @ Tue, 21 Apr 2015 14:07:22: 2000000 INFO @ Tue, 21 Apr 2015 14:07:22: 2000000 INFO @ Tue, 21 Apr 2015 14:07:26: 3000000 INFO @ Tue, 21 Apr 2015 14:07:28: 3000000 INFO @ Tue, 21 Apr 2015 14:07:28: 3000000 INFO @ Tue, 21 Apr 2015 14:07:32: 4000000 INFO @ Tue, 21 Apr 2015 14:07:34: 4000000 INFO @ Tue, 21 Apr 2015 14:07:34: 4000000 INFO @ Tue, 21 Apr 2015 14:07:37: 5000000 INFO @ Tue, 21 Apr 2015 14:07:41: 5000000 INFO @ Tue, 21 Apr 2015 14:07:41: 5000000 INFO @ Tue, 21 Apr 2015 14:07:43: 6000000 INFO @ Tue, 21 Apr 2015 14:07:47: 6000000 INFO @ Tue, 21 Apr 2015 14:07:47: 6000000 INFO @ Tue, 21 Apr 2015 14:07:49: 7000000 INFO @ Tue, 21 Apr 2015 14:07:53: 7000000 INFO @ Tue, 21 Apr 2015 14:07:53: 7000000 INFO @ Tue, 21 Apr 2015 14:07:54: 8000000 INFO @ Tue, 21 Apr 2015 14:07:59: 8000000 INFO @ Tue, 21 Apr 2015 14:07:59: 8000000 INFO @ Tue, 21 Apr 2015 14:08:00: 9000000 INFO @ Tue, 21 Apr 2015 14:08:05: 10000000 INFO @ Tue, 21 Apr 2015 14:08:06: 9000000 INFO @ Tue, 21 Apr 2015 14:08:06: 9000000 INFO @ Tue, 21 Apr 2015 14:08:11: 11000000 INFO @ Tue, 21 Apr 2015 14:08:12: 10000000 INFO @ Tue, 21 Apr 2015 14:08:12: 10000000 INFO @ Tue, 21 Apr 2015 14:08:17: 12000000 INFO @ Tue, 21 Apr 2015 14:08:18: 11000000 INFO @ Tue, 21 Apr 2015 14:08:18: 11000000 INFO @ Tue, 21 Apr 2015 14:08:19: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:08:19: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:08:19: #1 total tags in treatment: 12470821 INFO @ Tue, 21 Apr 2015 14:08:19: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:08:19: #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 14:08:22: #1 tags after filtering in treatment: 12465471 INFO @ Tue, 21 Apr 2015 14:08:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:08:22: #1 finished! INFO @ Tue, 21 Apr 2015 14:08:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:08:24: #2 number of paired peaks: 2845 INFO @ Tue, 21 Apr 2015 14:08:24: start model_add_line... INFO @ Tue, 21 Apr 2015 14:08:24: 12000000 INFO @ Tue, 21 Apr 2015 14:08:24: 12000000 INFO @ Tue, 21 Apr 2015 14:08:28: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:08:28: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:08:28: #1 total tags in treatment: 12470821 INFO @ Tue, 21 Apr 2015 14:08:28: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:08:28: #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 14:08:28: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:08:28: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:08:28: #1 total tags in treatment: 12470821 INFO @ Tue, 21 Apr 2015 14:08:28: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:08:28: #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 14:08:30: #1 tags after filtering in treatment: 12465471 INFO @ Tue, 21 Apr 2015 14:08:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:08:30: #1 finished! INFO @ Tue, 21 Apr 2015 14:08:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:08:30: #1 tags after filtering in treatment: 12465471 INFO @ Tue, 21 Apr 2015 14:08:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:08:30: #1 finished! INFO @ Tue, 21 Apr 2015 14:08:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:08:32: #2 number of paired peaks: 2845 INFO @ Tue, 21 Apr 2015 14:08:32: start model_add_line... INFO @ Tue, 21 Apr 2015 14:08:32: #2 number of paired peaks: 2845 INFO @ Tue, 21 Apr 2015 14:08:32: start model_add_line... INFO @ Tue, 21 Apr 2015 14:08:49: start X-correlation... INFO @ Tue, 21 Apr 2015 14:08:49: end of X-cor INFO @ Tue, 21 Apr 2015 14:08:49: #2 finished! INFO @ Tue, 21 Apr 2015 14:08:49: #2 predicted fragment length is 55 bps INFO @ Tue, 21 Apr 2015 14:08:49: #2 alternative fragment length(s) may be 4,55 bps INFO @ Tue, 21 Apr 2015 14:08:49: #2.2 Generate R script for model : SRX084582.10_model.r WARNING @ Tue, 21 Apr 2015 14:08:49: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:08:49: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Tue, 21 Apr 2015 14:08:49: #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 14:08:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:08:57: start X-correlation... INFO @ Tue, 21 Apr 2015 14:08:57: end of X-cor INFO @ Tue, 21 Apr 2015 14:08:57: #2 finished! INFO @ Tue, 21 Apr 2015 14:08:57: #2 predicted fragment length is 55 bps INFO @ Tue, 21 Apr 2015 14:08:57: #2 alternative fragment length(s) may be 4,55 bps INFO @ Tue, 21 Apr 2015 14:08:57: #2.2 Generate R script for model : SRX084582.05_model.r WARNING @ Tue, 21 Apr 2015 14:08:57: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:08:57: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Tue, 21 Apr 2015 14:08:57: #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 14:08:57: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:08:58: start X-correlation... INFO @ Tue, 21 Apr 2015 14:08:58: end of X-cor INFO @ Tue, 21 Apr 2015 14:08:58: #2 finished! INFO @ Tue, 21 Apr 2015 14:08:58: #2 predicted fragment length is 55 bps INFO @ Tue, 21 Apr 2015 14:08:58: #2 alternative fragment length(s) may be 4,55 bps INFO @ Tue, 21 Apr 2015 14:08:58: #2.2 Generate R script for model : SRX084582.20_model.r WARNING @ Tue, 21 Apr 2015 14:08:58: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:08:58: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Tue, 21 Apr 2015 14:08:58: #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 14:08:58: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:08:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:09:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:10:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:10:04: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:10:50: #4 Write output xls file... SRX084582.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:10:50: #4 Write peak in narrowPeak format file... SRX084582.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:10:51: #4 Write summits bed file... SRX084582.10_summits.bed INFO @ Tue, 21 Apr 2015 14:10:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7823 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:10:51: #4 Write output xls file... SRX084582.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:10:51: #4 Write peak in narrowPeak format file... SRX084582.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:10:51: #4 Write summits bed file... SRX084582.20_summits.bed INFO @ Tue, 21 Apr 2015 14:10:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3821 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:11:02: #4 Write output xls file... SRX084582.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:11:02: #4 Write peak in narrowPeak format file... SRX084582.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:11:03: #4 Write summits bed file... SRX084582.05_summits.bed INFO @ Tue, 21 Apr 2015 14:11:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13802 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。