Job ID = 11632716 sra ファイルのダウンロード中... Completed: 1171519K bytes transferred in 15 seconds (628355K 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... Read 45917020 spots for /home/okishinya/chipatlas/results/rn6/SRX3782475/SRR6826293.sra Written 45917020 spots for /home/okishinya/chipatlas/results/rn6/SRX3782475/SRR6826293.sra 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:20:48 45917020 reads; of these: 45917020 (100.00%) were unpaired; of these: 1662186 (3.62%) aligned 0 times 33454671 (72.86%) aligned exactly 1 time 10800163 (23.52%) aligned >1 times 96.38% overall alignment rate Time searching: 00:20:52 Overall time: 00:20:53 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] 3209659 / 44254834 = 0.0725 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, 15 Feb 2019 07:03:31: # Command line: callpeak -t SRX3782475.bam -f BAM -g 2.15e9 -n SRX3782475.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782475.20 # format = BAM # ChIP-seq file = ['SRX3782475.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, 15 Feb 2019 07:03:31: # Command line: callpeak -t SRX3782475.bam -f BAM -g 2.15e9 -n SRX3782475.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782475.10 # format = BAM # ChIP-seq file = ['SRX3782475.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, 15 Feb 2019 07:03:31: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:03:31: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:03:31: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:03:31: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:03:31: # Command line: callpeak -t SRX3782475.bam -f BAM -g 2.15e9 -n SRX3782475.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782475.05 # format = BAM # ChIP-seq file = ['SRX3782475.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, 15 Feb 2019 07:03:31: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:03:31: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:03:39: 1000000 INFO @ Fri, 15 Feb 2019 07:03:39: 1000000 INFO @ Fri, 15 Feb 2019 07:03:39: 1000000 INFO @ Fri, 15 Feb 2019 07:03:46: 2000000 INFO @ Fri, 15 Feb 2019 07:03:46: 2000000 INFO @ Fri, 15 Feb 2019 07:03:46: 2000000 INFO @ Fri, 15 Feb 2019 07:03:53: 3000000 INFO @ Fri, 15 Feb 2019 07:03:53: 3000000 INFO @ Fri, 15 Feb 2019 07:03:53: 3000000 INFO @ Fri, 15 Feb 2019 07:04:00: 4000000 INFO @ Fri, 15 Feb 2019 07:04:01: 4000000 INFO @ Fri, 15 Feb 2019 07:04:01: 4000000 INFO @ Fri, 15 Feb 2019 07:04:08: 5000000 INFO @ Fri, 15 Feb 2019 07:04:08: 5000000 INFO @ Fri, 15 Feb 2019 07:04:08: 5000000 INFO @ Fri, 15 Feb 2019 07:04:15: 6000000 INFO @ Fri, 15 Feb 2019 07:04:15: 6000000 INFO @ Fri, 15 Feb 2019 07:04:15: 6000000 INFO @ Fri, 15 Feb 2019 07:04:22: 7000000 INFO @ Fri, 15 Feb 2019 07:04:22: 7000000 INFO @ Fri, 15 Feb 2019 07:04:23: 7000000 INFO @ Fri, 15 Feb 2019 07:04:29: 8000000 INFO @ Fri, 15 Feb 2019 07:04:30: 8000000 INFO @ Fri, 15 Feb 2019 07:04:30: 8000000 INFO @ Fri, 15 Feb 2019 07:04:36: 9000000 INFO @ Fri, 15 Feb 2019 07:04:37: 9000000 INFO @ Fri, 15 Feb 2019 07:04:37: 9000000 INFO @ Fri, 15 Feb 2019 07:04:43: 10000000 INFO @ Fri, 15 Feb 2019 07:04:44: 10000000 INFO @ Fri, 15 Feb 