Job ID = 10194807 sra ファイルのダウンロード中... Completed: 1323803K bytes transferred in 19 seconds (555343K 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 49121925 spots for /home/okishinya/chipatlas/results/rn6/SRX1819033/SRR3624109.sra Written 49121925 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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:43:48 49121925 reads; of these: 49121925 (100.00%) were unpaired; of these: 2814216 (5.73%) aligned 0 times 34414763 (70.06%) aligned exactly 1 time 11892946 (24.21%) aligned >1 times 94.27% overall alignment rate Time searching: 00:43:54 Overall time: 00:43:54 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 12 files... [bam_rmdupse_core] 3938440 / 46307709 = 0.0850 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 @ Fri, 10 Nov 2017 22:52:11: # Command line: callpeak -t SRX1819033.bam -f BAM -g 2.15e9 -n SRX1819033.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1819033.10 # format = BAM # ChIP-seq file = ['SRX1819033.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 @ Fri, 10 Nov 2017 22:52:11: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:52:11: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:52:11: # Command line: callpeak -t SRX1819033.bam -f BAM -g 2.15e9 -n SRX1819033.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1819033.05 # format = BAM # ChIP-seq file = ['SRX1819033.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 @ Fri, 10 Nov 2017 22:52:11: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:52:11: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:52:11: # Command line: callpeak -t SRX1819033.bam -f BAM -g 2.15e9 -n SRX1819033.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1819033.20 # format = BAM # ChIP-seq file = ['SRX1819033.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 @ Fri, 10 Nov 2017 22:52:11: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:52:11: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:52:22: 1000000 INFO @ Fri, 10 Nov 2017 22:52:25: 1000000 INFO @ Fri, 10 Nov 2017 22:52:25: 1000000 INFO @ Fri, 10 Nov 2017 22:52:36: 2000000 INFO @ Fri, 10 Nov 2017 22:52:40: 2000000 INFO @ Fri, 10 Nov 2017 22:52:43: 2000000 INFO @ Fri, 10 Nov 2017 22:52:50: 3000000 INFO @ Fri, 10 Nov 2017 22:52:55: 3000000 INFO @ Fri, 10 Nov 2017 22:53:02: 3000000 INFO @ Fri, 10 Nov 2017 22:53:03: 4000000 INFO @ Fri, 10 Nov 2017 22:53:11: 5000000 INFO @ Fri, 10 Nov 2017 22:53:11: 4000000 INFO @ Fri, 10 Nov 2017 22:53:19: 4000000 INFO @ Fri, 10 Nov 2017 22:53:20: 6000000 INFO @ Fri, 10 Nov 2017 22:53:26: 5000000 INFO @ Fri, 10 Nov 2017 22:53:28: 7000000 INFO @ Fri, 10 Nov 2017 22:53:35: 5000000 INFO @ Fri, 10 Nov 2017 22:53:37: 8000000 INFO @ Fri, 10 Nov 2017 22:53:41: 6000000 INFO @ Fri, 10 Nov 2017 22:53:45: 9000000 INFO @ Fri, 10 Nov 2017 22:53:51: 6000000 INFO @ Fri, 10 Nov 2017 22:53:53: 10000000 INFO @ Fri, 10 Nov 2017 22:53:57: 7000000 INFO @ Fri, 10 Nov 2017 22:54:02: 11000000 INFO @ Fri, 10 Nov 2017 22:54:08: 7000000 INFO @ Fri, 10 Nov 2017 22:54:10: 12000000 INFO @ Fri, 10 Nov 2017 22:54:11: 8000000 INFO @ Fri, 10 Nov 2017 22:54:19: 13000000 INFO @ Fri, 10 Nov 2017 22:54:23: 8000000 INFO @ Fri, 10 Nov 2017 22:54:25: 9000000 INFO @ Fri, 10 Nov 2017 22:54:28: 14000000 INFO @ Fri, 10 Nov 2017 22:54:36: 