Job ID = 10487573 sra ファイルのダウンロード中... Completed: 3638609K bytes transferred in 66 seconds (448102K 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 54012219 spots for /home/okishinya/chipatlas/results/rn6/SRX2611104/SRR5311148.sra Written 54012219 spots total 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 03:06:02 54012219 reads; of these: 54012219 (100.00%) were unpaired; of these: 16745417 (31.00%) aligned 0 times 31878806 (59.02%) aligned exactly 1 time 5387996 (9.98%) aligned >1 times 69.00% overall alignment rate Time searching: 03:06:07 Overall time: 03:06:07 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 28 files... [bam_rmdupse_core] 8327376 / 37266802 = 0.2235 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, 18 Mar 2018 12:59:02: # Command line: callpeak -t SRX2611104.bam -f BAM -g 2.15e9 -n SRX2611104.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611104.20 # format = BAM # ChIP-seq file = ['SRX2611104.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 @ Sun, 18 Mar 2018 12:59:02: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:59:02: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:59:02: # Command line: callpeak -t SRX2611104.bam -f BAM -g 2.15e9 -n SRX2611104.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611104.05 # format = BAM # ChIP-seq file = ['SRX2611104.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 @ Sun, 18 Mar 2018 12:59:02: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:59:02: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:59:02: # Command line: callpeak -t SRX2611104.bam -f BAM -g 2.15e9 -n SRX2611104.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611104.10 # format = BAM # ChIP-seq file = ['SRX2611104.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 @ Sun, 18 Mar 2018 12:59:02: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:59:02: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:59:11: 1000000 INFO @ Sun, 18 Mar 2018 12:59:12: 1000000 INFO @ Sun, 18 Mar 2018 12:59:12: 1000000 INFO @ Sun, 18 Mar 2018 12:59:21: 2000000 INFO @ Sun, 18 Mar 2018 12:59:21: 2000000 INFO @ Sun, 18 Mar 2018 12:59:21: 2000000 INFO @ Sun, 18 Mar 2018 12:59:30: 3000000 INFO @ Sun, 18 Mar 2018 12:59:31: 3000000 INFO @ Sun, 18 Mar 2018 12:59:31: 3000000 INFO @ Sun, 18 Mar 2018 12:59:39: 4000000 INFO @ Sun, 18 Mar 2018 12:59:40: 4000000 INFO @ Sun, 18 Mar 2018 12:59:40: 4000000 INFO @ Sun, 18 Mar 2018 12:59:48: 5000000 INFO @ Sun, 18 Mar 2018 12:59:50: 5000000 INFO @ Sun, 18 Mar 2018 12:59:50: 5000000 INFO @ Sun, 18 Mar 2018 12:59:58: 6000000 INFO @ Sun, 18 Mar 2018 12:59:59: 6000000 INFO @ Sun, 18 Mar 2018 12:59:59: 6000000 INFO @ Sun, 18 Mar 2018 13:00:07: 7000000 INFO @ Sun, 18 Mar 2018 13:00:08: 7000000 INFO @ Sun, 18 Mar 2018 13:00:08: 7000000 INFO @ Sun, 18 Mar 2018 13:00:16: 8000000 INFO @ Sun, 18 Mar 2018 13:00:18: 8000000 INFO @ Sun, 18 Mar 2018 13:00:18: 8000000 INFO @ Sun, 18 Mar 2018 13:00:25: 9000000 INFO @ Sun, 18 Mar 2018 13:00:27: 9000000 INFO @ Sun, 18 Mar 2018 13:00:28: 9000000 INFO @ Sun, 18 Mar 2018 13:00:35: 10000000 INFO @ Sun, 18 Mar 2018 13:00:37: 10000000 INFO @ Sun, 18 Mar 2018 13:00:38: 10000000 INFO @ Sun, 18 Mar 2018 13:00:45: 11000000 INFO @ Sun, 18 Mar 2018 13:00:46: 11000000 INFO @ Sun, 18 Mar 2018 13:00:48: 11000000 INFO @ Sun, 18 Mar 2018 13:00:54: 12000000 INFO @ Sun, 18 Mar 2018 13:00:56: 12000000 INFO @ Sun, 18 Mar 2018 13:00:58: 12000000 INFO @ Sun, 18 Mar 2018 13:01:03: 13000000 INFO @ Sun, 18 Mar 2018 13:01:06: 13000000 INFO @ Sun, 18 Mar 2018 13:01:08: 13000000 INFO @ Sun, 18 Mar 2018 13:01:13: 14000000 INFO @ Sun, 18 Mar 2018 13:01:15: 14000000 INFO @ Sun, 18 Mar 2018 13:01:18: 14000000 INFO @ Sun, 18 Mar 2018 13:01:22: 