Job ID = 10487591 sra ファイルのダウンロード中... Completed: 4355835K bytes transferred in 161 seconds (221552K 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 64339419 spots for /home/okishinya/chipatlas/results/rn6/SRX2611114/SRR5311158.sra Written 64339419 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: 03:24:37 64339419 reads; of these: 64339419 (100.00%) were unpaired; of these: 23639103 (36.74%) aligned 0 times 32189179 (50.03%) aligned exactly 1 time 8511137 (13.23%) aligned >1 times 63.26% overall alignment rate Time searching: 03:24:42 Overall time: 03:24:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 32 files... [bam_rmdupse_core] 9895102 / 40700316 = 0.2431 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 13:34:30: # Command line: callpeak -t SRX2611114.bam -f BAM -g 2.15e9 -n SRX2611114.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611114.05 # format = BAM # ChIP-seq file = ['SRX2611114.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 13:34:30: # Command line: callpeak -t SRX2611114.bam -f BAM -g 2.15e9 -n SRX2611114.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611114.20 # format = BAM # ChIP-seq file = ['SRX2611114.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 13:34:30: # Command line: callpeak -t SRX2611114.bam -f BAM -g 2.15e9 -n SRX2611114.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611114.10 # format = BAM # ChIP-seq file = ['SRX2611114.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 13:34:30: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:34:30: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:34:30: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:34:30: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:34:30: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:34:30: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:34:39: 1000000 INFO @ Sun, 18 Mar 2018 13:34:39: 1000000 INFO @ Sun, 18 Mar 2018 13:34:39: 1000000 INFO @ Sun, 18 Mar 2018 13:34:49: 2000000 INFO @ Sun, 18 Mar 2018 13:34:49: 2000000 INFO @ Sun, 18 Mar 2018 13:34:50: 2000000 INFO @ Sun, 18 Mar 2018 13:34:59: 3000000 INFO @ Sun, 18 Mar 2018 13:34:59: 3000000 INFO @ Sun, 18 Mar 2018 13:35:02: 3000000 INFO @ Sun, 18 Mar 2018 13:35:09: 4000000 INFO @ Sun, 18 Mar 2018 13:35:09: 4000000 INFO @ Sun, 18 Mar 2018 13:35:14: 4000000 INFO @ Sun, 18 Mar 2018 13:35:18: 5000000 INFO @ Sun, 18 Mar 2018 13:35:18: 5000000 INFO @ Sun, 18 Mar 2018 13:35:25: 5000000 INFO @ Sun, 18 Mar 2018 13:35:27: 6000000 INFO @ Sun, 18 Mar 2018 13:35:28: 6000000 INFO @ Sun, 18 Mar 2018 13:35:34: 6000000 INFO @ Sun, 18 Mar 2018 13:35:36: 7000000 INFO @ Sun, 18 Mar 2018 13:35:37: 7000000 INFO @ Sun, 18 Mar 2018 13:35:43: 7000000 INFO @ Sun, 18 Mar 2018 13:35:45: 8000000 INFO @ Sun, 18 Mar 2018 13:35:47: 8000000 INFO @ Sun, 18 Mar 2018 13:35:53: 8000000 INFO @ Sun, 18 Mar 2018 13:35:54: 9000000 INFO @ Sun, 18 Mar 2018 13:35:57: 9000000 INFO @ Sun, 18 Mar 2018 13:36:02: 9000000 INFO @ Sun, 18 Mar 2018 13:36:03: 10000000 INFO @ Sun, 18 Mar 2018 13:36:06: 10000000 INFO @ Sun, 18 Mar 2018 13:36:12: 10000000 INFO @ Sun, 18 Mar 2018 13:36:12: 11000000 INFO @ Sun, 18 Mar 2018 13:36:16: 11000000 INFO @ Sun, 18 Mar 2018 13:36:21: 12000000 INFO @ Sun, 18 Mar 2018 13:36:21: 11000000 INFO @ Sun, 18 Mar 2018 13:36:25: 12000000 INFO @ Sun, 18 Mar 2018 13:36:30: 13000000 INFO @ Sun, 18 Mar 2018 13:36:30: 12000000 INFO @ Sun, 18 Mar 2018 13:36:35: 13000000 INFO @ Sun, 18 Mar 2018 13:36:39: 14000000 INFO @ Sun, 18 Mar 2018 13:36:39: 13000000 INFO @ Sun, 18 Mar 2018 13:36:44: 14000000 INFO @ Sun, 18 Mar 2018 13:36:48: 15000000 INFO @ Sun, 18 Mar 2018 13:36:49: 14000000 INFO @ Sun, 18 Mar 2018 13:36:54: 15000000 INFO @ Sun, 18 Mar 2018 13:36:57: 16000000 INFO @ Sun, 18 Mar 2018 13:37:00: 15000000 INFO @ Sun, 18 Mar 2018 13:37:06: 16000000 INFO @ Sun, 18 Mar 2018 13:37:08: 17000000 INFO @ Sun, 18 Mar 2018 13:37:12: 16000000 INFO @ Sun, 18 Mar 2018 13:37:17: 17000000 INFO @ Sun, 18 Mar 2018 13:37:19: 18000000 INFO @ Sun, 18 Mar 2018 13:37:23: 17000000 INFO @ Sun, 18 Mar 2018 13:37:27: 18000000 INFO @ Sun, 18 Mar 2018 13:37:29: 19000000 INFO @ Sun, 18 Mar 2018 13:37:35: 18000000 INFO @ Sun, 18 Mar 2018 13:37:38: 19000000 INFO @ Sun, 18 Mar 2018 13:37:40: 20000000 INFO @ Sun, 18 Mar 2018 13:37:45: 19000000 INFO @ Sun, 18 Mar 2018 13:37:49: 20000000 INFO @ Sun, 18 Mar 2018 13:37:50: 21000000 INFO @ Sun, 18 Mar 2018 13:37:56: 20000000 INFO @ Sun, 18 Mar 2018 13:37:58: 21000000 INFO @ Sun, 18 Mar 2018 13:38:00: 22000000 INFO @ Sun, 18 Mar 2018 13:38:06: 21000000 INFO @ Sun, 18 Mar 2018 13:38:07: 22000000 INFO @ Sun, 18 Mar 2018 13:38:09: 23000000 INFO @ Sun, 18 Mar 2018 13:38:16: 22000000 INFO @ Sun, 18 Mar 2018 13:38:16: 23000000 INFO @ Sun, 18 Mar 2018 13:38:19: 24000000 INFO @ Sun, 18 Mar 2018 13:38:25: 24000000 INFO @ Sun, 18 Mar 2018 13:38:25: 23000000 INFO @ Sun, 18 Mar 2018 13:38:28: 25000000 INFO @ Sun, 18 Mar 2018 13:38:34: 25000000 INFO @ Sun, 18 Mar 2018 13:38:34: 24000000 INFO @ Sun, 18 Mar 2018 13:38:37: 26000000 INFO @ Sun, 18 Mar 2018 13:38:43: 26000000 INFO @ Sun, 18 Mar 2018 13:38:45: 25000000 INFO @ Sun, 18 Mar 2018 13:38:47: 27000000 INFO @ Sun, 18 Mar 2018 13:38:54: 27000000 INFO @ Sun, 18 Mar 2018 13:38:56: 26000000 INFO @ Sun, 18 Mar 2018 13:38:58: 28000000 INFO @ Sun, 18 Mar 2018 13:39:04: 28000000 INFO @ Sun, 18 Mar 2018 13:39:08: 27000000 INFO @ Sun, 18 Mar 2018 13:39:09: 29000000 INFO @ Sun, 18 Mar 2018 13:39:15: 29000000 INFO @ Sun, 18 Mar 2018 13:39:20: 28000000 INFO @ Sun, 18 Mar 2018 13:39:20: 30000000 INFO @ Sun, 18 Mar 2018 13:39:26: 30000000 INFO @ Sun, 18 Mar 2018 13:39:29: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:39:29: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:39:29: #1 total tags in treatment: 30805214 INFO @ Sun, 18 Mar 2018 13:39:29: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:39:29: #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 13:39:30: #1 tags after filtering in treatment: 30805124 INFO @ Sun, 18 Mar 2018 13:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:39:30: #1 finished! INFO @ Sun, 18 Mar 2018 13:39:30: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:39:31: 29000000 INFO @ Sun, 18 Mar 2018 13:39:33: #2 number of paired peaks: 8595 INFO @ Sun, 18 Mar 2018 13:39:33: start model_add_line... INFO @ Sun, 18 Mar 2018 13:39:34: start X-correlation... INFO @ Sun, 18 Mar 2018 13:39:34: end of X-cor INFO @ Sun, 18 Mar 2018 13:39:34: #2 finished! INFO @ Sun, 18 Mar 2018 13:39:34: #2 predicted fragment length is 147 bps INFO @ Sun, 18 Mar 2018 13:39:34: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 18 Mar 2018 13:39:34: #2.2 Generate R script for model : SRX2611114.05_model.r WARNING @ Sun, 18 Mar 2018 13:39:34: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:39:34: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 18 Mar 2018 13:39:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 13:39:34: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:39:34: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:39:34: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:39:34: #1 total tags in treatment: 30805214 INFO @ Sun, 18 Mar 2018 13:39:34: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:39:34: #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 13:39:35: #1 tags after filtering in treatment: 30805124 INFO @ Sun, 18 Mar 2018 13:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:39:35: #1 finished! INFO @ Sun, 18 Mar 