Job ID = 10714495 sra ファイルのダウンロード中... Completed: 1414179K bytes transferred in 17 seconds (660025K 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 21947298 spots for /home/okishinya/chipatlas/results/ce10/SRX4085412/SRR7167441.sra Written 21947298 spots for /home/okishinya/chipatlas/results/ce10/SRX4085412/SRR7167441.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: 00:16:42 21947298 reads; of these: 21947298 (100.00%) were paired; of these: 11557162 (52.66%) aligned concordantly 0 times 8526667 (38.85%) aligned concordantly exactly 1 time 1863469 (8.49%) aligned concordantly >1 times ---- 11557162 pairs aligned concordantly 0 times; of these: 430132 (3.72%) aligned discordantly 1 time ---- 11127030 pairs aligned 0 times concordantly or discordantly; of these: 22254060 mates make up the pairs; of these: 17031690 (76.53%) aligned 0 times 4622949 (20.77%) aligned exactly 1 time 599421 (2.69%) aligned >1 times 61.20% overall alignment rate Time searching: 00:16:42 Overall time: 00:16:42 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_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] 1435203 / 10662308 = 0.1346 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 13:20:35: # Command line: callpeak -t SRX4085412.bam -f BAM -g ce -n SRX4085412.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085412.20 # format = BAM # ChIP-seq file = ['SRX4085412.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 13:20:35: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:20:35: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:20:35: # Command line: callpeak -t SRX4085412.bam -f BAM -g ce -n SRX4085412.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085412.10 # format = BAM # ChIP-seq file = ['SRX4085412.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 13:20:35: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:20:35: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:20:35: # Command line: callpeak -t SRX4085412.bam -f BAM -g ce -n SRX4085412.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085412.05 # format = BAM # ChIP-seq file = ['SRX4085412.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 13:20:35: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:20:35: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:20:41: 1000000 INFO @ Sun, 03 Jun 2018 13:20:41: 1000000 INFO @ Sun, 03 Jun 2018 13:20:41: 1000000 INFO @ Sun, 03 Jun 2018 13:20:47: 2000000 INFO @ Sun, 03 Jun 2018 13:20:47: 2000000 INFO @ Sun, 03 Jun 2018 13:20:47: 2000000 INFO @ Sun, 03 Jun 2018 13:20:53: 3000000 INFO @ Sun, 03 Jun 2018 13:20:53: 3000000 INFO @ Sun, 03 Jun 2018 13:20:53: 3000000 INFO @ Sun, 03 Jun 2018 13:20:59: 4000000 INFO @ Sun, 03 Jun 2018 13:20:59: 4000000 INFO @ Sun, 03 Jun 2018 13:20:59: 4000000 INFO @ Sun, 03 Jun 2018 13:21:05: 5000000 INFO @ Sun, 03 Jun 2018 13:21:05: 5000000 INFO @ Sun, 03 Jun 2018 13:21:05: 5000000 INFO @ Sun, 03 Jun 2018 13:21:11: 6000000 INFO @ Sun, 03 Jun 2018 13:21:12: 6000000 INFO @ Sun, 03 Jun 2018 13:21:12: 6000000 INFO @ Sun, 03 Jun 2018 13:21:17: 7000000 INFO @ Sun, 03 Jun 2018 13:21:18: 7000000 INFO @ Sun, 03 Jun 2018 13:21:18: 7000000 INFO @ Sun, 03 Jun 2018 13:21:24: 8000000 INFO @ Sun, 03 Jun 2018 13:21:24: 8000000 INFO @ Sun, 03 Jun 2018 13:21:25: 8000000 INFO @ Sun, 03 Jun 2018 13:21:30: 9000000 INFO @ Sun, 03 Jun 2018 13:21:30: 9000000 INFO @ Sun, 03 Jun 2018 13:21:31: 9000000 INFO @ Sun, 03 Jun 2018 13:21:36: 10000000 INFO @ Sun, 03 Jun 2018 13:21:36: 10000000 INFO @ Sun, 03 Jun 2018 13:21:37: 10000000 INFO @ Sun, 03 Jun 2018 13:21:42: 11000000 INFO @ Sun, 03 Jun 2018 13:21:42: 11000000 INFO @ Sun, 03 Jun 2018 13:21:44: 11000000 INFO @ Sun, 03 Jun 2018 13:21:48: 12000000 