Job ID = 9028855 sra ファイルのダウンロード中... Completed: 220318K bytes transferred in 5 seconds (318561K bits/sec), in 2 files, 3 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 22318 0 22318 0 0 2830 0 --:--:-- 0:00:07 --:--:-- 17504 100 41830 0 41830 0 0 4799 0 --:--:-- 0:00:08 --:--:-- 19871 100 56282 0 56282 0 0 6220 0 --:--:-- 0:00:09 --:--:-- 23094 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 3653806 spots for /home/okishinya/chipatlas/results/ce10/SRX982079/SRR1956561.sra Written 3653806 spots total Written 4416368 spots for /home/okishinya/chipatlas/results/ce10/SRX982079/SRR1956562.sra Written 4416368 spots total 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: 00:02:13 8070174 reads; of these: 8070174 (100.00%) were unpaired; of these: 1655268 (20.51%) aligned 0 times 5527058 (68.49%) aligned exactly 1 time 887848 (11.00%) aligned >1 times 79.49% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 342669 / 6414906 = 0.0534 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 12:07:28: # Command line: callpeak -t SRX982079.bam -f BAM -g ce -n SRX982079.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982079.05 # format = BAM # ChIP-seq file = ['SRX982079.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 12:07:28: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:07:28: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:07:28: # Command line: callpeak -t SRX982079.bam -f BAM -g ce -n SRX982079.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982079.20 # format = BAM # ChIP-seq file = ['SRX982079.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 12:07:28: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:07:28: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:07:28: # Command line: callpeak -t SRX982079.bam -f BAM -g ce -n SRX982079.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982079.10 # format = BAM # ChIP-seq file = ['SRX982079.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 12:07:28: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:07:28: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:07:36: 1000000 INFO @ Sat, 03 Jun 2017 12:07:36: 1000000 INFO @ Sat, 03 Jun 2017 12:07:36: 1000000 INFO @ Sat, 03 Jun 2017 12:07:43: 2000000 INFO @ Sat, 03 Jun 2017 12:07:44: 2000000 INFO @ Sat, 03 Jun 2017 12:07:44: 2000000 INFO @ Sat, 03 Jun 2017 12:07:51: 3000000 INFO @ Sat, 03 Jun 2017 12:07:51: 3000000 INFO @ Sat, 03 Jun 2017 12:07:52: 3000000 INFO @ Sat, 03 Jun 2017 12:07:59: 4000000 INFO @ Sat, 03 Jun 2017 12:07:59: 4000000 INFO @ Sat, 03 Jun 2017 12:08:00: 4000000 INFO @ Sat, 03 Jun 2017 12:08:06: 5000000 INFO @ Sat, 03 Jun 2017 12:08:07: 5000000 INFO @ Sat, 03 Jun 2017 12:08:08: 5000000 INFO @ Sat, 03 Jun 2017 12:08:14: 6000000 INFO @ Sat, 03 Jun 2017 12:08:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:08:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:08:14: #1 total tags in treatment: 6072237 INFO @ Sat, 03 Jun 2017 12:08:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:08:14: #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 12:08:15: 6000000 INFO @ Sat, 03 Jun 2017 12:08:15: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:08:15: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:08:15: #1 total tags in treatment: 6072237 INFO @ Sat, 03 Jun 2017 12:08:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:08:15: #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 12:08:16: #1 tags after filtering in treatment: 6070837 INFO @ Sat, 03 Jun 2017 12:08:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:08:16: #1 finished! INFO @ Sat, 03 Jun 2017 12:08:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:08:16: 6000000 INFO @ Sat, 03 Jun 2017 12:08:16: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:08:16: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:08:16: #1 total tags in treatment: 6072237 INFO @ Sat, 03 Jun 2017 12:08:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:08:16: #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 12:08:17: #1 tags after filtering in treatment: 6070837 INFO @ Sat, 03 Jun 2017 12:08:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:08:17: #1 finished! INFO @ Sat, 03 Jun 2017 12:08:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:08:17: #2 number of paired peaks: 598 WARNING @ Sat, 03 Jun 2017 12:08:17: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sat, 03 Jun 2017 12:08:17: start model_add_line... INFO @ Sat, 03 Jun 2017 12:08:17: #1 tags after filtering in treatment: 6070837 INFO @ Sat, 03 Jun 2017 12:08:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:08:17: #1 finished! INFO @ Sat, 03 Jun 2017 12:08:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:08:18: #2 number of paired peaks: 598 WARNING @ Sat, 03 Jun 2017 12:08:18: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sat, 03 Jun 2017 12:08:18: start model_add_line... INFO @ Sat, 03 Jun 2017 12:08:18: #2 number of paired peaks: 598 WARNING @ Sat, 03 Jun 2017 12:08:18: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sat, 03 Jun 2017 12:08:18: start model_add_line... INFO @ Sat, 03 Jun 2017 12:08:21: start X-correlation... INFO @ Sat, 03 Jun 2017 12:08:21: end of X-cor INFO @ Sat, 03 Jun 2017 12:08:21: #2 finished! INFO @ Sat, 03 Jun 2017 12:08:21: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 12:08:21: #2 alternative fragment length(s) may be 4,62 bps INFO @ Sat, 03 Jun 2017 12:08:21: #2.2 Generate R script for model : SRX982079.10_model.r WARNING @ Sat, 03 Jun 2017 12:08:21: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:08:21: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Sat, 03 Jun 2017 12:08:21: #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 12:08:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:08:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:08:22: start X-correlation... INFO @ Sat, 03 Jun 2017 12:08:22: end of X-cor INFO @ Sat, 03 Jun 2017 12:08:22: #2 finished! INFO @ Sat, 03 Jun 2017 12:08:22: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 12:08:22: #2 alternative fragment length(s) may be 4,62 bps INFO @ Sat, 03 Jun 2017 12:08:22: #2.2 Generate R script for model : SRX982079.05_model.r WARNING @ Sat, 03 Jun 2017 12:08:22: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:08:22: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Sat, 03 Jun 2017 12:08:22: #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 12:08:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:08:23: start X-correlation... INFO @ Sat, 03 Jun 2017 12:08:23: end of X-cor INFO @ Sat, 03 Jun 2017 12:08:23: #2 finished! INFO @ Sat, 03 Jun 2017 12:08:23: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 12:08:23: #2 alternative fragment length(s) may be 4,62 bps INFO @ Sat, 03 Jun 2017 12:08:23: #2.2 Generate R script for model : SRX982079.20_model.r WARNING @ Sat, 03 Jun 2017 12:08:23: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:08:23: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Sat, 03 Jun 2017 12:08:23: #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 12:08:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:08:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:08:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:08:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:08:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:09:20: #4 Write output xls file... SRX982079.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:09:20: #4 Write peak in narrowPeak format file... SRX982079.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:09:20: #4 Write summits bed file... SRX982079.10_summits.bed INFO @ Sat, 03 Jun 2017 12:09:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (292 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:09:22: #4 Write output xls file... SRX982079.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:09:22: #4 Write peak in narrowPeak format file... SRX982079.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:09:22: #4 Write summits bed file... SRX982079.20_summits.bed INFO @ Sat, 03 Jun 2017 12:09:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (123 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:09:23: #4 Write output xls file... SRX982079.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:09:23: #4 Write peak in narrowPeak format file... SRX982079.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:09:23: #4 Write summits bed file... SRX982079.05_summits.bed INFO @ Sat, 03 Jun 2017 12:09:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (662 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。