Job ID = 10714367 sra ファイルのダウンロード中... Completed: 1267787K bytes transferred in 143 seconds (72190K 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 25229792 spots for /home/okishinya/chipatlas/results/ce10/SRX2965748/SRR5766333.sra Written 25229792 spots for /home/okishinya/chipatlas/results/ce10/SRX2965748/SRR5766333.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:04 25229792 reads; of these: 25229792 (100.00%) were unpaired; of these: 2189653 (8.68%) aligned 0 times 19319120 (76.57%) aligned exactly 1 time 3721019 (14.75%) aligned >1 times 91.32% overall alignment rate Time searching: 00:13:05 Overall time: 00:13:05 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 12 files... [bam_rmdupse_core] 2626787 / 23040139 = 0.1140 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 @ Sun, 03 Jun 2018 12:52:11: # Command line: callpeak -t SRX2965748.bam -f BAM -g ce -n SRX2965748.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2965748.20 # format = BAM # ChIP-seq file = ['SRX2965748.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 @ Sun, 03 Jun 2018 12:52:11: # Command line: callpeak -t SRX2965748.bam -f BAM -g ce -n SRX2965748.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2965748.10 # format = BAM # ChIP-seq file = ['SRX2965748.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 @ Sun, 03 Jun 2018 12:52:11: # Command line: callpeak -t SRX2965748.bam -f BAM -g ce -n SRX2965748.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2965748.05 # format = BAM # ChIP-seq file = ['SRX2965748.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 @ Sun, 03 Jun 2018 12:52:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:52:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:52:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:52:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:52:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:52:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:52:18: 1000000 INFO @ Sun, 03 Jun 2018 12:52:18: 1000000 INFO @ Sun, 03 Jun 2018 12:52:18: 1000000 INFO @ Sun, 03 Jun 2018 12:52:25: 2000000 INFO @ Sun, 03 Jun 2018 12:52:25: 2000000 INFO @ Sun, 03 Jun 2018 12:52:26: 2000000 INFO @ Sun, 03 Jun 2018 12:52:32: 3000000 INFO @ Sun, 03 Jun 2018 12:52:32: 3000000 INFO @ Sun, 03 Jun 2018 12:52:33: 3000000 INFO @ Sun, 03 Jun 2018 12:52:39: 4000000 INFO @ Sun, 03 Jun 2018 12:52:40: 4000000 INFO @ Sun, 03 Jun 2018 12:52:41: 4000000 INFO @ Sun, 03 Jun 2018 12:52:46: 5000000 INFO @ Sun, 03 Jun 2018 12:52:47: 5000000 INFO @ Sun, 03 Jun 2018 12:52:48: 5000000 INFO @ Sun, 03 Jun 2018 12:52:53: 6000000 INFO @ Sun, 03 Jun 2018 12:52:54: 6000000 INFO @ Sun, 03 Jun 2018 12:52:55: 6000000 INFO @ Sun, 03 Jun 2018 12:53:00: 7000000 INFO @ Sun, 03 Jun 2018 12:53:01: 7000000 INFO @ Sun, 03 Jun 2018 12:53:03: 7000000 INFO @ Sun, 03 Jun 2018 12:53:07: 8000000 INFO @ Sun, 03 Jun 2018 12:53:08: 8000000 INFO @ Sun, 03 Jun 2018 12:53:10: 8000000 INFO @ Sun, 03 Jun 2018 12:53:14: 9000000 INFO @ Sun, 03 Jun 2018 12:53:16: 9000000 INFO @ Sun, 03 Jun 2018 12:53:18: 9000000 INFO @ Sun, 03 Jun 2018 12:53:20: 10000000 INFO @ Sun, 03 Jun 2018 12:53:23: 10000000 INFO @ Sun, 03 Jun 2018 12:53:25: 10000000 INFO @ Sun, 03 Jun 2018 12:53:27: 11000000 INFO @ Sun, 03 Jun 2018 12:53:30: 11000000 INFO @ Sun, 03 Jun 2018 12:53:33: 11000000 INFO @ Sun, 03 Jun 2018 12:53:34: 12000000 INFO @ Sun, 03 Jun 2018 12:53:37: 12000000 INFO @ Sun, 03 Jun 2018 12:53:40: 12000000 INFO @ Sun, 03 Jun 2018 12:53:41: 13000000 INFO @ Sun, 03 Jun 2018 12:53:44: 13000000 INFO @ Sun, 03 Jun 2018 12:53:48: 13000000 INFO @ Sun, 03 Jun 2018 12:53:48: 14000000 INFO @ Sun, 03 Jun 2018 12:53:52: 14000000 INFO @ Sun, 03 Jun 2018 12:53:55: 15000000 INFO @ Sun, 03 Jun 2018 12:53:55: 14000000 INFO @ Sun, 03 Jun 2018 12:53:59: 15000000 INFO @ Sun, 03 Jun 2018 12:54:01: 16000000 INFO @ Sun, 03 Jun 2018 12:54:03: 15000000 INFO @ Sun, 03 Jun 2018 12:54:06: 16000000 INFO @ Sun, 03 Jun 2018 12:54:08: 17000000 INFO @ Sun, 03 Jun 2018 12:54:10: 16000000 INFO @ Sun, 03 Jun 2018 12:54:13: 17000000 INFO @ Sun, 03 Jun 2018 12:54:15: 18000000 INFO @ Sun, 03 Jun 2018 12:54:18: 17000000 INFO @ Sun, 03 Jun 2018 12:54:20: 18000000 INFO @ Sun, 03 Jun 2018 12:54:22: 19000000 INFO @ Sun, 03 Jun 2018 12:54:25: 18000000 INFO @ Sun, 03 Jun 2018 12:54:27: 19000000 INFO @ Sun, 03 Jun 2018 12:54:29: 20000000 INFO @ Sun, 03 Jun 2018 12:54:32: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:54:32: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:54:32: #1 total tags in treatment: 20413352 INFO @ Sun, 03 Jun 2018 12:54:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:54:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:54:32: #1 tags after filtering in treatment: 20413352 INFO @ Sun, 03 Jun 2018 12:54:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:54:32: #1 finished! INFO @ Sun, 03 Jun 2018 12:54:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:54:32: 19000000 INFO @ Sun, 03 Jun 2018 12:54:34: #2 number of paired peaks: 140 WARNING @ Sun, 03 Jun 2018 12:54:34: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 03 Jun 2018 12:54:34: start model_add_line... INFO @ Sun, 03 Jun 