15000000 INFO @ Fri, 10 Nov 2017 22:54:38: 9000000 INFO @ Fri, 10 Nov 2017 22:54:40: 10000000 INFO @ Fri, 10 Nov 2017 22:54:45: 16000000 INFO @ Fri, 10 Nov 2017 22:54:53: 17000000 INFO @ Fri, 10 Nov 2017 22:54:54: 10000000 INFO @ Fri, 10 Nov 2017 22:54:55: 11000000 INFO @ Fri, 10 Nov 2017 22:55:04: 18000000 INFO @ Fri, 10 Nov 2017 22:55:09: 12000000 INFO @ Fri, 10 Nov 2017 22:55:11: 11000000 INFO @ Fri, 10 Nov 2017 22:55:22: 19000000 INFO @ Fri, 10 Nov 2017 22:55:23: 13000000 INFO @ Fri, 10 Nov 2017 22:55:28: 12000000 INFO @ Fri, 10 Nov 2017 22:55:37: 14000000 INFO @ Fri, 10 Nov 2017 22:55:39: 20000000 INFO @ Fri, 10 Nov 2017 22:55:47: 13000000 INFO @ Fri, 10 Nov 2017 22:55:50: 15000000 INFO @ Fri, 10 Nov 2017 22:55:58: 21000000 INFO @ Fri, 10 Nov 2017 22:56:03: 16000000 INFO @ Fri, 10 Nov 2017 22:56:04: 14000000 INFO @ Fri, 10 Nov 2017 22:56:15: 22000000 INFO @ Fri, 10 Nov 2017 22:56:17: 17000000 INFO @ Fri, 10 Nov 2017 22:56:19: 15000000 INFO @ Fri, 10 Nov 2017 22:56:29: 16000000 INFO @ Fri, 10 Nov 2017 22:56:31: 23000000 INFO @ Fri, 10 Nov 2017 22:56:31: 18000000 INFO @ Fri, 10 Nov 2017 22:56:40: 17000000 INFO @ Fri, 10 Nov 2017 22:56:44: 19000000 INFO @ Fri, 10 Nov 2017 22:56:48: 24000000 INFO @ Fri, 10 Nov 2017 22:56:56: 18000000 INFO @ Fri, 10 Nov 2017 22:56:58: 20000000 INFO @ Fri, 10 Nov 2017 22:57:03: 25000000 INFO @ Fri, 10 Nov 2017 22:57:12: 19000000 INFO @ Fri, 10 Nov 2017 22:57:13: 21000000 INFO @ Fri, 10 Nov 2017 22:57:17: 26000000 INFO @ Fri, 10 Nov 2017 22:57:28: 20000000 INFO @ Fri, 10 Nov 2017 22:57:29: 22000000 INFO @ Fri, 10 Nov 2017 22:57:32: 27000000 INFO @ Fri, 10 Nov 2017 22:57:44: 21000000 INFO @ Fri, 10 Nov 2017 22:57:45: 23000000 INFO @ Fri, 10 Nov 2017 22:57:49: 28000000 INFO @ Fri, 10 Nov 2017 22:58:00: 22000000 INFO @ Fri, 10 Nov 2017 22:58:00: 24000000 INFO @ Fri, 10 Nov 2017 22:58:04: 29000000 INFO @ Fri, 10 Nov 2017 22:58:14: 30000000 INFO @ Fri, 10 Nov 2017 22:58:15: 23000000 INFO @ Fri, 10 Nov 2017 22:58:16: 25000000 INFO @ Fri, 10 Nov 2017 22:58:25: 31000000 INFO @ Fri, 10 Nov 2017 22:58:30: 24000000 INFO @ Fri, 10 Nov 2017 22:58:31: 26000000 INFO @ Fri, 10 Nov 2017 22:58:37: 32000000 INFO @ Fri, 10 Nov 2017 22:58:43: 25000000 INFO @ Fri, 10 Nov 2017 22:58:44: 27000000 INFO @ Fri, 10 Nov 2017 22:58:49: 33000000 INFO @ Fri, 10 Nov 2017 22:58:54: 26000000 INFO @ Fri, 10 Nov 2017 22:58:59: 28000000 INFO @ Fri, 10 Nov 2017 22:59:01: 34000000 INFO @ Fri, 10 Nov 2017 22:59:05: 27000000 INFO @ Fri, 10 Nov 2017 22:59:14: 29000000 INFO @ Fri, 10 Nov 2017 22:59:16: 35000000 INFO @ Fri, 10 Nov 2017 22:59:19: 28000000 INFO @ Fri, 10 Nov 2017 22:59:29: 30000000 INFO @ Fri, 10 Nov 2017 22:59:31: 36000000 INFO @ Fri, 10 Nov 2017 22:59:33: 29000000 INFO @ Fri, 10 Nov 2017 22:59:46: 37000000 INFO @ Fri, 10 Nov 2017 22:59:46: 30000000 INFO @ Fri, 10 Nov 2017 22:59:47: 31000000 INFO @ Fri, 10 Nov 2017 22:59:59: 31000000 INFO @ Fri, 10 Nov 2017 23:00:00: 38000000 INFO @ Fri, 10 Nov 2017 23:00:07: 32000000 INFO @ Fri, 10 Nov 2017 23:00:13: 32000000 INFO @ Fri, 10 Nov 2017 23:00:15: 39000000 INFO @ Fri, 10 Nov 2017 23:00:27: 33000000 INFO @ Fri, 10 Nov 2017 23:00:28: 33000000 INFO @ Fri, 10 Nov 2017 23:00:30: 40000000 INFO @ Fri, 10 Nov 2017 23:00:43: 34000000 INFO @ Fri, 10 Nov 2017 23:00:44: 34000000 INFO @ Fri, 