Job ID = 9025446 sra ファイルのダウンロード中... Completed: 100064K bytes transferred in 4 seconds (185997K 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 --:--:-- 0:00:07 --:--:-- 0 100 24454 0 24454 0 0 2971 0 --:--:-- 0:00:08 --:--:-- 13902 100 46010 0 46010 0 0 5247 0 --:--:-- 0:00:08 --:--:-- 20030 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 6085075 spots for /home/okishinya/chipatlas/results/ce10/SRX1007131/SRR1993091.sra Written 6085075 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: 00:00:28 6085075 reads; of these: 6085075 (100.00%) were unpaired; of these: 5839301 (95.96%) aligned 0 times 205457 (3.38%) aligned exactly 1 time 40317 (0.66%) aligned >1 times 4.04% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 11679 / 245774 = 0.0475 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 03:48:55: # Command line: callpeak -t SRX1007131.bam -f BAM -g ce -n SRX1007131.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1007131.10 # format = BAM # ChIP-seq file = ['SRX1007131.bam'] # control file = None # effective genome size = 9.00e+07 # 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 03:48:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 03:48:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 03:48:55: # Command line: callpeak -t SRX1007131.bam -f BAM -g ce -n SRX1007131.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1007131.20 # format = BAM # ChIP-seq file = ['SRX1007131.bam'] # control file = None # effective genome size = 9.00e+07 # 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 03:48:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 03:48:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 03:48:55: # Command line: callpeak -t SRX1007131.bam -f BAM -g ce -n SRX1007131.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1007131.05 # format = BAM # ChIP-seq file = ['SRX1007131.bam'] # control file = None # effective genome size = 9.00e+07 # 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 03:48:55: #1 read tag files... INFO @ Sat, 03 Jun 2017 03:48:55: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 03:48:56: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 03:48:56: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 03:48:56: #1 total tags in treatment: 234095 INFO @ Sat, 03 Jun 2017 03:48:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 03:48:56: #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 03:48:56: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 03:48:56: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 03:48:56: #1 total tags in treatment: 234095 INFO @ Sat, 03 Jun 2017 03:48:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 03:48:56: #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 03:48:56: #1 tags after filtering in treatment: 234057 INFO @ Sat, 03 Jun 2017 03:48:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 03:48:56: #1 finished! INFO @ Sat, 03 Jun 2017 03:48:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 03:48:56: #1 tags after filtering in treatment: 234057 INFO @ Sat, 03 Jun 2017 03:48:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 03:48:56: #1 finished! INFO @ Sat, 03 Jun 2017 03:48:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 03:48:56: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 03:48:56: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 03:48:56: #1 total tags in treatment: 234095 INFO @ Sat, 03 Jun 2017 03:48:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 03:48:56: #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 03:48:56: #1 tags after filtering in treatment: 234057 INFO @ Sat, 03 Jun 2017 03:48:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 03:48:56: #1 finished! INFO @ Sat, 03 Jun 2017 03:48:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 03:48:57: #2 number of paired peaks: 2114 INFO @ Sat, 03 Jun 2017 03:48:57: start model_add_line... INFO @ Sat, 03 Jun 2017 03:48:57: #2 number of paired peaks: 2114 INFO @ Sat, 03 Jun 2017 03:48:57: start model_add_line... INFO @ Sat, 03 Jun 2017 03:48:57: #2 number of paired peaks: 2114 INFO @ Sat, 03 Jun 2017 03:48:57: start model_add_line... INFO @ Sat, 03 Jun 2017 03:48:57: start X-correlation... INFO @ Sat, 03 Jun 2017 03:48:57: end of X-cor INFO @ Sat, 03 Jun 2017 03:48:57: #2 finished! INFO @ Sat, 03 Jun 2017 03:48:57: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Jun 2017 03:48:57: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Jun 2017 03:48:57: #2.2 Generate R script for model : SRX1007131.20_model.r INFO @ Sat, 03 Jun 2017 03:48:57: start X-correlation... INFO @ Sat, 03 Jun 2017 03:48:57: end of X-cor INFO @ Sat, 03 Jun 2017 03:48:57: #2 finished! INFO @ Sat, 03 Jun 2017 03:48:57: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Jun 2017 03:48:57: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Jun 2017 03:48:57: #2.2 Generate R script for model : SRX1007131.10_model.r WARNING @ Sat, 03 Jun 2017 03:48:57: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 03:48:57: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Jun 2017 03:48:57: #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 03:48:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 03:48:57: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 03 Jun 2017 03:48:57: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 03:48:57: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Jun 2017 03:48:57: #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 03:48:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 03:48:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 03:48:57: start X-correlation... INFO @ Sat, 03 Jun 2017 03:48:57: end of X-cor INFO @ Sat, 03 Jun 2017 03:48:57: #2 finished! INFO @ Sat, 03 Jun 2017 03:48:57: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Jun 2017 03:48:57: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Jun 2017 03:48:57: #2.2 Generate R script for model : SRX1007131.05_model.r WARNING @ Sat, 03 Jun 2017 03:48:57: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 03:48:57: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Jun 2017 03:48:57: #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 03:48:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 03:48:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 03:48:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 03:48:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 03:48:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 03:49:00: #4 Write output xls file... SRX1007131.20_peaks.xls INFO @ Sat, 03 Jun 2017 03:49:00: #4 Write peak in narrowPeak format file... SRX1007131.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 03:49:00: #4 Write summits bed file... SRX1007131.20_summits.bed INFO @ Sat, 03 Jun 2017 03:49:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 03:49:00: #4 Write output xls file... SRX1007131.10_peaks.xls INFO @ Sat, 03 Jun 2017 03:49:00: #4 Write peak in narrowPeak format file... SRX1007131.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 03:49:00: #4 Write summits bed file... SRX1007131.10_summits.bed INFO @ Sat, 03 Jun 2017 03:49:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (395 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 03:49:00: #4 Write output xls file... SRX1007131.05_peaks.xls INFO @ Sat, 03 Jun 2017 03:49:00: #4 Write peak in narrowPeak format file... SRX1007131.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 03:49:00: #4 Write summits bed file... SRX1007131.05_summits.bed INFO @ Sat, 03 Jun 2017 03:49:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1153 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。