2018 12:54:34: start X-correlation... INFO @ Sun, 03 Jun 2018 12:54:34: end of X-cor INFO @ Sun, 03 Jun 2018 12:54:34: #2 finished! INFO @ Sun, 03 Jun 2018 12:54:34: #2 predicted fragment length is 96 bps INFO @ Sun, 03 Jun 2018 12:54:34: #2 alternative fragment length(s) may be 3,96,550 bps INFO @ Sun, 03 Jun 2018 12:54:34: #2.2 Generate R script for model : SRX2965748.20_model.r WARNING @ Sun, 03 Jun 2018 12:54:34: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:54:34: #2 You may need to consider one of the other alternative d(s): 3,96,550 WARNING @ Sun, 03 Jun 2018 12:54:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:54:34: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:54:35: 20000000 INFO @ Sun, 03 Jun 2018 12:54:38: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:54:38: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:54:38: #1 total tags in treatment: 20413352 INFO @ Sun, 03 Jun 2018 12:54:38: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:54:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:54:38: #1 tags after filtering in treatment: 20413352 INFO @ Sun, 03 Jun 2018 12:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:54:38: #1 finished! INFO @ Sun, 03 Jun 2018 12:54:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:54:39: #2 number of paired peaks: 140 WARNING @ Sun, 03 Jun 2018 12:54:39: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 03 Jun 2018 12:54:39: start model_add_line... INFO @ Sun, 03 Jun 2018 12:54:40: start X-correlation... INFO @ Sun, 03 Jun 2018 12:54:40: end of X-cor INFO @ Sun, 03 Jun 2018 12:54:40: #2 finished! INFO @ Sun, 03 Jun 2018 12:54:40: #2 predicted fragment length is 96 bps INFO @ Sun, 03 Jun 2018 12:54:40: #2 alternative fragment length(s) may be 3,96,550 bps INFO @ Sun, 03 Jun 2018 12:54:40: #2.2 Generate R script for model : SRX2965748.05_model.r WARNING @ Sun, 03 Jun 2018 12:54:40: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:54:40: #2 You may need to consider one of the other alternative d(s): 3,96,550 WARNING @ Sun, 03 Jun 2018 12:54:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:54:40: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:54:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:54:40: 20000000 INFO @ Sun, 03 Jun 2018 12:54:43: #1 tag size is determined as 101 bps INFO @ Sun, 03 Jun 2018 12:54:43: #1 tag size = 101 INFO @ Sun, 03 Jun 2018 12:54:43: #1 total tags in treatment: 20413352 INFO @ Sun, 03 Jun 2018 12:54:43: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:54:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:54:43: #1 tags after filtering in treatment: 20413352 INFO @ Sun, 03 Jun 2018 12:54:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:54:43: #1 finished! INFO @ Sun, 03 Jun 2018 12:54:43: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:54:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:54:45: #2 number of paired peaks: 140 WARNING @ Sun, 03 Jun 2018 12:54:45: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 03 Jun 2018 12:54:45: start model_add_line... INFO @ Sun, 03 Jun 2018 12:54:45: start X-correlation... INFO @ Sun, 03 Jun 2018 12:54:45: end of X-cor INFO @ Sun, 03 Jun 2018 12:54:45: #2 finished! INFO @ Sun, 03 Jun 2018 12:54:45: #2 predicted fragment length is 96 bps INFO @ Sun, 03 Jun 2018 12:54:45: #2 alternative fragment length(s) may be 3,96,550 bps INFO @ Sun, 03 Jun 2018 12:54:45: #2.2 Generate R script for model : SRX2965748.10_model.r WARNING @ Sun, 03 Jun 2018 12:54:45: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:54:45: #2 You may need to consider one of the other alternative d(s): 3,96,550 WARNING @ Sun, 03 Jun 2018 12:54:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:54:45: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:55:12: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:55:16: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:55:22: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:55:33: #4 Write output xls file... SRX2965748.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:55:33: #4 Write peak in narrowPeak format file... SRX2965748.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:55:33: #4 Write summits bed file... SRX2965748.20_summits.bed INFO @ Sun, 03 Jun 2018 12:55:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:55:35: #4 Write output xls file... SRX2965748.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:55:35: #4 Write peak in narrowPeak format file... SRX2965748.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:55:35: #4 Write summits bed file... SRX2965748.05_summits.bed INFO @ Sun, 03 Jun 2018 12:55:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (551 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:55:41: #4 Write output xls file... SRX2965748.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:55:41: #4 Write peak in narrowPeak format file... SRX2965748.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:55:41: #4 Write summits bed file... SRX2965748.10_summits.bed INFO @ Sun, 03 Jun 2018 12:55:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (421 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。