10 Nov 2017 23:00:47: 41000000 INFO @ Fri, 10 Nov 2017 23:00:59: 35000000 INFO @ Fri, 10 Nov 2017 23:01:00: 35000000 INFO @ Fri, 10 Nov 2017 23:01:02: 42000000 INFO @ Fri, 10 Nov 2017 23:01:09: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 23:01:09: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 23:01:09: #1 total tags in treatment: 42369269 INFO @ Fri, 10 Nov 2017 23:01:09: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:01:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:01:10: #1 tags after filtering in treatment: 42369185 INFO @ Fri, 10 Nov 2017 23:01:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:01:10: #1 finished! INFO @ Fri, 10 Nov 2017 23:01:10: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:01:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:01:15: #2 number of paired peaks: 2780 INFO @ Fri, 10 Nov 2017 23:01:15: start model_add_line... INFO @ Fri, 10 Nov 2017 23:01:15: 36000000 INFO @ Fri, 10 Nov 2017 23:01:15: start X-correlation... INFO @ Fri, 10 Nov 2017 23:01:15: end of X-cor INFO @ Fri, 10 Nov 2017 23:01:15: #2 finished! INFO @ Fri, 10 Nov 2017 23:01:15: #2 predicted fragment length is 39 bps INFO @ Fri, 10 Nov 2017 23:01:15: #2 alternative fragment length(s) may be 39,205,378 bps INFO @ Fri, 10 Nov 2017 23:01:15: #2.2 Generate R script for model : SRX1819033.10_model.r WARNING @ Fri, 10 Nov 2017 23:01:15: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:01:15: #2 You may need to consider one of the other alternative d(s): 39,205,378 WARNING @ Fri, 10 Nov 2017 23:01:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:01:15: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:01:19: 36000000 INFO @ Fri, 10 Nov 2017 23:01:30: 37000000 INFO @ Fri, 10 Nov 2017 23:01:39: 37000000 INFO @ Fri, 10 Nov 2017 23:01:46: 38000000 INFO @ Fri, 10 Nov 2017 23:01:57: 38000000 INFO @ Fri, 10 Nov 2017 23:02:02: 39000000 INFO @ Fri, 10 Nov 2017 23:02:11: 39000000 INFO @ Fri, 10 Nov 2017 23:02:18: 40000000 INFO @ Fri, 10 Nov 2017 23:02:26: 40000000 INFO @ Fri, 10 Nov 2017 23:02:36: 41000000 INFO @ Fri, 10 Nov 2017 23:02:42: 41000000 INFO @ Fri, 10 Nov 2017 23:02:52: 42000000 INFO @ Fri, 10 Nov 2017 23:02:57: 42000000 INFO @ Fri, 10 Nov 2017 23:02:58: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 23:02:58: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 23:02:58: #1 total tags in treatment: 42369269 INFO @ Fri, 10 Nov 2017 23:02:58: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:02:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:03:00: #1 tags after filtering in treatment: 42369185 INFO @ Fri, 10 Nov 2017 23:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:03:00: #1 finished! INFO @ Fri, 10 Nov 2017 23:03:00: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:03:02: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 23:03:02: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 23:03:02: #1 total tags in treatment: 42369269 INFO @ Fri, 10 Nov 2017 23:03:02: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:03:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:03:04: #1 tags after filtering in treatment: 42369185 INFO @ Fri, 10 Nov 2017 23:03:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:03:04: #1 finished! INFO @ Fri, 10 Nov 2017 