Job ID = 10453671 sra ファイルのダウンロード中... Completed: 563398K bytes transferred in 23 seconds (198605K 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... Written 33071916 spots for /home/okishinya/chipatlas/results/rn6/SRX3478276/SRR6384655.sra Written 33071916 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:02:26 33071916 reads; of these: 33071916 (100.00%) were unpaired; of these: 738206 (2.23%) aligned 0 times 22266572 (67.33%) aligned exactly 1 time 10067138 (30.44%) aligned >1 times 97.77% overall alignment rate Time searching: 01:02:31 Overall time: 01:02:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 935531 / 32333710 = 0.0289 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 @ Thu, 08 Feb 2018 18:57:11: # Command line: callpeak -t SRX3478276.bam -f BAM -g 2.15e9 -n SRX3478276.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3478276.05 # format = BAM # ChIP-seq file = ['SRX3478276.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Thu, 08 Feb 2018 18:57:11: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:57:11: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:57:11: # Command line: callpeak -t SRX3478276.bam -f BAM -g 2.15e9 -n SRX3478276.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3478276.10 # format = BAM # ChIP-seq file = ['SRX3478276.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Thu, 08 Feb 2018 18:57:11: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:57:11: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:57:11: # Command line: callpeak -t SRX3478276.bam -f BAM -g 2.15e9 -n SRX3478276.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3478276.20 # format = BAM # ChIP-seq file = ['SRX3478276.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Thu, 08 Feb 2018 18:57:11: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:57:11: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:57:22: 1000000 INFO @ Thu, 08 Feb 2018 18:57:23: 1000000 INFO @ Thu, 08 Feb 2018 18:57:29: 1000000 INFO @ Thu, 08 Feb 2018 18:57:35: 2000000 INFO @ Thu, 08 Feb 2018 18:57:36: 2000000 INFO @ Thu, 08 Feb 2018 18:57:47: 3000000 INFO @ Thu, 08 Feb 2018 18:57:48: 3000000 INFO @ Thu, 08 Feb 2018 18:57:48: 2000000 INFO @ Thu, 08 Feb 2018 18:57:57: 4000000 INFO @ Thu, 08 Feb 2018 18:58:03: 4000000 INFO @ Thu, 08 Feb 2018 18:58:06: 5000000 INFO @ Thu, 08 Feb 2018 18:58:07: 3000000 INFO @ Thu, 08 Feb 2018 18:58:17: 6000000 INFO @ Thu, 08 Feb 2018 18:58:17: 5000000 INFO @ Thu, 08 Feb 2018 18:58:25: 4000000 INFO @ Thu, 08 Feb 2018 18:58:27: 7000000 INFO @ Thu, 08 Feb 2018 18:58:30: 6000000 INFO @ Thu, 08 Feb 2018 18:58:38: 8000000 INFO @ Thu, 08 Feb 2018 18:58:41: 5000000 INFO @ Thu, 08 Feb 2018 18:58:46: 7000000 INFO @ Thu, 08 Feb 2018 18:58:47: 9000000 INFO @ Thu, 08 Feb 2018 18:58:56: 10000000 INFO @ Thu, 08 Feb 2018 18:58:59: 6000000 INFO @ Thu, 08 Feb 2018 18:59:00: 8000000 INFO @ Thu, 08 Feb 2018 18:59:06: 11000000 INFO @ Thu, 08 Feb 2018 18:59:14: 9000000 INFO @ Thu, 08 Feb 2018 18:59:16: 12000000 INFO @ Thu, 08 Feb 2018 18:59:18: 7000000 INFO @ Thu, 08 Feb 2018 18:59:27: 13000000 INFO @ Thu, 08 Feb 2018 18:59:31: 10000000 INFO @ Thu, 08 Feb 2018 18:59:35: 8000000 INFO @ Thu, 08 Feb 2018 18:59:38: 14000000 INFO @ Thu, 08 Feb 2018 18:59:48: 15000000 INFO @ Thu, 08 Feb 2018 18:59:48: 11000000 INFO @ Thu, 08 Feb 2018 18:59:52: 9000000 INFO @ Thu, 08 Feb 2018 18:59:58: 16000000 INFO @ Thu, 08 Feb 2018 19:00:05: 12000000 INFO @ Thu, 08 Feb 2018 19:00:06: 10000000 INFO @ Thu, 08 Feb 2018 19:00:09: 17000000 INFO @ Thu, 08 Feb 2018 19:00:19: 18000000 INFO @ Thu, 08 Feb 2018 19:00:23: 11000000 INFO @ Thu, 08 Feb 2018 19:00:24: 13000000 INFO @ Thu, 08 Feb 2018 19:00:30: 19000000 INFO @ Thu, 08 Feb 2018 19:00:38: 12000000 INFO @ Thu, 08 Feb 2018 19:00:40: 20000000 INFO @ Thu, 08 Feb 2018 19:00:40: 14000000 INFO @ Thu, 08 Feb 2018 19:00:49: 21000000 INFO @ Thu, 08 Feb 2018 19:00:53: 13000000 INFO @ Thu, 08 Feb 2018 19:00:57: 15000000 INFO @ Thu, 08 Feb 2018 19:00:58: 22000000 INFO @ Thu, 08 Feb 2018 19:01:07: 23000000 INFO @ Thu, 08 Feb 2018 19:01:09: 14000000 INFO @ Thu, 08 Feb 2018 19:01:15: 16000000 INFO @ Thu, 08 Feb 2018 19:01:16: 24000000 INFO @ Thu, 08 Feb 2018 19:01:25: 15000000 INFO @ Thu, 08 Feb 2018 19:01:25: 25000000 INFO @ Thu, 08 Feb 2018 19:01:33: 17000000 INFO @ Thu, 08 Feb 2018 19:01:34: 26000000 INFO @ Thu, 08 Feb 2018 19:01:41: 16000000 INFO @ Thu, 08 Feb 2018 19:01:43: 27000000 INFO @ Thu, 08 Feb 2018 19:01:50: 18000000 INFO @ Thu, 08 Feb 2018 19:01:52: 28000000 INFO @ Thu, 08 Feb 2018 19:01:56: 17000000 INFO @ Thu, 08 Feb 2018 19:02:01: 29000000 INFO @ Thu, 08 Feb 2018 19:02:07: 19000000 INFO @ Thu, 08 Feb 2018 19:02:10: 30000000 INFO @ Thu, 08 Feb 2018 19:02:11: 18000000 INFO @ Thu, 08 Feb 2018 19:02:19: 31000000 INFO @ Thu, 08 Feb 2018 19:02:21: 20000000 INFO @ Thu, 08 Feb 2018 19:02:23: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 19:02:23: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 19:02:23: #1 total tags in treatment: 31398179 INFO @ Thu, 08 Feb 2018 19:02:23: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 19:02:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 19:02:24: #1 tags after filtering in treatment: 31398096 INFO @ Thu, 08 Feb 2018 19:02:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 19:02:24: #1 finished! INFO @ Thu, 08 Feb 2018 19:02:24: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 19:02:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 19:02:25: 19000000 INFO @ Thu, 08 Feb 2018 19:02:28: #2 number of paired peaks: 5870 INFO @ Thu, 08 Feb 2018 19:02:28: start model_add_line... INFO @ Thu, 08 Feb 2018 19:02:28: start X-correlation... INFO @ Thu, 08 Feb 2018 19:02:28: end of X-cor INFO @ Thu, 08 Feb 2018 19:02:28: #2 finished! INFO @ Thu, 08 Feb 2018 19:02:28: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 19:02:28: #2 alternative fragment length(s) may be 50,228,401,408,489 bps INFO @ Thu, 08 Feb 2018 19:02:28: #2.2 Generate R script for model : SRX3478276.20_model.r WARNING @ Thu, 08 Feb 2018 19:02:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 19:02:28: #2 You may need to consider one of the other alternative d(s): 50,228,401,408,489 WARNING @ Thu, 08 Feb 2018 19:02:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 19:02:28: #3 Call peaks... INFO @ Thu, 08 Feb 2018 19:02:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 19:02:37: 21000000 INFO @ Thu, 08 Feb 2018 19:02:39: 20000000 INFO @ Thu, 08 Feb 2018 19:02:52: 22000000 INFO @ Thu, 08 Feb 2018 19:02:53: 21000000 INFO @ Thu, 08 Feb 2018 19:03:08: 22000000 INFO @ Thu, 08 Feb 2018 19:03:08: 23000000 INFO @ Thu, 08 Feb 2018 19:03:21: 24000000 INFO @ Thu, 08 Feb 2018 19:03:24: 23000000 INFO @ Thu, 08 Feb 2018 19:03:31: 25000000 INFO @ Thu, 08 Feb 2018 19:03:41: 24000000 INFO @ Thu, 08 Feb 2018 19:03:43: 26000000 INFO @ Thu, 08 Feb 2018 19:03:56: 27000000 INFO @ Thu, 08 Feb 2018 19:03:59: 25000000 INFO @ Thu, 08 Feb 2018 19:04:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 19:04:12: 28000000 INFO @ Thu, 08 Feb 2018 19:04:14: 26000000 INFO @ Thu, 08 Feb 2018 19:04:26: 27000000 INFO @ Thu, 08 Feb 2018 19:04:33: 29000000 INFO @ Thu, 08 Feb 2018 19:04:37: 28000000 INFO @ Thu, 08 Feb 2018 19:04:49: 29000000 INFO @ Thu, 08 Feb 2018 19:04:54: 30000000 INFO @ Thu, 08 Feb 2018 19:05:01: 30000000 INFO @ Thu, 08 Feb 2018 19:05:04: #4 Write output xls file... SRX3478276.20_peaks.xls INFO @ Thu, 08 Feb 2018 19:05:04: #4 Write peak in narrowPeak format file... SRX3478276.20_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 19:05:04: #4 Write summits bed file... SRX3478276.20_summits.bed INFO @ Thu, 08 Feb 2018 19:05:04: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (538 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 19:05:13: 31000000 INFO @ Thu, 08 Feb 2018 19:05:14: 31000000 INFO @ Thu, 08 Feb 2018 19:05:18: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 