Job ID = 11170836 sra ファイルのダウンロード中... Completed: 1026502K bytes transferred in 116 seconds (72340K 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 38739324 spots for /home/okishinya/chipatlas/results/ce10/SRX3583336/SRR6493992.sra Written 38739324 spots for /home/okishinya/chipatlas/results/ce10/SRX3583336/SRR6493992.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: 00:12:36 38739324 reads; of these: 38739324 (100.00%) were unpaired; of these: 7744576 (19.99%) aligned 0 times 26722162 (68.98%) aligned exactly 1 time 4272586 (11.03%) aligned >1 times 80.01% overall alignment rate Time searching: 00:12:36 Overall time: 00:12:36 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] 8957909 / 30994748 = 0.2890 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 11:48:40: # Command line: callpeak -t SRX3583336.bam -f BAM -g ce -n SRX3583336.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3583336.20 # format = BAM # ChIP-seq file = ['SRX3583336.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 11:48:40: # Command line: callpeak -t SRX3583336.bam -f BAM -g ce -n SRX3583336.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3583336.05 # format = BAM # ChIP-seq file = ['SRX3583336.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 11:48:40: # Command line: callpeak -t SRX3583336.bam -f BAM -g ce -n SRX3583336.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3583336.10 # format = BAM # ChIP-seq file = ['SRX3583336.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 11:48:40: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:48:40: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:48:40: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:48:40: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:48:40: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:48:40: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:48:46: 1000000 INFO @ Sat, 08 Sep 2018 11:48:47: 1000000 INFO @ Sat, 08 Sep 2018 11:48:47: 1000000 INFO @ Sat, 08 Sep 2018 11:48:53: 2000000 INFO @ Sat, 08 Sep 2018 11:48:53: 2000000 INFO @ Sat, 08 Sep 2018 11:48:54: 2000000 INFO @ Sat, 08 Sep 2018 11:48:59: 3000000 INFO @ Sat, 08 Sep 2018 11:49:00: 3000000 INFO @ Sat, 08 Sep 2018 11:49:00: 3000000 INFO @ Sat, 08 Sep 2018 11:49:06: 4000000 INFO @ Sat, 08 Sep 2018 11:49:07: 4000000 INFO @ Sat, 08 Sep 2018 11:49:07: 4000000 INFO @ Sat, 08 Sep 2018 11:49:12: 5000000 INFO @ Sat, 08 Sep 2018 11:49:13: 5000000 INFO @ Sat, 08 Sep 2018 11:49:13: 5000000 INFO @ Sat, 08 Sep 2018 11:49:19: 6000000 INFO @ Sat, 08 Sep 2018 11:49:20: 6000000 INFO @ Sat, 08 Sep 2018 11:49:20: 6000000 INFO @ Sat, 08 Sep 2018 11:49:25: 7000000 INFO @ Sat, 08 Sep 2018 11:49:26: 7000000 INFO @ Sat, 08 Sep 2018 11:49:27: 7000000 INFO @ Sat, 08 Sep 2018 11:49:32: 8000000 INFO @ Sat, 08 Sep 2018 11:49:33: 8000000 INFO @ Sat, 08 Sep 2018 11:49:34: 8000000 INFO @ Sat, 08 Sep 2018 11:49:38: 9000000 INFO @ Sat, 08 Sep 2018 11:49:39: 9000000 INFO @ Sat, 08 Sep 2018 11:49:40: 9000000 INFO @ Sat, 08 Sep 2018 11:49:45: 10000000 INFO @ Sat, 08 Sep 2018 11:49:46: 10000000 INFO @ Sat, 08 Sep 2018 11:49:47: 10000000 INFO @ Sat, 08 Sep 2018 11:49:51: 11000000 INFO @ Sat, 08 Sep 2018 11:49:52: 11000000 INFO @ Sat, 08 Sep 2018 11:49:54: 11000000 INFO @ Sat, 08 Sep 2018 11:49:58: 12000000 INFO @ Sat, 08 Sep 2018 11:49:59: 12000000 INFO @ Sat, 08 Sep 2018 11:50:01: 12000000 INFO @ Sat, 08 Sep 2018 11:50:05: 13000000 INFO @ Sat, 08 Sep 2018 11:50:05: 13000000 INFO @ Sat, 08 Sep 2018 11:50:07: 13000000 INFO @ Sat, 08 Sep 2018 11:50:11: 14000000 INFO @ Sat, 08 Sep 2018 11:50:12: 14000000 INFO @ Sat, 08 Sep 2018 11:50:14: 14000000 INFO @ Sat, 08 Sep 2018 11:50:18: 15000000 INFO @ Sat, 08 Sep 2018 11:50:18: 15000000 INFO @ Sat, 08 Sep 2018 11:50:21: 15000000 INFO @ Sat, 08 Sep 2018 11:50:24: 16000000 INFO @ Sat, 08 Sep 2018 11:50:25: 16000000 INFO @ Sat, 08 Sep 2018 11:50:27: 16000000 INFO @ Sat, 08 Sep 2018 11:50:31: 17000000 INFO @ Sat, 08 Sep 2018 11:50:31: 17000000 INFO @ Sat, 08 Sep 2018 11:50:34: 17000000 INFO @ Sat, 08 Sep 2018 11:50:37: 18000000 INFO @ Sat, 08 Sep 2018 11:50:38: 18000000 INFO @ Sat, 08 Sep 2018 11:50:41: 18000000 INFO @ Sat, 08 Sep 2018 11:50:44: 19000000 INFO @ Sat, 08 Sep 2018 11:50:44: 19000000 INFO @ Sat, 08 Sep 2018 11:50:47: 19000000 INFO @ Sat, 08 Sep 2018 11:50:51: 20000000 INFO @ Sat, 08 Sep 2018 11:50:51: 20000000 INFO @ Sat, 08 Sep 2018 11:50:54: 20000000 INFO @ Sat, 08 Sep 2018 11:50:57: 21000000 INFO @ Sat, 08 Sep 2018 11:50:57: 21000000 INFO @ Sat, 08 Sep 2018 11:51:01: 21000000 INFO @ Sat, 08 Sep 2018 11:51:04: 22000000 INFO @ Sat, 08 Sep 2018 11:51:04: 22000000 INFO @ Sat, 08 Sep 2018 11:51:04: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:51:04: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:51:04: #1 total tags in treatment: 22036839 INFO @ Sat, 08 Sep 2018 11:51:04: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:51:04: #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 11:51:04: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:51:04: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:51:04: #1 total tags in treatment: 22036839 INFO @ Sat, 08 Sep 2018 11:51:04: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:51:04: #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 11:51:04: #1 tags after filtering in treatment: 22036839 INFO @ Sat, 08 Sep 2018 11:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:51:04: #1 finished! INFO @ Sat, 08 Sep 2018 11:51:04: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:51:05: #1 tags after filtering in treatment: 22036839 INFO @ Sat, 08 Sep 2018 11:51:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:51:05: #1 finished! INFO @ Sat, 08 Sep 2018 11:51:05: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:51:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:51:06: #2 number of paired peaks: 123 WARNING @ Sat, 08 Sep 2018 11:51:06: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 08 Sep 2018 11:51:06: start model_add_line... INFO @ Sat, 08 Sep 2018 11:51:06: start X-correlation... INFO @ Sat, 08 Sep 2018 11:51:06: end of X-cor INFO @ Sat, 08 Sep 2018 11:51:06: #2 finished! INFO @ Sat, 08 Sep 2018 11:51:06: #2 predicted fragment length is 59 bps INFO @ Sat, 08 Sep 2018 11:51:06: #2 alternative fragment length(s) may be 1,59,531,545,548,583 bps INFO @ Sat, 08 Sep 2018 11:51:06: #2.2 Generate R script for model : SRX3583336.05_model.r WARNING @ Sat, 08 Sep 2018 11:51:06: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:51:06: #2 You may need to consider one of the other alternative d(s): 1,59,531,545,548,583 WARNING @ Sat, 08 Sep 2018 11:51:06: #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 11:51:06: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:51:06: #2 number of paired peaks: 123 WARNING @ Sat, 08 Sep 2018 11:51:06: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 08 Sep 2018 11:51:06: start model_add_line... INFO @ Sat, 08 Sep 2018 11:51:06: start X-correlation... INFO @ Sat, 08 Sep 2018 11:51:06: end of X-cor INFO @ Sat, 08 Sep 2018 11:51:06: #2 finished! INFO @ Sat, 08 Sep 2018 11:51:06: #2 predicted fragment length is 59 bps INFO @ Sat, 08 Sep 2018 11:51:06: #2 alternative fragment length(s) may be 1,59,531,545,548,583 bps INFO @ Sat, 08 Sep 2018 11:51:06: #2.2 Generate R script for model : SRX3583336.10_model.r WARNING @ Sat, 08 Sep 2018 11:51:06: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:51:06: #2 You may need to consider one of the other alternative d(s): 1,59,531,545,548,583 WARNING @ Sat, 08 Sep 2018 11:51:06: #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 11:51:06: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:51:07: 22000000 INFO @ Sat, 08 Sep 2018 11:51:08: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:51:08: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:51:08: #1 total tags in treatment: 22036839 INFO @ Sat, 08 Sep 2018 11:51:08: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:51:08: #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 11:51:08: #1 tags after filtering in treatment: 22036839 INFO @ Sat, 08 Sep 2018 11:51:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:51:08: #1 finished! INFO @ Sat, 08 Sep 2018 11:51:08: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:51:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:51:10: #2 number of paired peaks: 123 WARNING @ Sat, 08 Sep 2018 11:51:10: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 08 Sep 2018 11:51:10: start model_add_line... INFO @ Sat, 08 Sep 2018 11:51:10: start X-correlation... INFO @ Sat, 08 Sep 2018 11:51:10: end of X-cor INFO @ Sat, 08 Sep 2018 11:51:10: #2 finished! INFO @ Sat, 08 Sep 2018 11:51:10: #2 predicted fragment length is 59 bps INFO @ Sat, 08 Sep 2018 11:51:10: #2 alternative fragment length(s) may be 1,59,531,545,548,583 bps INFO @ Sat, 08 Sep 2018 11:51:10: #2.2 Generate R script for model : SRX3583336.20_model.r WARNING @ Sat, 08 Sep 2018 11:51:10: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:51:10: #2 You may need to consider one of the other alternative d(s): 1,59,531,545,548,583 WARNING @ Sat, 08 Sep 2018 11:51:10: #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 11:51:10: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:51:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:51:45: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:51:45: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:51:50: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:52:06: #4 Write output xls file... SRX3583336.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:52:06: #4 Write peak in narrowPeak format file... SRX3583336.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:52:06: #4 Write summits bed file... SRX3583336.10_summits.bed INFO @ Sat, 08 Sep 2018 11:52:06: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1831 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:52:07: #4 Write output xls file... SRX3583336.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:52:07: #4 Write peak in narrowPeak format file... SRX3583336.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:52:07: #4 Write summits bed file... SRX3583336.05_summits.bed INFO @ Sat, 08 Sep 2018 11:52:07: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3386 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:52:11: #4 Write output xls file... SRX3583336.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:52:11: #4 Write peak in narrowPeak format file... SRX3583336.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:52:11: #4 Write summits bed file... SRX3583336.20_summits.bed INFO @ Sat, 08 Sep 2018 11:52:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (256 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。