Job ID = 10194750 sra ファイルのダウンロード中... Completed: 506240K bytes transferred in 6 seconds (660174K 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 38197337 spots for /home/okishinya/chipatlas/results/rn6/SRX1091088/SRR2095965.sra Written 38197337 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:28:42 38197337 reads; of these: 38197337 (100.00%) were unpaired; of these: 1421430 (3.72%) aligned 0 times 27112789 (70.98%) aligned exactly 1 time 9663118 (25.30%) aligned >1 times 96.28% overall alignment rate Time searching: 00:28:45 Overall time: 00:28:45 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] 1486478 / 36775907 = 0.0404 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 @ Sat, 11 Nov 2017 00:54:39: # Command line: callpeak -t SRX1091088.bam -f BAM -g 2.15e9 -n SRX1091088.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1091088.10 # format = BAM # ChIP-seq file = ['SRX1091088.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 @ Sat, 11 Nov 2017 00:54:39: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:54:39: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:54:39: # Command line: callpeak -t SRX1091088.bam -f BAM -g 2.15e9 -n SRX1091088.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1091088.20 # format = BAM # ChIP-seq file = ['SRX1091088.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 @ Sat, 11 Nov 2017 00:54:39: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:54:39: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:54:39: # Command line: callpeak -t SRX1091088.bam -f BAM -g 2.15e9 -n SRX1091088.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1091088.05 # format = BAM # ChIP-seq file = ['SRX1091088.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 @ Sat, 11 Nov 2017 00:54:39: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:54:39: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:54:46: 1000000 INFO @ Sat, 11 Nov 2017 00:54:46: 1000000 INFO @ Sat, 11 Nov 2017 00:54:46: 1000000 INFO @ Sat, 11 Nov 2017 00:54:54: 2000000 INFO @ Sat, 11 Nov 2017 00:54:54: 2000000 INFO @ Sat, 11 Nov 2017 00:54:54: 2000000 INFO @ Sat, 11 Nov 2017 00:55:01: 3000000 INFO @ Sat, 11 Nov 2017 00:55:02: 3000000 INFO @ Sat, 11 Nov 2017 00:55:02: 3000000 INFO @ Sat, 11 Nov 2017 00:55:08: 4000000 INFO @ Sat, 11 Nov 2017 00:55:10: 4000000 INFO @ Sat, 11 Nov 2017 00:55:10: 4000000 INFO @ Sat, 11 Nov 2017 00:55:15: 5000000 INFO @ Sat, 11 Nov 2017 00:55:17: 5000000 INFO @ Sat, 11 Nov 2017 00:55:17: 5000000 INFO @ Sat, 11 Nov 2017 00:55:22: 6000000 INFO @ Sat, 11 Nov 2017 00:55:25: 6000000 INFO @ Sat, 11 Nov 2017 00:55:25: 6000000 INFO @ Sat, 11 Nov 2017 00:55:29: 7000000 INFO @ Sat, 11 Nov 2017 00:55:33: 7000000 INFO @ Sat, 11 Nov 2017 00:55:33: 7000000 INFO @ Sat, 11 Nov 2017 00:55:37: 8000000 INFO @ Sat, 11 Nov 2017 00:55:40: 8000000 INFO @ Sat, 11 Nov 2017 00:55:41: 8000000 INFO @ Sat, 11 Nov 2017 00:55:45: 9000000 INFO @ Sat, 11 Nov 2017 00:55:48: 9000000 INFO @ Sat, 11 Nov 2017 00:55:50: 9000000 INFO @ Sat, 11 Nov 2017 00:55:53: 10000000 INFO @ Sat, 11 Nov 2017 00:55:56: 10000000 INFO @ Sat, 11 Nov 2017 00:55:58: 10000000 INFO @ Sat, 11 Nov 2017 00:56:01: 11000000 INFO @ Sat, 11 Nov 2017 00:56:03: 11000000 INFO @ Sat, 11 Nov 2017 00:56:06: 11000000 INFO @ Sat, 11 Nov 2017 00:56:09: 12000000 INFO @ Sat, 11 Nov 2017 00:56:11: 12000000 INFO @ Sat, 11 Nov 2017 00:56:14: 12000000 INFO @ Sat, 11 Nov 2017 00:56:17: 13000000 INFO @ Sat, 11 Nov 2017 00:56:18: 13000000 INFO @ Sat, 11 Nov 2017 00:56:22: 13000000 INFO @ Sat, 11 Nov 2017 00:56:25: 14000000 INFO @ Sat, 11 Nov 2017 00:56:25: 14000000 INFO @ Sat, 11 Nov 2017 00:56:30: 14000000 INFO @ Sat, 11 Nov 2017 00:56:33: 15000000 INFO @ Sat, 11 Nov 2017 00:56:33: 15000000 INFO @ Sat, 11 Nov 2017 00:56:39: 15000000 INFO @ Sat, 11 Nov 2017 00:56:40: 16000000 INFO @ Sat, 11 Nov 2017 00:56:41: 16000000 INFO @ Sat, 11 Nov 2017 00:56:47: 16000000 INFO @ Sat, 11 Nov 2017 00:56:48: 17000000 INFO @ Sat, 11 Nov 2017 