19:05:18: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 19:05:18: #1 total tags in treatment: 31398179 INFO @ Thu, 08 Feb 2018 19:05:18: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 19:05:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 19:05:20: #1 tags after filtering in treatment: 31398096 INFO @ Thu, 08 Feb 2018 19:05:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 19:05:20: #1 finished! INFO @ Thu, 08 Feb 2018 19:05:20: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 19:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 19:05:21: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 19:05:21: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 19:05:21: #1 total tags in treatment: 31398179 INFO @ Thu, 08 Feb 2018 19:05:21: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 19:05:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 19:05:23: #1 tags after filtering in treatment: 31398096 INFO @ Thu, 08 Feb 2018 19:05:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 19:05:23: #1 finished! INFO @ Thu, 08 Feb 2018 19:05:23: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 19:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 19:05:23: #2 number of paired peaks: 5870 INFO @ Thu, 08 Feb 2018 19:05:23: start model_add_line... INFO @ Thu, 08 Feb 2018 19:05:24: start X-correlation... INFO @ Thu, 08 Feb 2018 19:05:24: end of X-cor INFO @ Thu, 08 Feb 2018 19:05:24: #2 finished! INFO @ Thu, 08 Feb 2018 19:05:24: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 19:05:24: #2 alternative fragment length(s) may be 50,228,401,408,489 bps INFO @ Thu, 08 Feb 2018 19:05:24: #2.2 Generate R script for model : SRX3478276.10_model.r WARNING @ Thu, 08 Feb 2018 19:05:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 19:05:24: #2 You may need to consider one of the other alternative d(s): 50,228,401,408,489 WARNING @ Thu, 08 Feb 2018 19:05:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 19:05:24: #3 Call peaks... INFO @ Thu, 08 Feb 2018 19:05:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 19:05:26: #2 number of paired peaks: 5870 INFO @ Thu, 08 Feb 2018 19:05:26: start model_add_line... INFO @ Thu, 08 Feb 2018 19:05:27: start X-correlation... INFO @ Thu, 08 Feb 2018 19:05:27: end of X-cor INFO @ Thu, 08 Feb 2018 19:05:27: #2 finished! INFO @ Thu, 08 Feb 2018 19:05:27: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 19:05:27: #2 alternative fragment length(s) may be 50,228,401,408,489 bps INFO @ Thu, 08 Feb 2018 19:05:27: #2.2 Generate R script for model : SRX3478276.05_model.r WARNING @ Thu, 08 Feb 2018 19:05:27: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 19:05:27: #2 You may need to consider one of the other alternative d(s): 50,228,401,408,489 WARNING @ Thu, 08 Feb 2018 19:05:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 19:05:27: #3 Call peaks... INFO @ Thu, 08 Feb 2018 19:05:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 19:06:59: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 19:07:03: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 19:07:58: #4 Write output xls file... SRX3478276.10_peaks.xls INFO @ Thu, 08 Feb 2018 19:07:58: #4 Write peak in narrowPeak format file... SRX3478276.10_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 19:07:58: #4 Write summits bed file... SRX3478276.10_summits.bed INFO @ Thu, 08 Feb 2018 19:07:58: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (1105 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 19:08:03: #4 Write output xls file... SRX3478276.05_peaks.xls INFO @ Thu, 08 Feb 2018 19:08:03: #4 Write peak in narrowPeak format file... SRX3478276.05_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 19:08:03: #4 Write summits bed file... SRX3478276.05_summits.bed INFO @ Thu, 08 Feb 2018 19:08:03: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (1930 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。