15000000 INFO @ Sun, 18 Mar 2018 13:01:24: 15000000 INFO @ Sun, 18 Mar 2018 13:01:28: 15000000 INFO @ Sun, 18 Mar 2018 13:01:32: 16000000 INFO @ Sun, 18 Mar 2018 13:01:34: 16000000 INFO @ Sun, 18 Mar 2018 13:01:38: 16000000 INFO @ Sun, 18 Mar 2018 13:01:42: 17000000 INFO @ Sun, 18 Mar 2018 13:01:43: 17000000 INFO @ Sun, 18 Mar 2018 13:01:48: 17000000 INFO @ Sun, 18 Mar 2018 13:01:51: 18000000 INFO @ Sun, 18 Mar 2018 13:01:53: 18000000 INFO @ Sun, 18 Mar 2018 13:01:58: 18000000 INFO @ Sun, 18 Mar 2018 13:02:01: 19000000 INFO @ Sun, 18 Mar 2018 13:02:02: 19000000 INFO @ Sun, 18 Mar 2018 13:02:08: 19000000 INFO @ Sun, 18 Mar 2018 13:02:10: 20000000 INFO @ Sun, 18 Mar 2018 13:02:12: 20000000 INFO @ Sun, 18 Mar 2018 13:02:18: 20000000 INFO @ Sun, 18 Mar 2018 13:02:20: 21000000 INFO @ Sun, 18 Mar 2018 13:02:21: 21000000 INFO @ Sun, 18 Mar 2018 13:02:28: 21000000 INFO @ Sun, 18 Mar 2018 13:02:29: 22000000 INFO @ Sun, 18 Mar 2018 13:02:30: 22000000 INFO @ Sun, 18 Mar 2018 13:02:38: 22000000 INFO @ Sun, 18 Mar 2018 13:02:39: 23000000 INFO @ Sun, 18 Mar 2018 13:02:40: 23000000 INFO @ Sun, 18 Mar 2018 13:02:48: 23000000 INFO @ Sun, 18 Mar 2018 13:02:48: 24000000 INFO @ Sun, 18 Mar 2018 13:02:49: 24000000 INFO @ Sun, 18 Mar 2018 13:02:58: 25000000 INFO @ Sun, 18 Mar 2018 13:02:58: 24000000 INFO @ Sun, 18 Mar 2018 13:02:59: 25000000 INFO @ Sun, 18 Mar 2018 13:03:07: 26000000 INFO @ Sun, 18 Mar 2018 13:03:08: 25000000 INFO @ Sun, 18 Mar 2018 13:03:08: 26000000 INFO @ Sun, 18 Mar 2018 13:03:17: 27000000 INFO @ Sun, 18 Mar 2018 13:03:18: 27000000 INFO @ Sun, 18 Mar 2018 13:03:18: 26000000 INFO @ Sun, 18 Mar 2018 13:03:27: 28000000 INFO @ Sun, 18 Mar 2018 13:03:27: 28000000 INFO @ Sun, 18 Mar 2018 13:03:28: 27000000 INFO @ Sun, 18 Mar 2018 13:03:37: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:03:37: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:03:37: #1 total tags in treatment: 28939426 INFO @ Sun, 18 Mar 2018 13:03:37: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:03:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 13:03:37: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:03:37: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:03:37: #1 total tags in treatment: 28939426 INFO @ Sun, 18 Mar 2018 13:03:37: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:03:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 13:03:37: #1 tags after filtering in treatment: 28939297 INFO @ Sun, 18 Mar 2018 13:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:03:37: #1 finished! INFO @ Sun, 18 Mar 2018 13:03:37: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:03:37: #1 tags after filtering in treatment: 28939297 INFO @ Sun, 18 Mar 2018 13:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:03:37: #1 finished! INFO @ Sun, 18 Mar 2018 13:03:37: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:03:38: 28000000 INFO @ Sun, 18 Mar 2018 13:03:40: #2 number of paired peaks: 7718 INFO @ Sun, 18 Mar 2018 13:03:40: start model_add_line... INFO @ Sun, 18 Mar 2018 13:03:40: #2 number of paired peaks: 7718 INFO @ Sun, 18 Mar 2018 13:03:40: start model_add_line... INFO @ Sun, 18 Mar 2018 13:03:41: start X-correlation... INFO @ Sun, 18 Mar 2018 13:03:41: end of X-cor INFO @ Sun, 18 Mar 2018 13:03:41: #2 finished! INFO @ Sun, 18 Mar 2018 13:03:41: #2 predicted fragment length is 151 bps INFO @ Sun, 18 Mar 2018 13:03:41: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 18 Mar 2018 13:03:41: #2.2 Generate R script for model : SRX2611104.20_model.r WARNING @ Sun, 18 Mar 2018 13:03:41: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:03:41: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Sun, 18 Mar 2018 