Job ID = 11170843 sra ファイルのダウンロード中... Completed: 924647K bytes transferred in 67 seconds (111911K bits/sec), in 1 file. 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... Read 32500265 spots for /home/okishinya/chipatlas/results/ce10/SRX3583343/SRR6493999.sra Written 32500265 spots for /home/okishinya/chipatlas/results/ce10/SRX3583343/SRR6493999.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:11:49 32500265 reads; of these: 32500265 (100.00%) were unpaired; of these: 827038 (2.54%) aligned 0 times 27372045 (84.22%) aligned exactly 1 time 4301182 (13.23%) aligned >1 times 97.46% overall alignment rate Time searching: 00:11:49 Overall time: 00:11:49 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_sort_core] merging from 16 files... [bam_rmdupse_core] 5331514 / 31673227 = 0.1683 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, 08 Sep 2018 11:48:06: # Command line: callpeak -t SRX3583343.bam -f BAM -g ce -n SRX3583343.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3583343.05 # format = BAM # ChIP-seq file = ['SRX3583343.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 11:48:06: # Command line: callpeak -t SRX3583343.bam -f BAM -g ce -n SRX3583343.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3583343.10 # format = BAM # ChIP-seq file = ['SRX3583343.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 11:48:06: # Command line: callpeak -t SRX3583343.bam -f BAM -g ce -n SRX3583343.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3583343.20 # format = BAM # ChIP-seq file = ['SRX3583343.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 11:48:06: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:48:06: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:48:06: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:48:06: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:48:06: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:48:06: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:48:13: 1000000 INFO @ Sat, 08 Sep 2018 11:48:14: 1000000 INFO @ Sat, 08 Sep 2018 11:48:14: 1000000 INFO @ Sat, 08 Sep 2018 11:48:21: 2000000 INFO @ Sat, 08 Sep 2018 11:48:22: 2000000 INFO @ Sat, 08 Sep 2018 11:48:22: 2000000 INFO @ Sat, 08 Sep 2018 11:48:28: 3000000 INFO @ Sat, 08 Sep 2018 11:48:30: 3000000 INFO @ Sat, 08 Sep 2018 11:48:30: 3000000 INFO @ Sat, 08 Sep 2018 11:48:35: 4000000 INFO @ Sat, 08 Sep 2018 11:48:38: 4000000 INFO @ Sat, 08 Sep 2018 11:48:38: 4000000 INFO @ Sat, 08 Sep 2018 11:48:42: 5000000 INFO @ Sat, 08 Sep 2018 11:48:46: 5000000 INFO @ Sat, 08 Sep 2018 11:48:46: 5000000 INFO @ Sat, 08 Sep 2018 11:48:50: 6000000 INFO @ Sat, 08 Sep 2018 11:48:54: 6000000 INFO @ Sat, 08 Sep 2018 11:48:54: 6000000 INFO @ Sat, 08 Sep 2018 11:48:57: 7000000 INFO @ Sat, 08 Sep 2018 11:49:02: 7000000 INFO @ Sat, 08 Sep 2018 11:49:02: 7000000 INFO @ Sat, 08 Sep 2018 11:49:04: 8000000 INFO @ Sat, 08 Sep 2018 11:49:10: 8000000 INFO @ Sat, 08 Sep 2018 11:49:10: 8000000 INFO @ Sat, 08 Sep 2018 11:49:11: 9000000 INFO @ Sat, 08 Sep 2018 11:49:18: 9000000 INFO @ Sat, 08 Sep 2018 11:49:18: 9000000 INFO @ Sat, 08 Sep 2018 11:49:19: 10000000 INFO @ Sat, 08 Sep 2018 11:49:26: 10000000 INFO @ Sat, 08 Sep 2018 11:49:26: 10000000 INFO @ Sat, 08 Sep 2018 11:49:26: 11000000 INFO @ Sat, 08 Sep 2018 11:49:33: 12000000 INFO @ Sat, 08 Sep 2018 11:49:34: 11000000 INFO @ Sat, 08 Sep 2018 11:49:34: 11000000 INFO @ Sat, 08 Sep 2018 11:49:41: 13000000 INFO @ Sat, 08 Sep 2018 11:49:42: 12000000 INFO @ Sat, 08 Sep 2018 11:49:42: 12000000 INFO @ Sat, 08 Sep 2018 11:49:48: 14000000 INFO @ Sat, 08 Sep 2018 11:49:50: 13000000 INFO @ Sat, 08 Sep 2018 11:49:50: 13000000 INFO @ Sat, 08 Sep 2018 11:49:55: 15000000 INFO @ Sat, 08 Sep 2018 11:49:58: 14000000 INFO @ Sat, 08 Sep 