INFO @ Sun, 03 Jun 2018 13:21:48: 12000000 INFO @ Sun, 03 Jun 2018 13:21:50: 12000000 INFO @ Sun, 03 Jun 2018 13:21:54: 13000000 INFO @ Sun, 03 Jun 2018 13:21:55: 13000000 INFO @ Sun, 03 Jun 2018 13:21:56: 13000000 INFO @ Sun, 03 Jun 2018 13:22:00: 14000000 INFO @ Sun, 03 Jun 2018 13:22:01: 14000000 INFO @ Sun, 03 Jun 2018 13:22:03: 14000000 INFO @ Sun, 03 Jun 2018 13:22:06: 15000000 INFO @ Sun, 03 Jun 2018 13:22:07: 15000000 INFO @ Sun, 03 Jun 2018 13:22:09: 15000000 INFO @ Sun, 03 Jun 2018 13:22:12: 16000000 INFO @ Sun, 03 Jun 2018 13:22:13: 16000000 INFO @ Sun, 03 Jun 2018 13:22:15: 16000000 INFO @ Sun, 03 Jun 2018 13:22:18: 17000000 INFO @ Sun, 03 Jun 2018 13:22:20: 17000000 INFO @ Sun, 03 Jun 2018 13:22:22: 17000000 INFO @ Sun, 03 Jun 2018 13:22:25: 18000000 INFO @ Sun, 03 Jun 2018 13:22:26: 18000000 INFO @ Sun, 03 Jun 2018 13:22:28: 18000000 INFO @ Sun, 03 Jun 2018 13:22:31: 19000000 INFO @ Sun, 03 Jun 2018 13:22:32: 19000000 INFO @ Sun, 03 Jun 2018 13:22:35: 19000000 INFO @ Sun, 03 Jun 2018 13:22:37: 20000000 INFO @ Sun, 03 Jun 2018 13:22:38: 20000000 INFO @ Sun, 03 Jun 2018 13:22:41: 20000000 INFO @ Sun, 03 Jun 2018 13:22:43: 21000000 INFO @ Sun, 03 Jun 2018 13:22:44: 21000000 INFO @ Sun, 03 Jun 2018 13:22:47: 21000000 INFO @ Sun, 03 Jun 2018 13:22:49: 22000000 INFO @ Sun, 03 Jun 2018 13:22:51: 22000000 INFO @ Sun, 03 Jun 2018 13:22:53: 22000000 INFO @ Sun, 03 Jun 2018 13:22:54: 23000000 INFO @ Sun, 03 Jun 2018 13:22:56: 23000000 INFO @ Sun, 03 Jun 2018 13:22:59: 23000000 INFO @ Sun, 03 Jun 2018 13:23:00: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:23:00: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:23:00: #1 total tags in treatment: 8992558 INFO @ Sun, 03 Jun 2018 13:23:00: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:23:00: #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 13:23:00: #1 tags after filtering in treatment: 7237958 INFO @ Sun, 03 Jun 2018 13:23:00: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 13:23:00: #1 finished! INFO @ Sun, 03 Jun 2018 13:23:00: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:23:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:23:00: #2 number of paired peaks: 940 WARNING @ Sun, 03 Jun 2018 13:23:00: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Sun, 03 Jun 2018 13:23:00: start model_add_line... INFO @ Sun, 03 Jun 2018 13:23:01: start X-correlation... INFO @ Sun, 03 Jun 2018 13:23:01: end of X-cor INFO @ Sun, 03 Jun 2018 13:23:01: #2 finished! INFO @ Sun, 03 Jun 2018 13:23:01: #2 predicted fragment length is 86 bps INFO @ Sun, 03 Jun 2018 13:23:01: #2 alternative fragment length(s) may be 86 bps INFO @ Sun, 03 Jun 2018 13:23:01: #2.2 Generate R script for model : SRX4085412.05_model.r WARNING @ Sun, 03 Jun 2018 13:23:01: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:23:01: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sun, 03 Jun 2018 13:23:01: #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 13:23:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:23:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:23:01: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:23:01: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:23:01: #1 total tags in treatment: 8992558 INFO @ Sun, 03 Jun 2018 13:23:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:23:01: #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 13:23:02: #1 tags after filtering in treatment: 7237958 INFO @ Sun, 03 Jun 2018 13:23:02: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 13:23:02: #1 finished! INFO @ Sun, 03 Jun 2018 13:23:02: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:23:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:23:02: #2 