Job ID = 10194929 sra ファイルのダウンロード中... Completed: 539307K bytes transferred in 8 seconds (528760K bits/sec), in 1 file. Completed: 1393026K bytes transferred in 17 seconds (656122K 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 15215412 spots for /home/okishinya/chipatlas/results/rn6/SRX2224391/SRR4370051.sra Written 15215412 spots total Written 39160061 spots for /home/okishinya/chipatlas/results/rn6/SRX2224391/SRR4370052.sra Written 39160061 spots total rm: cannot remove `[DSE]RX*': 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:09:55 54375473 reads; of these: 54375473 (100.00%) were unpaired; of these: 9559036 (17.58%) aligned 0 times 31346665 (57.65%) aligned exactly 1 time 13469772 (24.77%) aligned >1 times 82.42% overall alignment rate Time searching: 01:09:59 Overall time: 01:09:59 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 20 files... [bam_rmdupse_core] 4314922 / 44816437 = 0.0963 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 00:58:02: # Command line: callpeak -t SRX2224391.bam -f BAM -g 2.15e9 -n SRX2224391.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2224391.10 # format = BAM # ChIP-seq file = ['SRX2224391.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 00:58:02: # Command line: callpeak -t SRX2224391.bam -f BAM -g 2.15e9 -n SRX2224391.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2224391.05 # format = BAM # ChIP-seq file = ['SRX2224391.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 00:58:02: # Command line: callpeak -t SRX2224391.bam -f BAM -g 2.15e9 -n SRX2224391.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2224391.20 # format = BAM # ChIP-seq file = ['SRX2224391.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 00:58:02: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:58:02: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:58:02: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:58:02: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:58:02: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:58:02: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:58:16: 1000000 INFO @ Sat, 11 Nov 2017 00:58:18: 1000000 INFO @ Sat, 11 Nov 2017 00:58:19: 1000000 INFO @ Sat, 11 Nov 2017 00:58:29: 2000000 INFO @ Sat, 11 Nov 2017 00:58:31: 2000000 INFO @ Sat, 11 Nov 2017 00:58:36: 2000000 INFO @ Sat, 11 Nov 2017 00:58:42: 3000000 INFO @ Sat, 11 Nov 2017 00:58:43: 3000000 INFO @ Sat, 11 Nov 2017 00:58:53: 3000000 INFO @ Sat, 11 Nov 2017 00:58:54: 4000000 INFO @ Sat, 11 Nov 2017 00:58:54: 4000000 INFO @ Sat, 11 Nov 2017 00:59:05: 5000000 INFO @ Sat, 11 Nov 2017 00:59:09: 5000000 INFO @ Sat, 11 Nov 2017 00:59:10: 4000000 INFO @ Sat, 11 Nov 2017 00:59:20: 6000000 INFO @ Sat, 11 Nov 2017 00:59:23: 6000000 INFO @ Sat, 11 Nov 2017 00:59:27: 5000000 INFO @ Sat, 11 Nov 2017 00:59:35: 7000000 INFO @ Sat, 11 Nov 2017 00:59:38: 7000000 INFO @ Sat, 11 Nov 2017 00:59:41: 6000000 INFO @ Sat, 11 Nov 2017 00:59:51: 8000000 INFO @ Sat, 11 Nov 2017 00:59:51: 8000000 INFO @ Sat, 11 Nov 2017 00:59:58: 7000000 INFO @ Sat, 11 Nov 2017 01:00:03: 9000000 INFO @ Sat, 11 Nov 2017 01:00:06: 9000000 INFO @ Sat, 11 Nov 2017 01:00:14: 10000000 INFO @ Sat, 11 Nov 2017 01:00:16: 8000000 INFO @ Sat, 11 Nov 2017 01:00:21: 10000000 INFO @ Sat, 11 Nov 2017 01:00:25: 11000000 INFO @ Sat, 11 Nov 2017 01:00:33: 9000000 INFO @ Sat, 11 Nov 2017 01:00:36: 12000000 INFO @ Sat, 11 Nov 2017 01:00:36: 11000000 INFO @ Sat, 11 Nov 2017 01:00:46: 13000000 INFO @ Sat, 11 Nov 2017 01:00:51: 10000000 INFO @ Sat, 11 Nov 2017 01:00:51: 12000000 INFO @ Sat, 11 Nov 2017 01:00:57: 14000000 INFO @ Sat, 11 Nov 2017 01:01:06: 13000000 INFO @ Sat, 11 Nov 2017 01:01:07: 11000000 INFO @ Sat, 11 Nov 2017 01:01:08: 15000000 INFO @ Sat, 11 Nov 2017 01:01:18: 16000000 INFO @ Sat, 11 Nov 2017 01:01:19: 14000000 INFO @ Sat, 11 Nov 2017 01:01:22: 12000000 INFO @ Sat, 11 Nov 2017 01:01:29: 17000000 INFO @ Sat, 11 Nov 2017 01:01:33: 15000000 INFO @ Sat, 11 Nov 2017 01:01:36: 13000000 INFO @ Sat, 11 Nov 2017 01:01:41: 18000000 INFO @ Sat, 11 Nov 2017 01:01:46: 16000000 INFO @ Sat, 11 Nov 2017 01:01:50: 14000000 INFO @ Sat, 11 Nov 2017 01:01:53: 19000000 INFO @ Sat, 11 Nov 2017 01:01:59: 17000000 INFO @ Sat, 11 Nov 2017 01:02:03: 15000000 INFO @ Sat, 11 Nov 2017 01:02:04: 20000000 INFO @ Sat, 11 