13:03:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 13:03:41: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:03:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:03:41: start X-correlation... INFO @ Sun, 18 Mar 2018 13:03:41: end of X-cor INFO @ Sun, 18 Mar 2018 13:03:41: #2 finished! INFO @ Sun, 18 Mar 2018 13:03:41: #2 predicted fragment length is 151 bps INFO @ Sun, 18 Mar 2018 13:03:41: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 18 Mar 2018 13:03:41: #2.2 Generate R script for model : SRX2611104.10_model.r WARNING @ Sun, 18 Mar 2018 13:03:41: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:03:41: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Sun, 18 Mar 2018 13:03:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 13:03:41: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:03:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:03:48: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:03:48: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:03:48: #1 total tags in treatment: 28939426 INFO @ Sun, 18 Mar 2018 13:03:48: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:03:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 13:03:48: #1 tags after filtering in treatment: 28939297 INFO @ Sun, 18 Mar 2018 13:03:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:03:48: #1 finished! INFO @ Sun, 18 Mar 2018 13:03:48: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:03:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:03:51: #2 number of paired peaks: 7718 INFO @ Sun, 18 Mar 2018 13:03:51: start model_add_line... INFO @ Sun, 18 Mar 2018 13:03:51: start X-correlation... INFO @ Sun, 18 Mar 2018 13:03:51: end of X-cor INFO @ Sun, 18 Mar 2018 13:03:51: #2 finished! INFO @ Sun, 18 Mar 2018 13:03:51: #2 predicted fragment length is 151 bps INFO @ Sun, 18 Mar 2018 13:03:51: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 18 Mar 2018 13:03:51: #2.2 Generate R script for model : SRX2611104.05_model.r WARNING @ Sun, 18 Mar 2018 13:03:51: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:03:51: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Sun, 18 Mar 2018 13:03:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 13:03:51: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:04:51: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:04:57: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:05:05: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:05:33: #4 Write output xls file... SRX2611104.20_peaks.xls INFO @ Sun, 18 Mar 2018 13:05:33: #4 Write peak in narrowPeak format file... SRX2611104.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:05:33: #4 Write summits bed file... SRX2611104.20_summits.bed INFO @ Sun, 18 Mar 2018 13:05:33: Done! pass1 - making usageList (28 chroms): 0 millis pass2 - checking and writing primary data (356 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:05:40: #4 Write output xls file... SRX2611104.10_peaks.xls INFO @ Sun, 18 Mar 2018 13:05:40: #4 Write peak in narrowPeak format file... SRX2611104.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:05:40: #4 Write summits bed file... SRX2611104.10_summits.bed INFO @ Sun, 18 Mar 2018 13:05:40: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (832 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:05:47: #4 Write output xls file... SRX2611104.05_peaks.xls INFO @ Sun, 18 Mar 2018 13:05:47: #4 Write peak in narrowPeak format file... SRX2611104.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:05:47: #4 Write summits bed file... SRX2611104.05_summits.bed INFO @ Sun, 18 Mar 2018 13:05:47: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (2531 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。