Job ID = 9029237 sra ファイルのダウンロード中... Completed: 1226518K bytes transferred in 15 seconds (628059K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 20109 0 20109 0 0 2651 0 --:--:-- 0:00:07 --:--:-- 16442 100 67893 0 67893 0 0 7761 0 --:--:-- 0:00:08 --:--:-- 28466 100 122k 0 122k 0 0 13138 0 --:--:-- 0:00:09 --:--:-- 39492 100 196k 0 196k 0 0 19012 0 --:--:-- 0:00:10 --:--:-- 47737 100 198k 0 198k 0 0 19187 0 --:--:-- 0:00:10 --:--:-- 53113 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 49969825 spots for /home/okishinya/chipatlas/results/dm3/SRX1433377/SRR2919842.sra Written 49969825 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: 00:15:01 49969825 reads; of these: 49969825 (100.00%) were unpaired; of these: 31360242 (62.76%) aligned 0 times 11829683 (23.67%) aligned exactly 1 time 6779900 (13.57%) aligned >1 times 37.24% overall alignment rate Time searching: 00:15:01 Overall time: 00:15:01 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] 10212053 / 18609583 = 0.5488 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 @ Sat, 03 Jun 2017 13:14:52: # Command line: callpeak -t SRX1433377.bam -f BAM -g dm -n SRX1433377.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433377.05 # format = BAM # ChIP-seq file = ['SRX1433377.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 @ Sat, 03 Jun 2017 13:14:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:52: # Command line: callpeak -t SRX1433377.bam -f BAM -g dm -n SRX1433377.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433377.10 # format = BAM # ChIP-seq file = ['SRX1433377.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 @ Sat, 03 Jun 2017 13:14:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:52: # Command line: callpeak -t SRX1433377.bam -f BAM -g dm -n SRX1433377.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433377.20 # format = BAM # ChIP-seq file = ['SRX1433377.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 @ Sat, 03 Jun 2017 13:14:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:14:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:14:58: 1000000 INFO @ Sat, 03 Jun 2017 13:14:58: 1000000 INFO @ Sat, 03 Jun 2017 13:14:58: 1000000 INFO @ Sat, 03 Jun 2017 13:15:04: 2000000 INFO @ Sat, 03 Jun 2017 13:15:05: 2000000 INFO @ Sat, 03 Jun 2017 13:15:05: 2000000 INFO @ Sat, 03 Jun 2017 13:15:10: 3000000 INFO @ Sat, 03 Jun 2017 13:15:11: 3000000 INFO @ Sat, 03 Jun 2017 13:15:11: 3000000 INFO @ Sat, 03 Jun 2017 13:15:16: 4000000 INFO @ Sat, 03 Jun 2017 13:15:18: 4000000 INFO @ Sat, 03 Jun 2017 13:15:18: 4000000 INFO @ Sat, 03 Jun 2017 13:15:23: 5000000 INFO @ Sat, 03 Jun 2017 13:15:25: 5000000 INFO @ Sat, 03 Jun 2017 13:15:25: 5000000 INFO @ Sat, 03 Jun 2017 13:15:29: 6000000 INFO @ Sat, 03 Jun 2017 13:15:32: 6000000 INFO @ Sat, 03 Jun 2017 13:15:32: 6000000 INFO @ Sat, 03 Jun 2017 13:15:35: 7000000 INFO @ Sat, 03 Jun 2017 13:15:39: 7000000 INFO @ Sat, 03 Jun 2017 13:15:39: 7000000 INFO @ Sat, 03 Jun 2017 13:15:41: 8000000 INFO @ Sat, 03 Jun 2017 13:15:44: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:15:44: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:15:44: #1 total tags in treatment: 8397530 INFO @ Sat, 03 Jun 2017 13:15:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:15:45: 8000000 INFO @ Sat, 03 Jun 2017 13:15:45: 8000000 INFO @ Sat, 03 Jun 2017 13:15:45: #1 tags after filtering in treatment: 8395064 INFO @ Sat, 03 Jun 2017 13:15:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:45: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:15:47: #2 number of paired peaks: 1373 INFO @ Sat, 03 Jun 2017 13:15:47: start model_add_line... INFO @ Sat, 03 Jun 2017 13:15:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:15:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:15:48: #1 total tags in treatment: 8397530 INFO @ Sat, 03 Jun 2017 13:15:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:15:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:15:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:15:48: #1 total tags in treatment: 8397530 INFO @ Sat, 03 Jun 2017 13:15:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:15:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:15:49: #1 tags after filtering in treatment: 8395064 INFO @ Sat, 03 Jun 2017 13:15:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:49: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:15:50: #1 tags after filtering in treatment: 8395064 INFO @ Sat, 03 Jun 2017 13:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:15:50: #1 finished! INFO @ Sat, 03 Jun 2017 13:15:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:15:51: #2 number of paired peaks: 1373 INFO @ Sat, 03 Jun 2017 13:15:51: start model_add_line... INFO @ Sat, 03 Jun 2017 13:15:52: #2 number of paired peaks: 1373 INFO @ Sat, 03 Jun 2017 13:15:52: start model_add_line... INFO @ Sat, 03 Jun 2017 13:15:54: start X-correlation... INFO @ Sat, 03 Jun 2017 13:15:54: end of X-cor INFO @ Sat, 03 Jun 2017 13:15:54: #2 finished! INFO @ Sat, 03 Jun 2017 13:15:54: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:15:54: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 03 Jun 2017 13:15:54: #2.2 Generate R script for model : SRX1433377.05_model.r WARNING @ Sat, 03 Jun 2017 13:15:54: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:15:54: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 03 Jun 2017 13:15:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:15:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:15:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:15:58: start X-correlation... INFO @ Sat, 03 Jun 2017 13:15:58: end of X-cor INFO @ Sat, 03 Jun 2017 13:15:58: #2 finished! INFO @ Sat, 03 Jun 2017 13:15:58: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:15:58: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 03 Jun 2017 13:15:58: #2.2 Generate R script for model : SRX1433377.10_model.r WARNING @ Sat, 03 Jun 2017 13:15:58: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:15:58: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 03 Jun 2017 13:15:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:15:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:15:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:15:59: start X-correlation... INFO @ Sat, 03 Jun 2017 13:15:59: end of X-cor INFO @ Sat, 03 Jun 2017 13:15:59: #2 finished! INFO @ Sat, 03 Jun 2017 13:15:59: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 13:15:59: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 03 Jun 2017 13:15:59: #2.2 Generate R script for model : SRX1433377.20_model.r WARNING @ Sat, 03 Jun 2017 13:15:59: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:15:59: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 03 Jun 2017 13:15:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:15:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:15:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:16:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:16:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:16:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:17:19: #4 Write output xls file... SRX1433377.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:19: #4 Write peak in narrowPeak format file... SRX1433377.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:19: #4 Write summits bed file... SRX1433377.05_summits.bed INFO @ Sat, 03 Jun 2017 13:17:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4004 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:17:21: #4 Write output xls file... SRX1433377.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:21: #4 Write peak in narrowPeak format file... SRX1433377.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:21: #4 Write summits bed file... SRX1433377.10_summits.bed INFO @ Sat, 03 Jun 2017 13:17:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2666 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:17:22: #4 Write output xls file... SRX1433377.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:17:22: #4 Write peak in narrowPeak format file... SRX1433377.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:17:22: #4 Write summits bed file... SRX1433377.20_summits.bed INFO @ Sat, 03 Jun 2017 13:17:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1747 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。