Job ID = 9029235 sra ファイルのダウンロード中... Completed: 725533K bytes transferred in 13 seconds (450704K 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 1094 0 --:--:-- 0:00:06 --:--:-- 10313 100 25901 0 25901 0 0 3307 0 --:--:-- 0:00:07 --:--:-- 16465 100 54861 0 54861 0 0 6215 0 --:--:-- 0:00:08 --:--:-- 21346 100 125k 0 125k 0 0 13047 0 --:--:-- 0:00:09 --:--:-- 35940 100 147k 0 147k 0 0 15081 0 --:--:-- 0:00:09 --:--:-- 40358 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 29269261 spots for /home/okishinya/chipatlas/results/dm3/SRX1433375/SRR2919840.sra Written 29269261 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: 00:08:43 29269261 reads; of these: 29269261 (100.00%) were unpaired; of these: 17718491 (60.54%) aligned 0 times 7648128 (26.13%) aligned exactly 1 time 3902642 (13.33%) aligned >1 times 39.46% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 5081306 / 11550770 = 0.4399 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 13:05:46: # Command line: callpeak -t SRX1433375.bam -f BAM -g dm -n SRX1433375.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433375.20 # format = BAM # ChIP-seq file = ['SRX1433375.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 13:05:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:05:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:05:46: # Command line: callpeak -t SRX1433375.bam -f BAM -g dm -n SRX1433375.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433375.05 # format = BAM # ChIP-seq file = ['SRX1433375.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 13:05:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:05:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:05:46: # Command line: callpeak -t SRX1433375.bam -f BAM -g dm -n SRX1433375.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433375.10 # format = BAM # ChIP-seq file = ['SRX1433375.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 13:05:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:05:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:05:52: 1000000 INFO @ Sat, 03 Jun 2017 13:05:52: 1000000 INFO @ Sat, 03 Jun 2017 13:05:52: 1000000 INFO @ Sat, 03 Jun 2017 13:05:58: 2000000 INFO @ Sat, 03 Jun 2017 13:05:58: 2000000 INFO @ Sat, 03 Jun 2017 13:05:59: 2000000 INFO @ Sat, 03 Jun 2017 13:06:04: 3000000 INFO @ Sat, 03 Jun 2017 13:06:04: 3000000 INFO @ Sat, 03 Jun 2017 13:06:05: 3000000 INFO @ Sat, 03 Jun 2017 13:06:09: 4000000 INFO @ Sat, 03 Jun 2017 13:06:10: 4000000 INFO @ Sat, 03 Jun 2017 13:06:12: 4000000 INFO @ Sat, 03 Jun 2017 13:06:15: 5000000 INFO @ Sat, 03 Jun 2017 13:06:17: 5000000 INFO @ Sat, 03 Jun 2017 13:06:20: 5000000 INFO @ Sat, 03 Jun 2017 13:06:20: 6000000 INFO @ Sat, 03 Jun 2017 13:06:23: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:06:23: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:06:23: #1 total tags in treatment: 6469464 INFO @ Sat, 03 Jun 2017 13:06:23: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:06:23: #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 13:06:24: #1 tags after filtering in treatment: 6467959 INFO @ Sat, 03 Jun 2017 13:06:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:06:24: #1 finished! INFO @ Sat, 03 Jun 2017 13:06:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:06:24: 6000000 INFO @ Sat, 03 Jun 2017 13:06:25: #2 number of paired peaks: 1518 INFO @ Sat, 03 Jun 2017 13:06:25: start model_add_line... INFO @ Sat, 03 Jun 2017 13:06:27: 6000000 INFO @ Sat, 03 Jun 2017 13:06:28: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:06:28: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:06:28: #1 total tags in treatment: 6469464 INFO @ Sat, 03 Jun 2017 13:06:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:06:28: #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 13:06:29: #1 tags after filtering in treatment: 6467959 INFO @ Sat, 03 Jun 2017 13:06:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:06:29: #1 finished! INFO @ Sat, 03 Jun 2017 13:06:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:06:30: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:06:30: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:06:30: #1 total tags in treatment: 6469464 INFO @ Sat, 03 Jun 2017 13:06:30: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:06:30: #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 13:06:30: #2 number of paired peaks: 1518 INFO @ Sat, 03 Jun 2017 13:06:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:06:31: #1 tags after filtering in treatment: 6467959 INFO @ Sat, 03 Jun 2017 13:06:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:06:31: #1 finished! INFO @ Sat, 03 Jun 2017 13:06:31: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:06:32: start X-correlation... INFO @ Sat, 03 Jun 2017 13:06:32: end of X-cor INFO @ Sat, 03 Jun 2017 13:06:32: #2 finished! INFO @ Sat, 03 Jun 2017 13:06:32: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 13:06:32: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Jun 2017 13:06:32: #2.2 Generate R script for model : SRX1433375.10_model.r WARNING @ Sat, 03 Jun 2017 13:06:32: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:06:32: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Jun 2017 13:06:32: #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 13:06:32: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:06:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:06:32: #2 number of paired peaks: 1518 INFO @ Sat, 03 Jun 2017 13:06:32: start model_add_line... INFO @ Sat, 03 Jun 2017 13:06:36: start X-correlation... INFO @ Sat, 03 Jun 2017 13:06:36: end of X-cor INFO @ Sat, 03 Jun 2017 13:06:36: #2 finished! INFO @ Sat, 03 Jun 2017 13:06:36: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 13:06:36: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Jun 2017 13:06:36: #2.2 Generate R script for model : SRX1433375.05_model.r WARNING @ Sat, 03 Jun 2017 13:06:36: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:06:36: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Jun 2017 13:06:36: #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 13:06:36: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:06:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:06:39: start X-correlation... INFO @ Sat, 03 Jun 2017 13:06:39: end of X-cor INFO @ Sat, 03 Jun 2017 13:06:39: #2 finished! INFO @ Sat, 03 Jun 2017 13:06:39: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 13:06:39: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Jun 2017 13:06:39: #2.2 Generate R script for model : SRX1433375.20_model.r WARNING @ Sat, 03 Jun 2017 13:06:39: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:06:39: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Jun 2017 13:06:39: #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 13:06:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:06:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:07:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:07:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:07:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:07:37: #4 Write output xls file... SRX1433375.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:07:37: #4 Write peak in narrowPeak format file... SRX1433375.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:07:37: #4 Write summits bed file... SRX1433375.10_summits.bed INFO @ Sat, 03 Jun 2017 13:07:37: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2311 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:07:46: #4 Write output xls file... SRX1433375.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:07:46: #4 Write peak in narrowPeak format file... SRX1433375.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:07:46: #4 Write summits bed file... SRX1433375.05_summits.bed INFO @ Sat, 03 Jun 2017 13:07:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3180 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:07:49: #4 Write output xls file... SRX1433375.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:07:49: #4 Write peak in narrowPeak format file... SRX1433375.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:07:49: #4 Write summits bed file... SRX1433375.20_summits.bed INFO @ Sat, 03 Jun 2017 13:07:49: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1492 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。