Nov 2017 01:02:13: 18000000 INFO @ Sat, 11 Nov 2017 01:02:14: 16000000 INFO @ Sat, 11 Nov 2017 01:02:15: 21000000 INFO @ Sat, 11 Nov 2017 01:02:26: 17000000 INFO @ Sat, 11 Nov 2017 01:02:26: 19000000 INFO @ Sat, 11 Nov 2017 01:02:26: 22000000 INFO @ Sat, 11 Nov 2017 01:02:38: 18000000 INFO @ Sat, 11 Nov 2017 01:02:39: 20000000 INFO @ Sat, 11 Nov 2017 01:02:41: 23000000 INFO @ Sat, 11 Nov 2017 01:02:50: 19000000 INFO @ Sat, 11 Nov 2017 01:02:52: 21000000 INFO @ Sat, 11 Nov 2017 01:03:02: 24000000 INFO @ Sat, 11 Nov 2017 01:03:03: 20000000 INFO @ Sat, 11 Nov 2017 01:03:05: 22000000 INFO @ Sat, 11 Nov 2017 01:03:18: 21000000 INFO @ Sat, 11 Nov 2017 01:03:18: 25000000 INFO @ Sat, 11 Nov 2017 01:03:18: 23000000 INFO @ Sat, 11 Nov 2017 01:03:29: 24000000 INFO @ Sat, 11 Nov 2017 01:03:30: 26000000 INFO @ Sat, 11 Nov 2017 01:03:35: 22000000 INFO @ Sat, 11 Nov 2017 01:03:40: 25000000 INFO @ Sat, 11 Nov 2017 01:03:42: 27000000 INFO @ Sat, 11 Nov 2017 01:03:47: 23000000 INFO @ Sat, 11 Nov 2017 01:03:52: 26000000 INFO @ Sat, 11 Nov 2017 01:03:53: 28000000 INFO @ Sat, 11 Nov 2017 01:04:01: 24000000 INFO @ Sat, 11 Nov 2017 01:04:02: 27000000 INFO @ Sat, 11 Nov 2017 01:04:06: 29000000 INFO @ Sat, 11 Nov 2017 01:04:13: 28000000 INFO @ Sat, 11 Nov 2017 01:04:16: 30000000 INFO @ Sat, 11 Nov 2017 01:04:18: 25000000 INFO @ Sat, 11 Nov 2017 01:04:24: 29000000 INFO @ Sat, 11 Nov 2017 01:04:26: 31000000 INFO @ Sat, 11 Nov 2017 01:04:34: 26000000 INFO @ Sat, 11 Nov 2017 01:04:37: 30000000 INFO @ Sat, 11 Nov 2017 01:04:40: 32000000 INFO @ Sat, 11 Nov 2017 01:04:50: 31000000 INFO @ Sat, 11 Nov 2017 01:04:50: 27000000 INFO @ Sat, 11 Nov 2017 01:04:57: 33000000 INFO @ Sat, 11 Nov 2017 01:05:02: 32000000 INFO @ Sat, 11 Nov 2017 01:05:09: 28000000 INFO @ Sat, 11 Nov 2017 01:05:14: 33000000 INFO @ Sat, 11 Nov 2017 01:05:15: 34000000 INFO @ Sat, 11 Nov 2017 01:05:26: 34000000 INFO @ Sat, 11 Nov 2017 01:05:28: 29000000 INFO @ Sat, 11 Nov 2017 01:05:34: 35000000 INFO @ Sat, 11 Nov 2017 01:05:37: 35000000 INFO @ Sat, 11 Nov 2017 01:05:47: 30000000 INFO @ Sat, 11 Nov 2017 01:05:48: 36000000 INFO @ Sat, 11 Nov 2017 01:05:53: 36000000 INFO @ Sat, 11 Nov 2017 01:05:59: 37000000 INFO @ Sat, 11 Nov 2017 01:06:05: 31000000 INFO @ Sat, 11 Nov 2017 01:06:10: 38000000 INFO @ Sat, 11 Nov 2017 01:06:12: 37000000 INFO @ Sat, 11 Nov 2017 01:06:21: 39000000 INFO @ Sat, 11 Nov 2017 01:06:24: 32000000 INFO @ Sat, 11 Nov 2017 01:06:31: 38000000 INFO @ Sat, 11 Nov 2017 01:06:32: 40000000 INFO @ Sat, 11 Nov 2017 01:06:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 01:06:38: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 01:06:38: #1 total tags in treatment: 40501515 INFO @ Sat, 11 Nov 2017 01:06:38: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:06:38: #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 01:06:40: #1 tags after filtering in treatment: 40501456 INFO @ Sat, 11 Nov 2017 01:06:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:06:40: #1 finished! INFO @ Sat, 11 Nov 2017 01:06:40: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:06:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:06:41: 33000000 INFO @ Sat, 11 Nov 2017 01:06:44: #2 number of paired peaks: 5835 INFO @ Sat, 11 Nov 2017 01:06:44: start model_add_line... INFO @ Sat, 11 Nov 2017 01:06:45: start X-correlation... INFO @ Sat, 11 Nov 2017 01:06:45: end of X-cor INFO @ Sat, 11 Nov 2017 01:06:45: #2 finished! INFO @ Sat, 11 Nov 2017 01:06:45: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 01:06:45: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Nov 2017 01:06:45: #2.2 Generate R script for model : SRX2224391.20_model.r WARNING @ Sat, 11 Nov 2017 01:06:45: #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 01:06:45: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Nov 2017 01:06:45: #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 01:06:45: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:06:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:06:50: 39000000 INFO @ Sat, 11 Nov 2017 01:06:59: 34000000 INFO @ Sat, 11 Nov 2017 01:07:07: 40000000 INFO @ Sat, 11 Nov 2017 01:07:15: 35000000 INFO @ Sat, 11 Nov 2017 01:07:17: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 01:07:17: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 