2018 13:39:35: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:39:38: #2 number of paired peaks: 8595 INFO @ Sun, 18 Mar 2018 13:39:38: start model_add_line... INFO @ Sun, 18 Mar 2018 13:39:39: start X-correlation... INFO @ Sun, 18 Mar 2018 13:39:39: end of X-cor INFO @ Sun, 18 Mar 2018 13:39:39: #2 finished! INFO @ Sun, 18 Mar 2018 13:39:39: #2 predicted fragment length is 147 bps INFO @ Sun, 18 Mar 2018 13:39:39: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 18 Mar 2018 13:39:39: #2.2 Generate R script for model : SRX2611114.20_model.r WARNING @ Sun, 18 Mar 2018 13:39:39: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:39:39: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 18 Mar 2018 13:39:39: #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 13:39:39: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:39:40: 30000000 INFO @ Sun, 18 Mar 2018 13:39:48: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:39:48: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:39:48: #1 total tags in treatment: 30805214 INFO @ Sun, 18 Mar 2018 13:39:48: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:39:48: #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 13:39:49: #1 tags after filtering in treatment: 30805124 INFO @ Sun, 18 Mar 2018 13:39:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:39:49: #1 finished! INFO @ Sun, 18 Mar 2018 13:39:49: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:39:52: #2 number of paired peaks: 8595 INFO @ Sun, 18 Mar 2018 13:39:52: start model_add_line... INFO @ Sun, 18 Mar 2018 13:39:52: start X-correlation... INFO @ Sun, 18 Mar 2018 13:39:52: end of X-cor INFO @ Sun, 18 Mar 2018 13:39:52: #2 finished! INFO @ Sun, 18 Mar 2018 13:39:52: #2 predicted fragment length is 147 bps INFO @ Sun, 18 Mar 2018 13:39:52: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 18 Mar 2018 13:39:52: #2.2 Generate R script for model : SRX2611114.10_model.r WARNING @ Sun, 18 Mar 2018 13:39:52: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:39:52: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 18 Mar 2018 13:39:52: #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 13:39:52: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:39:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:40:49: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:40:53: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:41:04: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:41:33: #4 Write output xls file... SRX2611114.05_peaks.xls INFO @ Sun, 18 Mar 2018 13:41:33: #4 Write peak in narrowPeak format file... SRX2611114.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:41:33: #4 Write summits bed file... SRX2611114.05_summits.bed INFO @ Sun, 18 Mar 2018 13:41:33: Done! pass1 - making usageList (76 chroms): 2 millis pass2 - checking and writing primary data (3380 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:41:39: #4 Write output xls file... SRX2611114.20_peaks.xls INFO @ Sun, 18 Mar 2018 13:41:39: #4 Write peak in narrowPeak format file... SRX2611114.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:41:39: #4 Write summits bed file... SRX2611114.20_summits.bed INFO @ Sun, 18 Mar 2018 13:41:39: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (734 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:41:46: #4 Write output xls file... SRX2611114.10_peaks.xls INFO @ Sun, 18 Mar 2018 13:41:46: #4 Write peak in narrowPeak format file... SRX2611114.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:41:46: #4 Write summits bed file... SRX2611114.10_summits.bed INFO @ Sun, 18 Mar 2018 13:41:46: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1625 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。