2018 11:49:58: 14000000 INFO @ Sat, 08 Sep 2018 11:50:02: 16000000 INFO @ Sat, 08 Sep 2018 11:50:06: 15000000 INFO @ Sat, 08 Sep 2018 11:50:06: 15000000 INFO @ Sat, 08 Sep 2018 11:50:10: 17000000 INFO @ Sat, 08 Sep 2018 11:50:14: 16000000 INFO @ Sat, 08 Sep 2018 11:50:14: 16000000 INFO @ Sat, 08 Sep 2018 11:50:17: 18000000 INFO @ Sat, 08 Sep 2018 11:50:22: 17000000 INFO @ Sat, 08 Sep 2018 11:50:22: 17000000 INFO @ Sat, 08 Sep 2018 11:50:24: 19000000 INFO @ Sat, 08 Sep 2018 11:50:30: 18000000 INFO @ Sat, 08 Sep 2018 11:50:30: 18000000 INFO @ Sat, 08 Sep 2018 11:50:31: 20000000 INFO @ Sat, 08 Sep 2018 11:50:37: 19000000 INFO @ Sat, 08 Sep 2018 11:50:37: 19000000 INFO @ Sat, 08 Sep 2018 11:50:38: 21000000 INFO @ Sat, 08 Sep 2018 11:50:45: 20000000 INFO @ Sat, 08 Sep 2018 11:50:45: 20000000 INFO @ Sat, 08 Sep 2018 11:50:46: 22000000 INFO @ Sat, 08 Sep 2018 11:50:53: 23000000 INFO @ Sat, 08 Sep 2018 11:50:54: 21000000 INFO @ Sat, 08 Sep 2018 11:50:54: 21000000 INFO @ Sat, 08 Sep 2018 11:51:01: 24000000 INFO @ Sat, 08 Sep 2018 11:51:02: 22000000 INFO @ Sat, 08 Sep 2018 11:51:02: 22000000 INFO @ Sat, 08 Sep 2018 11:51:08: 25000000 INFO @ Sat, 08 Sep 2018 11:51:10: 23000000 INFO @ Sat, 08 Sep 2018 11:51:10: 23000000 INFO @ Sat, 08 Sep 2018 11:51:16: 26000000 INFO @ Sat, 08 Sep 2018 11:51:18: 24000000 INFO @ Sat, 08 Sep 2018 11:51:18: 24000000 INFO @ Sat, 08 Sep 2018 11:51:18: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:51:18: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:51:18: #1 total tags in treatment: 26341713 INFO @ Sat, 08 Sep 2018 11:51:18: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:51:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:51:19: #1 tags after filtering in treatment: 26341713 INFO @ Sat, 08 Sep 2018 11:51:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:51:19: #1 finished! INFO @ Sat, 08 Sep 2018 11:51:19: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:51:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:51:20: #2 number of paired peaks: 148 WARNING @ Sat, 08 Sep 2018 11:51:20: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 08 Sep 2018 11:51:20: start model_add_line... INFO @ Sat, 08 Sep 2018 11:51:21: start X-correlation... INFO @ Sat, 08 Sep 2018 11:51:21: end of X-cor INFO @ Sat, 08 Sep 2018 11:51:21: #2 finished! INFO @ Sat, 08 Sep 2018 11:51:21: #2 predicted fragment length is 78 bps INFO @ Sat, 08 Sep 2018 11:51:21: #2 alternative fragment length(s) may be 2,78 bps INFO @ Sat, 08 Sep 2018 11:51:21: #2.2 Generate R script for model : SRX3583343.20_model.r WARNING @ Sat, 08 Sep 2018 11:51:21: #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, 08 Sep 2018 11:51:21: #2 You may need to consider one of the other alternative d(s): 2,78 WARNING @ Sat, 08 Sep 2018 11:51:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:51:21: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:51:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:51:26: 25000000 INFO @ Sat, 08 Sep 2018 11:51:26: 25000000 INFO @ Sat, 08 Sep 2018 11:51:33: 26000000 INFO @ Sat, 08 Sep 2018 11:51:33: 26000000 INFO @ Sat, 08 Sep 2018 11:51:36: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:51:36: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:51:36: #1 total tags in treatment: 26341713 INFO @ Sat, 08 Sep 2018 11:51:36: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:51:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:51:36: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:51:36: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:51:36: #1 total tags in treatment: 26341713 INFO @ Sat, 08 Sep 2018 11:51:36: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:51:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:51:36: #1 tags after filtering in treatment: 26341713 INFO @ Sat, 08 Sep 2018 11:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:51:36: #1 finished! INFO @ Sat, 08 Sep 2018 11:51:36: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:51:36: #1 tags after filtering in treatment: 26341713 INFO @ Sat, 08 Sep 2018 11:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:51:36: #1 finished! INFO @ Sat, 08 Sep 2018 11:51:36: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:51:38: #2 number of paired peaks: 148 WARNING @ Sat, 08 Sep 2018 11:51:38: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 08 Sep 2018 11:51:38: start model_add_line... INFO @ Sat, 08 Sep 2018 11:51:38: #2 number of paired peaks: 148 WARNING @ Sat, 08 Sep 2018 11:51:38: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 08 Sep 2018 11:51:38: start model_add_line... INFO @ Sat, 08 Sep 2018 11:51:38: start X-correlation... INFO @ Sat, 08 Sep 2018 11:51:38: end of X-cor INFO @ Sat, 08 Sep 2018 11:51:38: #2 finished! INFO @ Sat, 08 Sep 2018 11:51:38: #2 predicted fragment length is 78 bps INFO @ Sat, 08 Sep 2018 11:51:38: #2 alternative fragment length(s) may be 2,78 bps INFO @ Sat, 08 Sep 2018 11:51:38: #2.2 Generate R script for model : SRX3583343.05_model.r WARNING @ Sat, 08 Sep 2018 11:51:38: #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, 08 Sep 2018 11:51:38: #2 You may need to consider one of the other alternative d(s): 2,78 WARNING @ Sat, 08 Sep 2018 11:51:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:51:38: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:51:38: start X-correlation... INFO @ Sat, 08 Sep 2018 11:51:38: end of X-cor INFO @ Sat, 08 Sep 2018 11:51:38: #2 finished! INFO @ Sat, 08 Sep 2018 11:51:38: #2 predicted fragment length is 78 bps INFO @ Sat, 08 Sep 2018 11:51:38: #2 alternative fragment length(s) may be 2,78 bps INFO @ Sat, 08 Sep 2018 11:51:38: #2.2 Generate R script for model : SRX3583343.10_model.r WARNING @ Sat, 08 Sep 2018 11:51:38: #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, 08 Sep 2018 11:51:38: #2 You may need to consider one of the other alternative d(s): 2,78 WARNING @ Sat, 08 Sep 2018 11:51:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:51:38: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:52:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:52:24: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:52:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:52:32: #4 Write output xls file... SRX3583343.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:52:32: #4 Write peak in narrowPeak format file... SRX3583343.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:52:32: #4 Write summits bed file... SRX3583343.20_summits.bed INFO @ Sat, 08 Sep 2018 11:52:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1696 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:52:51: #4 Write output xls file... SRX3583343.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:52:51: #4 Write output xls file... SRX3583343.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:52:51: #4 Write peak in narrowPeak format file... SRX3583343.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:52:51: #4 Write summits bed file... SRX3583343.10_summits.bed INFO @ Sat, 08 Sep 2018 11:52:51: #4 Write peak in narrowPeak format file... SRX3583343.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:52:51: Done! INFO @ Sat, 08 Sep 2018 11:52:51: #4 Write summits bed file... SRX3583343.05_summits.bed INFO @ Sat, 08 Sep 2018 11:52:51: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3054 records, 4 fields): 20 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4169 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。