01:07:17: #1 total tags in treatment: 40501515 INFO @ Sat, 11 Nov 2017 01:07:17: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:07:17: #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 01:07:19: #1 tags after filtering in treatment: 40501456 INFO @ Sat, 11 Nov 2017 01:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:07:19: #1 finished! INFO @ Sat, 11 Nov 2017 01:07:19: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:07:23: #2 number of paired peaks: 5835 INFO @ Sat, 11 Nov 2017 01:07:23: start model_add_line... INFO @ Sat, 11 Nov 2017 01:07:24: start X-correlation... INFO @ Sat, 11 Nov 2017 01:07:24: end of X-cor INFO @ Sat, 11 Nov 2017 01:07:24: #2 finished! INFO @ Sat, 11 Nov 2017 01:07:24: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 01:07:24: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Nov 2017 01:07:24: #2.2 Generate R script for model : SRX2224391.10_model.r WARNING @ Sat, 11 Nov 2017 01:07:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:07:24: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Nov 2017 01:07:24: #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 01:07:24: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:07:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:07:33: 36000000 INFO @ Sat, 11 Nov 2017 01:07:51: 37000000 INFO @ Sat, 11 Nov 2017 01:08:09: 38000000 INFO @ Sat, 11 Nov 2017 01:08:28: 39000000 INFO @ Sat, 11 Nov 2017 01:08:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:08:47: 40000000 INFO @ Sat, 11 Nov 2017 01:08:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 01:08:57: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 01:08:57: #1 total tags in treatment: 40501515 INFO @ Sat, 11 Nov 2017 01:08:57: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:08:57: #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 01:08:59: #1 tags after filtering in treatment: 40501456 INFO @ Sat, 11 Nov 2017 01:08:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:08:59: #1 finished! INFO @ Sat, 11 Nov 2017 01:08:59: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:09:03: #2 number of paired peaks: 5835 INFO @ Sat, 11 Nov 2017 01:09:03: start model_add_line... INFO @ Sat, 11 Nov 2017 01:09:04: start X-correlation... INFO @ Sat, 11 Nov 2017 01:09:04: end of X-cor INFO @ Sat, 11 Nov 2017 01:09:04: #2 finished! INFO @ Sat, 11 Nov 2017 01:09:04: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 01:09:04: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Nov 2017 01:09:04: #2.2 Generate R script for model : SRX2224391.05_model.r WARNING @ Sat, 11 Nov 2017 01:09:04: #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 01:09:04: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Nov 2017 01:09:04: #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 01:09:04: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:09:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:09:44: #4 Write output xls file... SRX2224391.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:09:44: #4 Write peak in narrowPeak format file... SRX2224391.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:09:44: #4 Write summits bed file... SRX2224391.20_summits.bed INFO @ Sat, 11 Nov 2017 01:09:44: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (684 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:10:24: #4 Write output xls file... SRX2224391.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:10:24: #4 Write peak in narrowPeak format file... SRX2224391.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:10:24: #4 Write summits bed file... SRX2224391.10_summits.bed INFO @ Sat, 11 Nov 2017 01:10:24: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (1441 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:11:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:12:16: #4 Write output xls file... SRX2224391.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:12:16: #4 Write peak in narrowPeak format file... SRX2224391.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:12:16: #4 Write summits bed file... SRX2224391.05_summits.bed INFO @ Sat, 11 Nov 2017 01:12:16: Done! pass1 - making usageList (84 chroms): 1 millis pass2 - checking and writing primary data (2863 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。