Job ID = 10714470 sra ファイルのダウンロード中... Completed: 1240531K bytes transferred in 22 seconds (456688K 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: PAIRED fastq に変換中... Read 20259317 spots for /home/okishinya/chipatlas/results/ce10/SRX4085386/SRR7167415.sra Written 20259317 spots for /home/okishinya/chipatlas/results/ce10/SRX4085386/SRR7167415.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: 00:17:56 20259317 reads; of these: 20259317 (100.00%) were paired; of these: 7397941 (36.52%) aligned concordantly 0 times 10954774 (54.07%) aligned concordantly exactly 1 time 1906602 (9.41%) aligned concordantly >1 times ---- 7397941 pairs aligned concordantly 0 times; of these: 451740 (6.11%) aligned discordantly 1 time ---- 6946201 pairs aligned 0 times concordantly or discordantly; of these: 13892402 mates make up the pairs; of these: 9785941 (70.44%) aligned 0 times 3576797 (25.75%) aligned exactly 1 time 529664 (3.81%) aligned >1 times 75.85% overall alignment rate Time searching: 00:17:56 Overall time: 00:17:56 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1038045 / 13123984 = 0.0791 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 13:09:26: # Command line: callpeak -t SRX4085386.bam -f BAM -g ce -n SRX4085386.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085386.10 # format = BAM # ChIP-seq file = ['SRX4085386.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 13:09:26: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:09:26: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:09:26: # Command line: callpeak -t SRX4085386.bam -f BAM -g ce -n SRX4085386.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085386.20 # format = BAM # ChIP-seq file = ['SRX4085386.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 13:09:26: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:09:26: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:09:26: # Command line: callpeak -t SRX4085386.bam -f BAM -g ce -n SRX4085386.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085386.05 # format = BAM # ChIP-seq file = ['SRX4085386.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 13:09:26: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:09:26: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:09:33: 1000000 INFO @ Sun, 03 Jun 2018 13:09:34: 1000000 INFO @ Sun, 03 Jun 2018 13:09:34: 1000000 INFO @ Sun, 03 Jun 2018 13:09:39: 2000000 INFO @ Sun, 03 Jun 2018 13:09:41: 2000000 INFO @ Sun, 03 Jun 2018 13:09:41: 2000000 INFO @ Sun, 03 Jun 2018 13:09:45: 3000000 INFO @ Sun, 03 Jun 2018 13:09:48: 3000000 INFO @ Sun, 03 Jun 2018 13:09:48: 3000000 INFO @ Sun, 03 Jun 2018 13:09:51: 4000000 INFO @ Sun, 03 Jun 2018 13:09:56: 4000000 INFO @ Sun, 03 Jun 2018 13:09:56: 4000000 INFO @ Sun, 03 Jun 2018 13:09:57: 5000000 INFO @ Sun, 03 Jun 2018 13:10:03: 5000000 INFO @ Sun, 03 Jun 2018 13:10:03: 5000000 INFO @ Sun, 03 Jun 2018 13:10:03: 6000000 INFO @ Sun, 03 Jun 2018 13:10:09: 7000000 INFO @ Sun, 03 Jun 2018 13:10:10: 6000000 INFO @ Sun, 03 Jun 2018 13:10:10: 6000000 INFO @ Sun, 03 Jun 2018 13:10:16: 8000000 INFO @ Sun, 03 Jun 2018 13:10:17: 7000000 INFO @ Sun, 03 Jun 2018 13:10:17: 7000000 INFO @ Sun, 03 Jun 2018 13:10:22: 9000000 INFO @ Sun, 03 Jun 2018 13:10:24: 8000000 INFO @ Sun, 03 Jun 2018 13:10:24: 8000000 INFO @ Sun, 03 Jun 2018 13:10:28: 10000000 INFO @ Sun, 03 Jun 2018 13:10:32: 9000000 INFO @ Sun, 03 Jun 2018 13:10:32: 9000000 INFO @ Sun, 03 Jun 2018 13:10:34: 11000000 INFO @ Sun, 03 Jun 2018 13:10:39: 10000000 INFO @ Sun, 03 Jun 2018 13:10:39: 10000000 INFO @ Sun, 03 Jun 2018 13:10:40: 12000000 INFO @ Sun, 03 Jun 2018 13:10:46: 13000000 INFO @ Sun, 03 Jun 2018 13:10:46: 11000000 INFO @ Sun, 03 Jun 2018 13:10:46: 11000000 INFO @ Sun, 03 Jun 2018 13:10:52: 14000000 INFO @ Sun, 03 Jun 2018 13:10:53: 12000000 INFO @ Sun, 03 Jun 2018 13:10:53: 12000000 INFO @ Sun, 03 Jun 2018 13:10:58: 15000000 INFO @ Sun, 03 Jun 2018 13:11:00: 13000000 INFO @ Sun, 03 Jun 2018 13:11:00: 13000000 INFO @ Sun, 03 Jun 2018 13:11:04: 16000000 INFO @ Sun, 03 Jun 2018 13:11:07: 14000000 INFO @ Sun, 03 Jun 2018 13:11:07: 14000000 INFO @ Sun, 03 Jun 2018 13:11:10: 17000000 INFO @ Sun, 03 Jun 2018 13:11:14: 15000000 INFO @ Sun, 03 Jun 2018 13:11:14: 15000000 INFO @ Sun, 03 Jun 2018 13:11:16: 18000000 INFO @ Sun, 03 Jun 2018 13:11:21: 16000000 INFO @ Sun, 03 Jun 2018 13:11:21: 16000000 INFO @ Sun, 03 Jun 2018 13:11:22: 19000000 INFO @ Sun, 03 Jun 2018 13:11:28: 20000000 INFO @ Sun, 03 Jun 2018 13:11:28: 17000000 INFO @ Sun, 03 Jun 2018 13:11:28: 17000000 INFO @ Sun, 03 Jun 2018 13:11:34: 21000000 INFO @ Sun, 03 Jun 2018 13:11:35: 18000000 INFO @ Sun, 03 Jun 2018 13:11:35: 18000000 INFO @ Sun, 03 Jun 2018 13:11:40: 22000000 INFO @ Sun, 03 Jun 2018 13:11:42: 19000000 INFO @ Sun, 03 Jun 2018 13:11:42: 19000000 INFO @ Sun, 03 Jun 2018 13:11:46: 23000000 INFO @ Sun, 03 Jun 2018 13:11:49: 20000000 INFO @ Sun, 03 Jun 2018 13:11:49: 20000000 INFO @ Sun, 03 Jun 2018 13:11:52: 24000000 INFO @ Sun, 03 Jun 2018 13:11:56: 21000000 INFO @ Sun, 03 Jun 2018 13:11:56: 21000000 INFO @ Sun, 03 Jun 2018 13:11:58: 25000000 INFO @ Sun, 03 Jun 2018 13:12:03: 22000000 INFO @ Sun, 03 Jun 2018 13:12:03: 22000000 INFO @ Sun, 03 Jun 2018 13:12:04: 26000000 INFO @ Sun, 03 Jun 2018 13:12:10: 23000000 INFO @ Sun, 03 Jun 2018 13:12:10: 23000000 INFO @ Sun, 03 Jun 2018 13:12:10: 27000000 INFO @ Sun, 03 Jun 2018 13:12:16: 28000000 INFO @ Sun, 03 Jun 2018 13:12:17: 24000000 INFO @ Sun, 03 Jun 2018 13:12:17: 24000000 INFO @ Sun, 03 Jun 2018 13:12:20: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:12:20: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:12:20: #1 total tags in treatment: 11842836 INFO @ Sun, 03 Jun 2018 13:12:20: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:12:20: #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 13:12:20: #1 tags after filtering in treatment: 10202813 INFO @ Sun, 03 Jun 2018 13:12:20: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:12:20: #1 finished! INFO @ Sun, 03 Jun 2018 13:12:20: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:12:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:12:21: #2 number of paired peaks: 276 WARNING @ Sun, 03 Jun 2018 13:12:21: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 03 Jun 2018 13:12:21: start model_add_line... INFO @ Sun, 03 Jun 2018 13:12:21: start X-correlation... INFO @ Sun, 03 Jun 2018 13:12:21: end of X-cor INFO @ Sun, 03 Jun 2018 13:12:21: #2 finished! INFO @ Sun, 03 Jun 2018 13:12:21: #2 predicted fragment length is 79 bps INFO @ Sun, 03 Jun 2018 13:12:21: #2 alternative fragment length(s) may be 4,79,590,595 bps INFO @ Sun, 03 Jun 2018 13:12:21: #2.2 Generate R script for model : SRX4085386.20_model.r WARNING @ Sun, 03 Jun 2018 13:12:21: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:12:21: #2 You may need to consider one of the other alternative d(s): 4,79,590,595 WARNING @ Sun, 03 Jun 2018 13:12:21: #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 13:12:21: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:12:24: 25000000 INFO @ Sun, 03 Jun 2018 13:12:24: 25000000 INFO @ Sun, 03 Jun 2018 13:12:30: 26000000 INFO @ Sun, 03 Jun 2018 13:12:30: 26000000 INFO @ Sun, 03 Jun 2018 13:12:37: 27000000 INFO @ Sun, 03 Jun 2018 13:12:37: 27000000 INFO @ Sun, 03 Jun 2018 13:12:43: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:12:44: 28000000 INFO @ Sun, 03 Jun 2018 13:12:44: 28000000 INFO @ Sun, 03 Jun 2018 13:12:48: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:12:48: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:12:48: #1 total tags in treatment: 11842836 INFO @ Sun, 03 Jun 2018 13:12:48: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:12:48: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:12:48: #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 13:12:48: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:12:48: #1 total tags in treatment: 11842836 INFO @ Sun, 03 Jun 2018 