number of paired peaks: 940 WARNING @ Sun, 03 Jun 2018 13:23:02: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Sun, 03 Jun 2018 13:23:02: start model_add_line... INFO @ Sun, 03 Jun 2018 13:23:02: start X-correlation... INFO @ Sun, 03 Jun 2018 13:23:02: end of X-cor INFO @ Sun, 03 Jun 2018 13:23:02: #2 finished! INFO @ Sun, 03 Jun 2018 13:23:02: #2 predicted fragment length is 86 bps INFO @ Sun, 03 Jun 2018 13:23:02: #2 alternative fragment length(s) may be 86 bps INFO @ Sun, 03 Jun 2018 13:23:02: #2.2 Generate R script for model : SRX4085412.20_model.r WARNING @ Sun, 03 Jun 2018 13:23:02: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:23:02: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sun, 03 Jun 2018 13:23:02: #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 13:23:02: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:23:04: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:23:04: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:23:04: #1 total tags in treatment: 8992558 INFO @ Sun, 03 Jun 2018 13:23:04: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:23:04: #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 13:23:04: #1 tags after filtering in treatment: 7237958 INFO @ Sun, 03 Jun 2018 13:23:04: #1 Redundant rate of treatment: 0.20 INFO @ Sun, 03 Jun 2018 13:23:04: #1 finished! INFO @ Sun, 03 Jun 2018 13:23:04: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:23:05: #2 number of paired peaks: 940 WARNING @ Sun, 03 Jun 2018 13:23:05: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Sun, 03 Jun 2018 13:23:05: start model_add_line... INFO @ Sun, 03 Jun 2018 13:23:05: start X-correlation... INFO @ Sun, 03 Jun 2018 13:23:05: end of X-cor INFO @ Sun, 03 Jun 2018 13:23:05: #2 finished! INFO @ Sun, 03 Jun 2018 13:23:05: #2 predicted fragment length is 86 bps INFO @ Sun, 03 Jun 2018 13:23:05: #2 alternative fragment length(s) may be 86 bps INFO @ Sun, 03 Jun 2018 13:23:05: #2.2 Generate R script for model : SRX4085412.10_model.r WARNING @ Sun, 03 Jun 2018 13:23:05: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:23:05: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sun, 03 Jun 2018 13:23:05: #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 13:23:05: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:23:18: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:23:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:23:22: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write output xls file... SRX4085412.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write peak in narrowPeak format file... SRX4085412.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write summits bed file... SRX4085412.05_summits.bed INFO @ Sun, 03 Jun 2018 13:23:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7654 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:23:28: #4 Write output xls file... SRX4085412.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:23:29: #4 Write peak in narrowPeak format file... SRX4085412.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:23:29: #4 Write summits bed file... SRX4085412.20_summits.bed INFO @ Sun, 03 Jun 2018 13:23:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2512 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:23:31: #4 Write output xls file... SRX4085412.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:23:31: #4 Write peak in narrowPeak format file... SRX4085412.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:23:31: #4 Write summits bed file... SRX4085412.10_summits.bed INFO @ Sun, 03 Jun 2018 13:23:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4810 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。