Job ID = 9041023 sra ファイルのダウンロード中... Completed: 813111K bytes transferred in 8 seconds (744806K 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 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1059 0 --:--:-- 0:00:07 --:--:-- 10540 100 23765 0 23765 0 0 2948 0 --:--:-- 0:00:08 --:--:-- 15263 100 53413 0 53413 0 0 5896 0 --:--:-- 0:00:09 --:--:-- 20905 100 131k 0 131k 0 0 13395 0 --:--:-- 0:00:10 --:--:-- 37916 100 193k 0 193k 0 0 18438 0 --:--:-- 0:00:10 --:--:-- 46888 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 11161947 spots for /home/okishinya/chipatlas/results/dm3/SRX1158171/SRR2173470.sra Written 11161947 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:31 11161947 reads; of these: 11161947 (100.00%) were unpaired; of these: 6135570 (54.97%) aligned 0 times 3712498 (33.26%) aligned exactly 1 time 1313879 (11.77%) aligned >1 times 45.03% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 1642714 / 5026377 = 0.3268 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 @ Mon, 05 Jun 2017 00:23:20: # Command line: callpeak -t SRX1158171.bam -f BAM -g dm -n SRX1158171.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1158171.05 # format = BAM # ChIP-seq file = ['SRX1158171.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 @ Mon, 05 Jun 2017 00:23:20: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:23:20: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:23:20: # Command line: callpeak -t SRX1158171.bam -f BAM -g dm -n SRX1158171.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1158171.20 # format = BAM # ChIP-seq file = ['SRX1158171.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 @ Mon, 05 Jun 2017 00:23:20: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:23:20: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:23:20: # Command line: callpeak -t SRX1158171.bam -f BAM -g dm -n SRX1158171.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1158171.10 # format = BAM # ChIP-seq file = ['SRX1158171.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 @ Mon, 05 Jun 2017 00:23:20: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:23:20: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:23:27: 1000000 INFO @ Mon, 05 Jun 2017 00:23:27: 1000000 INFO @ Mon, 05 Jun 2017 00:23:27: 1000000 INFO @ Mon, 05 Jun 2017 00:23:35: 2000000 INFO @ Mon, 05 Jun 2017 00:23:35: 2000000 INFO @ Mon, 05 Jun 2017 00:23:35: 2000000 INFO @ Mon, 05 Jun 2017 00:23:42: 3000000 INFO @ Mon, 05 Jun 2017 00:23:42: 3000000 INFO @ Mon, 05 Jun 2017 00:23:42: 3000000 INFO @ Mon, 05 Jun 2017 00:23:45: #1 tag size is determined as 101 bps INFO @ Mon, 05 Jun 2017 00:23:45: #1 tag size is determined as 101 bps INFO @ Mon, 05 Jun 2017 00:23:45: #1 tag size = 101 INFO @ Mon, 05 Jun 2017 00:23:45: #1 tag size = 101 INFO @ Mon, 05 Jun 2017 00:23:45: #1 total tags in treatment: 3383663 INFO @ Mon, 05 Jun 2017 00:23:45: #1 total tags in treatment: 3383663 INFO @ Mon, 05 Jun 2017 00:23:45: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:23:45: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:23:45: #1 tag size is determined as 101 bps INFO @ Mon, 05 Jun 2017 00:23:45: #1 tag size = 101 INFO @ Mon, 05 Jun 2017 00:23:45: #1 total tags in treatment: 3383663 INFO @ Mon, 05 Jun 2017 00:23:45: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:23:45: #1 tags after filtering in treatment: 3380148 INFO @ Mon, 05 Jun 2017 00:23:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:23:45: #1 finished! INFO @ Mon, 05 Jun 2017 00:23:45: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:23:45: #1 tags after filtering in treatment: 3380148 INFO @ Mon, 05 Jun 2017 00:23:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:23:45: #1 finished! INFO @ Mon, 05 Jun 2017 00:23:45: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:23:46: #1 tags after filtering in treatment: 3380148 INFO @ Mon, 05 Jun 2017 00:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:23:46: #1 finished! INFO @ Mon, 05 Jun 2017 00:23:46: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:23:47: #2 number of paired peaks: 5601 INFO @ Mon, 05 Jun 2017 00:23:47: start model_add_line... INFO @ Mon, 05 Jun 2017 00:23:47: #2 number of paired peaks: 5601 INFO @ Mon, 05 Jun 2017 00:23:47: start model_add_line... INFO @ Mon, 05 Jun 2017 00:23:47: #2 number of paired peaks: 5601 INFO @ Mon, 05 Jun 2017 00:23:47: start model_add_line... INFO @ Mon, 05 Jun 2017 00:23:59: start X-correlation... INFO @ Mon, 05 Jun 2017 00:23:59: end of X-cor INFO @ Mon, 05 Jun 2017 00:23:59: #2 finished! INFO @ Mon, 05 Jun 2017 00:23:59: #2 predicted fragment length is 162 bps INFO @ Mon, 05 Jun 2017 00:23:59: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 05 Jun 2017 00:23:59: #2.2 Generate R script for model : SRX1158171.20_model.r WARNING @ Mon, 05 Jun 2017 00:23:59: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:23:59: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Mon, 05 Jun 2017 00:23:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:23:59: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:23:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:23:59: start X-correlation... INFO @ Mon, 05 Jun 2017 00:23:59: end of X-cor INFO @ Mon, 05 Jun 2017 00:23:59: #2 finished! INFO @ Mon, 05 Jun 2017 00:23:59: #2 predicted fragment length is 162 bps INFO @ Mon, 05 Jun 2017 00:23:59: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 05 Jun 2017 00:23:59: #2.2 Generate R script for model : SRX1158171.05_model.r WARNING @ Mon, 05 Jun 2017 00:23:59: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:23:59: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Mon, 05 Jun 2017 00:23:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:23:59: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:23:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:24:00: start X-correlation... INFO @ Mon, 05 Jun 2017 00:24:00: end of X-cor INFO @ Mon, 05 Jun 2017 00:24:00: #2 finished! INFO @ Mon, 05 Jun 2017 00:24:00: #2 predicted fragment length is 162 bps INFO @ Mon, 05 Jun 2017 00:24:00: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 05 Jun 2017 00:24:00: #2.2 Generate R script for model : SRX1158171.10_model.r WARNING @ Mon, 05 Jun 2017 00:24:00: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:24:00: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Mon, 05 Jun 2017 00:24:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 00:24:00: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:24:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:24:20: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:24:20: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:24:21: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:24:37: #4 Write output xls file... SRX1158171.20_peaks.xls INFO @ Mon, 05 Jun 2017 00:24:37: #4 Write peak in narrowPeak format file... SRX1158171.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:24:37: #4 Write summits bed file... SRX1158171.20_summits.bed INFO @ Mon, 05 Jun 2017 00:24:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1298 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:24:38: #4 Write output xls file... SRX1158171.10_peaks.xls INFO @ Mon, 05 Jun 2017 00:24:38: #4 Write peak in narrowPeak format file... SRX1158171.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:24:39: #4 Write summits bed file... SRX1158171.10_summits.bed INFO @ Mon, 05 Jun 2017 00:24:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3890 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:24:40: #4 Write output xls file... SRX1158171.05_peaks.xls INFO @ Mon, 05 Jun 2017 00:24:40: #4 Write peak in narrowPeak format file... SRX1158171.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:24:40: #4 Write summits bed file... SRX1158171.05_summits.bed INFO @ Mon, 05 Jun 2017 00:24:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6890 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。