13:12:48: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:12:48: #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 13:12:48: #1 tags after filtering in treatment: 10202813 INFO @ Sun, 03 Jun 2018 13:12:48: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:12:48: #1 finished! INFO @ Sun, 03 Jun 2018 13:12:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:12:48: #1 tags after filtering in treatment: 10202813 INFO @ Sun, 03 Jun 2018 13:12:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:12:48: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Jun 2018 13:12:48: #1 finished! INFO @ Sun, 03 Jun 2018 13:12:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:12:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:12:48: #2 number of paired peaks: 276 WARNING @ Sun, 03 Jun 2018 13:12:48: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 03 Jun 2018 13:12:48: start model_add_line... INFO @ Sun, 03 Jun 2018 13:12:49: #2 number of paired peaks: 276 WARNING @ Sun, 03 Jun 2018 13:12:49: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 03 Jun 2018 13:12:49: start model_add_line... INFO @ Sun, 03 Jun 2018 13:12:49: start X-correlation... INFO @ Sun, 03 Jun 2018 13:12:49: end of X-cor INFO @ Sun, 03 Jun 2018 13:12:49: #2 finished! INFO @ Sun, 03 Jun 2018 13:12:49: #2 predicted fragment length is 79 bps INFO @ Sun, 03 Jun 2018 13:12:49: #2 alternative fragment length(s) may be 4,79,590,595 bps INFO @ Sun, 03 Jun 2018 13:12:49: #2.2 Generate R script for model : SRX4085386.10_model.r WARNING @ Sun, 03 Jun 2018 13:12:49: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:12:49: #2 You may need to consider one of the other alternative d(s): 4,79,590,595 WARNING @ Sun, 03 Jun 2018 13:12:49: #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 13:12:49: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:12:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:12:49: start X-correlation... INFO @ Sun, 03 Jun 2018 13:12:49: end of X-cor INFO @ Sun, 03 Jun 2018 13:12:49: #2 finished! INFO @ Sun, 03 Jun 2018 13:12:49: #2 predicted fragment length is 79 bps INFO @ Sun, 03 Jun 2018 13:12:49: #2 alternative fragment length(s) may be 4,79,590,595 bps INFO @ Sun, 03 Jun 2018 13:12:49: #2.2 Generate R script for model : SRX4085386.05_model.r WARNING @ Sun, 03 Jun 2018 13:12:49: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:12:49: #2 You may need to consider one of the other alternative d(s): 4,79,590,595 WARNING @ Sun, 03 Jun 2018 13:12:49: #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 13:12:49: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:12:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:12:54: #4 Write output xls file... SRX4085386.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:12:54: #4 Write peak in narrowPeak format file... SRX4085386.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:12:54: #4 Write summits bed file... SRX4085386.20_summits.bed INFO @ Sun, 03 Jun 2018 13:12:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:13:09: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:13:11: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:13:21: #4 Write output xls file... SRX4085386.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:13:21: #4 Write peak in narrowPeak format file... SRX4085386.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:13:21: #4 Write summits bed file... SRX4085386.05_summits.bed INFO @ Sun, 03 Jun 2018 13:13:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2403 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:13:23: #4 Write output xls file... SRX4085386.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:13:23: #4 Write peak in narrowPeak format file... SRX4085386.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:13:23: #4 Write summits bed file... SRX4085386.10_summits.bed INFO @ Sun, 03 Jun 2018 13:13:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1237 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。