23:03:04: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:03:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:03:04: #2 number of paired peaks: 2780 INFO @ Fri, 10 Nov 2017 23:03:04: start model_add_line... INFO @ Fri, 10 Nov 2017 23:03:05: start X-correlation... INFO @ Fri, 10 Nov 2017 23:03:05: end of X-cor INFO @ Fri, 10 Nov 2017 23:03:05: #2 finished! INFO @ Fri, 10 Nov 2017 23:03:05: #2 predicted fragment length is 39 bps INFO @ Fri, 10 Nov 2017 23:03:05: #2 alternative fragment length(s) may be 39,205,378 bps INFO @ Fri, 10 Nov 2017 23:03:05: #2.2 Generate R script for model : SRX1819033.05_model.r WARNING @ Fri, 10 Nov 2017 23:03:05: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:03:05: #2 You may need to consider one of the other alternative d(s): 39,205,378 WARNING @ Fri, 10 Nov 2017 23:03:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:03:05: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:03:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:03:08: #2 number of paired peaks: 2780 INFO @ Fri, 10 Nov 2017 23:03:08: start model_add_line... INFO @ Fri, 10 Nov 2017 23:03:09: start X-correlation... INFO @ Fri, 10 Nov 2017 23:03:09: end of X-cor INFO @ Fri, 10 Nov 2017 23:03:09: #2 finished! INFO @ Fri, 10 Nov 2017 23:03:09: #2 predicted fragment length is 39 bps INFO @ Fri, 10 Nov 2017 23:03:09: #2 alternative fragment length(s) may be 39,205,378 bps INFO @ Fri, 10 Nov 2017 23:03:09: #2.2 Generate R script for model : SRX1819033.20_model.r WARNING @ Fri, 10 Nov 2017 23:03:09: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:03:09: #2 You may need to consider one of the other alternative d(s): 39,205,378 WARNING @ Fri, 10 Nov 2017 23:03:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:03:09: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:03:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:04:25: #4 Write output xls file... SRX1819033.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:04:25: #4 Write peak in narrowPeak format file... SRX1819033.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:04:25: #4 Write summits bed file... SRX1819033.10_summits.bed INFO @ Fri, 10 Nov 2017 23:04:25: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (1062 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:05:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:05:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:06:11: #4 Write output xls file... SRX1819033.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:06:11: #4 Write peak in narrowPeak format file... SRX1819033.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:06:11: #4 Write summits bed file... SRX1819033.20_summits.bed INFO @ Fri, 10 Nov 2017 23:06:11: Done! pass1 - making usageList (29 chroms): 2 millis pass2 - checking and writing primary data (501 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:06:13: #4 Write output xls file... SRX1819033.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:06:13: #4 Write peak in narrowPeak format file... SRX1819033.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:06:13: #4 Write summits bed file... SRX1819033.05_summits.bed INFO @ Fri, 10 Nov 2017 23:06:13: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (1835 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。