Job ID = 9025624 sra ファイルのダウンロード中... Completed: 513898K bytes transferred in 7 seconds (553835K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:11 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:12 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:13 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:14 --:--:-- 0 100 28797 0 28797 0 0 1852 0 --:--:-- 0:00:15 --:--:-- 5617 100 41247 0 41247 0 0 2625 0 --:--:-- 0:00:15 --:--:-- 9614 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 13809537 spots for /home/okishinya/chipatlas/results/ce10/SRX208766/SRR628900.sra Written 13809537 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: 00:04:20 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 4716172 (34.15%) aligned 0 times 7951390 (57.58%) aligned exactly 1 time 1141975 (8.27%) aligned >1 times 65.85% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 2016367 / 9093365 = 0.2217 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 04:46:04: # Command line: callpeak -t SRX208766.bam -f BAM -g ce -n SRX208766.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208766.05 # format = BAM # ChIP-seq file = ['SRX208766.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 04:46:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:46:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:46:04: # Command line: callpeak -t SRX208766.bam -f BAM -g ce -n SRX208766.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208766.10 # format = BAM # ChIP-seq file = ['SRX208766.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 04:46:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:46:04: # Command line: callpeak -t SRX208766.bam -f BAM -g ce -n SRX208766.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208766.20 # format = BAM # ChIP-seq file = ['SRX208766.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 04:46:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:46:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:46:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:46:11: 1000000 INFO @ Sat, 03 Jun 2017 04:46:13: 1000000 INFO @ Sat, 03 Jun 2017 04:46:13: 1000000 INFO @ Sat, 03 Jun 2017 04:46:19: 2000000 INFO @ Sat, 03 Jun 2017 04:46:22: 2000000 INFO @ Sat, 03 Jun 2017 04:46:22: 2000000 INFO @ Sat, 03 Jun 2017 04:46:27: 3000000 INFO @ Sat, 03 Jun 2017 04:46:32: 3000000 INFO @ Sat, 03 Jun 2017 04:46:32: 3000000 INFO @ Sat, 03 Jun 2017 04:46:36: 4000000 INFO @ Sat, 03 Jun 2017 04:46:42: 4000000 INFO @ Sat, 03 Jun 2017 04:46:42: 4000000 INFO @ Sat, 03 Jun 2017 04:46:44: 5000000 INFO @ Sat, 03 Jun 2017 04:46:51: 5000000 INFO @ Sat, 03 Jun 2017 04:46:51: 5000000 INFO @ Sat, 03 Jun 2017 04:46:52: 6000000 INFO @ Sat, 03 Jun 2017 04:47:00: 7000000 INFO @ Sat, 03 Jun 2017 04:47:00: 6000000 INFO @ Sat, 03 Jun 2017 04:47:00: 6000000 INFO @ Sat, 03 Jun 2017 04:47:01: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:47:01: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:47:01: #1 total tags in treatment: 7076998 INFO @ Sat, 03 Jun 2017 04:47:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:47:01: #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 04:47:02: #1 tags after filtering in treatment: 7006143 INFO @ Sat, 03 Jun 2017 04:47:02: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 03 Jun 2017 04:47:02: #1 finished! INFO @ Sat, 03 Jun 2017 04:47:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:47:04: #2 number of paired peaks: 119 WARNING @ Sat, 03 Jun 2017 04:47:04: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 03 Jun 2017 04:47:04: start model_add_line... INFO @ Sat, 03 Jun 2017 04:47:05: start X-correlation... INFO @ Sat, 03 Jun 2017 04:47:05: end of X-cor INFO @ Sat, 03 Jun 2017 04:47:05: #2 finished! INFO @ Sat, 03 Jun 2017 04:47:05: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 04:47:05: #2 alternative fragment length(s) may be 2,56,108,135,564,596 bps INFO @ Sat, 03 Jun 2017 04:47:05: #2.2 Generate R script for model : SRX208766.05_model.r WARNING @ Sat, 03 Jun 2017 04:47:05: #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 04:47:05: #2 You may need to consider one of the other alternative d(s): 2,56,108,135,564,596 WARNING @ Sat, 03 Jun 2017 04:47:05: #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 04:47:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:47:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:47:09: 7000000 INFO @ Sat, 03 Jun 2017 04:47:09: 7000000 INFO @ Sat, 03 Jun 2017 04:47:10: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:47:10: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:47:10: #1 total tags in treatment: 7076998 INFO @ Sat, 03 Jun 2017 04:47:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:47:10: #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 04:47:10: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:47:10: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:47:10: #1 total tags in treatment: 7076998 INFO @ Sat, 03 Jun 2017 04:47:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:47:10: #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 04:47:11: #1 tags after filtering in treatment: 7006143 INFO @ Sat, 03 Jun 2017 04:47:11: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 03 Jun 2017 04:47:11: #1 finished! INFO @ Sat, 03 Jun 2017 04:47:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:47:11: #1 tags after filtering in treatment: 7006143 INFO @ Sat, 03 Jun 2017 04:47:11: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 03 Jun 2017 04:47:11: #1 finished! INFO @ Sat, 03 Jun 2017 04:47:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:47:12: #2 number of paired peaks: 119 WARNING @ Sat, 03 Jun 2017 04:47:12: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 03 Jun 2017 04:47:12: start model_add_line... INFO @ Sat, 03 Jun 2017 04:47:12: #2 number of paired peaks: 119 WARNING @ Sat, 03 Jun 2017 04:47:12: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 03 Jun 2017 04:47:12: start model_add_line... INFO @ Sat, 03 Jun 2017 04:47:14: start X-correlation... INFO @ Sat, 03 Jun 2017 04:47:14: end of X-cor INFO @ Sat, 03 Jun 2017 04:47:14: #2 finished! INFO @ Sat, 03 Jun 2017 04:47:14: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 04:47:14: #2 alternative fragment length(s) may be 2,56,108,135,564,596 bps INFO @ Sat, 03 Jun 2017 04:47:14: #2.2 Generate R script for model : SRX208766.20_model.r WARNING @ Sat, 03 Jun 2017 04:47:14: #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 04:47:14: #2 You may need to consider one of the other alternative d(s): 2,56,108,135,564,596 WARNING @ Sat, 03 Jun 2017 04:47:14: #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 04:47:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:47:14: start X-correlation... INFO @ Sat, 03 Jun 2017 04:47:14: end of X-cor INFO @ Sat, 03 Jun 2017 04:47:14: #2 finished! INFO @ Sat, 03 Jun 2017 04:47:14: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 04:47:14: #2 alternative fragment length(s) may be 2,56,108,135,564,596 bps INFO @ Sat, 03 Jun 2017 04:47:14: #2.2 Generate R script for model : SRX208766.10_model.r WARNING @ Sat, 03 Jun 2017 04:47:14: #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 04:47:14: #2 You may need to consider one of the other alternative d(s): 2,56,108,135,564,596 WARNING @ Sat, 03 Jun 2017 04:47:14: #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 04:47:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:47:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:47:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:47:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:48:13: #4 Write output xls file... SRX208766.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:48:13: #4 Write peak in narrowPeak format file... SRX208766.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:48:13: #4 Write summits bed file... SRX208766.05_summits.bed INFO @ Sat, 03 Jun 2017 04:48:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (175 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:48:20: #4 Write output xls file... SRX208766.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:48:20: #4 Write peak in narrowPeak format file... SRX208766.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:48:20: #4 Write summits bed file... SRX208766.10_summits.bed INFO @ Sat, 03 Jun 2017 04:48:20: 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 04:48:25: #4 Write output xls file... SRX208766.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:48:25: #4 Write peak in narrowPeak format file... SRX208766.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:48:25: #4 Write summits bed file... SRX208766.20_summits.bed INFO @ Sat, 03 Jun 2017 04:48:25: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (12 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。