00:56:50: 17000000 INFO @ Sat, 11 Nov 2017 00:56:55: 18000000 INFO @ Sat, 11 Nov 2017 00:56:55: 17000000 INFO @ Sat, 11 Nov 2017 00:56:58: 18000000 INFO @ Sat, 11 Nov 2017 00:57:02: 19000000 INFO @ Sat, 11 Nov 2017 00:57:04: 18000000 INFO @ Sat, 11 Nov 2017 00:57:06: 19000000 INFO @ Sat, 11 Nov 2017 00:57:10: 20000000 INFO @ Sat, 11 Nov 2017 00:57:12: 19000000 INFO @ Sat, 11 Nov 2017 00:57:14: 20000000 INFO @ Sat, 11 Nov 2017 00:57:17: 21000000 INFO @ Sat, 11 Nov 2017 00:57:21: 20000000 INFO @ Sat, 11 Nov 2017 00:57:23: 21000000 INFO @ Sat, 11 Nov 2017 00:57:24: 22000000 INFO @ Sat, 11 Nov 2017 00:57:29: 21000000 INFO @ Sat, 11 Nov 2017 00:57:31: 22000000 INFO @ Sat, 11 Nov 2017 00:57:32: 23000000 INFO @ Sat, 11 Nov 2017 00:57:38: 22000000 INFO @ Sat, 11 Nov 2017 00:57:39: 24000000 INFO @ Sat, 11 Nov 2017 00:57:39: 23000000 INFO @ Sat, 11 Nov 2017 00:57:46: 25000000 INFO @ Sat, 11 Nov 2017 00:57:46: 23000000 INFO @ Sat, 11 Nov 2017 00:57:47: 24000000 INFO @ Sat, 11 Nov 2017 00:57:54: 26000000 INFO @ Sat, 11 Nov 2017 00:57:55: 24000000 INFO @ Sat, 11 Nov 2017 00:57:56: 25000000 INFO @ Sat, 11 Nov 2017 00:58:01: 27000000 INFO @ Sat, 11 Nov 2017 00:58:03: 25000000 INFO @ Sat, 11 Nov 2017 00:58:04: 26000000 INFO @ Sat, 11 Nov 2017 00:58:08: 28000000 INFO @ Sat, 11 Nov 2017 00:58:12: 26000000 INFO @ Sat, 11 Nov 2017 00:58:12: 27000000 INFO @ Sat, 11 Nov 2017 00:58:16: 29000000 INFO @ Sat, 11 Nov 2017 00:58:20: 28000000 INFO @ Sat, 11 Nov 2017 00:58:20: 27000000 INFO @ Sat, 11 Nov 2017 00:58:23: 30000000 INFO @ Sat, 11 Nov 2017 00:58:28: 29000000 INFO @ Sat, 11 Nov 2017 00:58:29: 28000000 INFO @ Sat, 11 Nov 2017 00:58:30: 31000000 INFO @ Sat, 11 Nov 2017 00:58:37: 30000000 INFO @ Sat, 11 Nov 2017 00:58:37: 29000000 INFO @ Sat, 11 Nov 2017 00:58:38: 32000000 INFO @ Sat, 11 Nov 2017 00:58:45: 31000000 INFO @ Sat, 11 Nov 2017 00:58:45: 33000000 INFO @ Sat, 11 Nov 2017 00:58:46: 30000000 INFO @ Sat, 11 Nov 2017 00:58:53: 34000000 INFO @ Sat, 11 Nov 2017 00:58:53: 32000000 INFO @ Sat, 11 Nov 2017 00:58:54: 31000000 INFO @ Sat, 11 Nov 2017 00:59:00: 35000000 INFO @ Sat, 11 Nov 2017 00:59:01: 33000000 INFO @ Sat, 11 Nov 2017 00:59:02: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:59:02: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:59:02: #1 total tags in treatment: 35289429 INFO @ Sat, 11 Nov 2017 00:59:02: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:59:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:59:03: 32000000 INFO @ Sat, 11 Nov 2017 00:59:03: #1 tags after filtering in treatment: 35289343 INFO @ Sat, 11 Nov 2017 00:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:59:03: #1 finished! INFO @ Sat, 11 Nov 2017 00:59:03: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:59:07: #2 number of paired peaks: 4435 INFO @ Sat, 11 Nov 2017 00:59:07: start model_add_line... INFO @ Sat, 11 Nov 2017 00:59:07: start X-correlation... INFO @ Sat, 11 Nov 2017 00:59:07: end of X-cor INFO @ Sat, 11 Nov 2017 00:59:07: #2 finished! INFO @ Sat, 11 Nov 2017 00:59:07: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 00:59:07: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Nov 2017 00:59:07: #2.2 Generate R script for model : SRX1091088.20_model.r WARNING @ Sat, 11 Nov 2017 00:59:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:59:07: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Nov 2017 00:59:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:59:07: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:59:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:59:10: 34000000 INFO @ Sat, 11 Nov 2017 00:59:11: 33000000 INFO @ Sat, 11 Nov 2017 00:59:18: 35000000 INFO @ Sat, 11 Nov 2017 00:59:20: 34000000 INFO @ Sat, 11 Nov 2017 00:59:21: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:59:21: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:59:21: #1 total tags in treatment: 35289429 INFO @ Sat, 11 Nov 2017 00:59:21: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:59:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:59:22: #1 tags after filtering in treatment: 35289343 INFO @ Sat, 11 Nov 2017 00:59:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:59:22: #1 finished! INFO @ Sat, 11 Nov 2017 00:59:22: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:59:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:59:25: #2 number of paired peaks: 4435 INFO @ Sat, 11 Nov 2017 00:59:25: start model_add_line... INFO @ Sat, 11 Nov 2017 00:59:25: start X-correlation... INFO @ Sat, 11 Nov 2017 00:59:25: end of X-cor INFO @ Sat, 11 Nov 2017 00:59:25: #2 finished! INFO @ Sat, 11 Nov 2017 00:59:25: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 00:59:25: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Nov 2017 00:59:25: #2.2 Generate R script for model : SRX1091088.05_model.r WARNING @ Sat, 11 Nov 2017 00:59:25: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:59:25: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Nov 2017 00:59:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:59:25: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:59:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:59:28: 35000000 INFO @ Sat, 11 Nov 2017 00:59:30: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:59:30: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:59:30: #1 total tags in treatment: 35289429 INFO @ Sat, 11 Nov 2017 00:59:30: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:59:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:59:31: #1 tags after filtering in treatment: 35289343 INFO @ Sat, 11 Nov 2017 00:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:59:31: #1 finished! INFO @ Sat, 11 Nov 2017 00:59:31: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:59:34: #2 number of paired peaks: 4435 INFO @ Sat, 11 Nov 2017 00:59:34: start model_add_line... INFO @ Sat, 11 Nov 2017 00:59:35: start X-correlation... INFO @ Sat, 11 Nov 2017 00:59:35: end of X-cor INFO @ Sat, 11 Nov 2017 00:59:35: #2 finished! INFO @ Sat, 11 Nov 2017 00:59:35: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 00:59:35: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Nov 2017 00:59:35: #2.2 Generate R script for model : SRX1091088.10_model.r WARNING @ Sat, 11 Nov 2017 00:59:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:59:35: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Nov 2017 00:59:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:59:35: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:00:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:00:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:00:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:01:15: #4 Write output xls file... SRX1091088.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:01:15: #4 Write peak in narrowPeak format file... SRX1091088.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:01:15: #4 Write summits bed file... SRX1091088.20_summits.bed INFO @ Sat, 11 Nov 2017 01:01:15: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (533 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:01:43: #4 Write output xls file... SRX1091088.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:01:43: #4 Write peak in narrowPeak format file... SRX1091088.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:01:43: #4 Write summits bed file... SRX1091088.05_summits.bed INFO @ Sat, 11 Nov 2017 01:01:43: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1793 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:01:50: #4 Write output xls file... SRX1091088.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:01:50: #4 Write peak in narrowPeak format file... SRX1091088.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:01:50: #4 Write summits bed file... SRX1091088.10_summits.bed INFO @ Sat, 11 Nov 2017 01:01:50: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (1075 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。