2019 07:04:45: 10000000 INFO @ Fri, 15 Feb 2019 07:04:50: 11000000 INFO @ Fri, 15 Feb 2019 07:04:52: 11000000 INFO @ Fri, 15 Feb 2019 07:04:52: 11000000 INFO @ Fri, 15 Feb 2019 07:04:58: 12000000 INFO @ Fri, 15 Feb 2019 07:04:59: 12000000 INFO @ Fri, 15 Feb 2019 07:05:00: 12000000 INFO @ Fri, 15 Feb 2019 07:05:05: 13000000 INFO @ Fri, 15 Feb 2019 07:05:07: 13000000 INFO @ Fri, 15 Feb 2019 07:05:07: 13000000 INFO @ Fri, 15 Feb 2019 07:05:12: 14000000 INFO @ Fri, 15 Feb 2019 07:05:14: 14000000 INFO @ Fri, 15 Feb 2019 07:05:15: 14000000 INFO @ Fri, 15 Feb 2019 07:05:19: 15000000 INFO @ Fri, 15 Feb 2019 07:05:22: 15000000 INFO @ Fri, 15 Feb 2019 07:05:23: 15000000 INFO @ Fri, 15 Feb 2019 07:05:26: 16000000 INFO @ Fri, 15 Feb 2019 07:05:30: 16000000 INFO @ Fri, 15 Feb 2019 07:05:30: 16000000 INFO @ Fri, 15 Feb 2019 07:05:33: 17000000 INFO @ Fri, 15 Feb 2019 07:05:37: 17000000 INFO @ Fri, 15 Feb 2019 07:05:38: 17000000 INFO @ Fri, 15 Feb 2019 07:05:41: 18000000 INFO @ Fri, 15 Feb 2019 07:05:45: 18000000 INFO @ Fri, 15 Feb 2019 07:05:46: 18000000 INFO @ Fri, 15 Feb 2019 07:05:48: 19000000 INFO @ Fri, 15 Feb 2019 07:05:52: 19000000 INFO @ Fri, 15 Feb 2019 07:05:53: 19000000 INFO @ Fri, 15 Feb 2019 07:05:55: 20000000 INFO @ Fri, 15 Feb 2019 07:06:00: 20000000 INFO @ Fri, 15 Feb 2019 07:06:01: 20000000 INFO @ Fri, 15 Feb 2019 07:06:02: 21000000 INFO @ Fri, 15 Feb 2019 07:06:08: 21000000 INFO @ Fri, 15 Feb 2019 07:06:09: 21000000 INFO @ Fri, 15 Feb 2019 07:06:10: 22000000 INFO @ Fri, 15 Feb 2019 07:06:15: 22000000 INFO @ Fri, 15 Feb 2019 07:06:16: 22000000 INFO @ Fri, 15 Feb 2019 07:06:17: 23000000 INFO @ Fri, 15 Feb 2019 07:06:23: 23000000 INFO @ Fri, 15 Feb 2019 07:06:24: 23000000 INFO @ Fri, 15 Feb 2019 07:06:24: 24000000 INFO @ Fri, 15 Feb 2019 07:06:30: 24000000 INFO @ Fri, 15 Feb 2019 07:06:31: 25000000 INFO @ Fri, 15 Feb 2019 07:06:32: 24000000 INFO @ Fri, 15 Feb 2019 07:06:38: 25000000 INFO @ Fri, 15 Feb 2019 07:06:39: 26000000 INFO @ Fri, 15 Feb 2019 07:06:40: 25000000 INFO @ Fri, 15 Feb 2019 07:06:46: 27000000 INFO @ Fri, 15 Feb 2019 07:06:46: 26000000 INFO @ Fri, 15 Feb 2019 07:06:48: 26000000 INFO @ Fri, 15 Feb 2019 07:06:53: 28000000 INFO @ Fri, 15 Feb 2019 07:06:54: 27000000 INFO @ Fri, 15 Feb 2019 07:06:56: 27000000 INFO @ Fri, 15 Feb 2019 07:07:01: 29000000 INFO @ Fri, 15 Feb 2019 07:07:02: 28000000 INFO @ Fri, 15 Feb 2019 07:07:04: 28000000 INFO @ Fri, 15 Feb 2019 07:07:08: 30000000 INFO @ Fri, 15 Feb 2019 07:07:09: 29000000 INFO @ Fri, 15 Feb 2019 07:07:11: 29000000 INFO @ Fri, 15 Feb 2019 07:07:16: 31000000 INFO @ Fri, 15 Feb 2019 07:07:17: 30000000 INFO @ Fri, 15 Feb 2019 07:07:19: 30000000 INFO @ Fri, 15 Feb 2019 07:07:23: 32000000 INFO @ Fri, 15 Feb 2019 07:07:25: 31000000 INFO @ Fri, 15 Feb 2019 07:07:27: 31000000 INFO @ Fri, 15 Feb 2019 07:07:31: 33000000 INFO @ Fri, 15 Feb 2019 07:07:32: 32000000 INFO @ Fri, 15 Feb 2019 07:07:34: 32000000 INFO @ Fri, 15 Feb 2019 07:07:38: 34000000 INFO @ Fri, 15 Feb 2019 07:07:40: 33000000 INFO @ Fri, 15 Feb 2019 07:07:42: 33000000 INFO @ Fri, 15 Feb 2019 07:07:46: 35000000 INFO @ Fri, 15 Feb 2019 07:07:47: 34000000 INFO @ Fri, 15 Feb 2019 07:07:50: 34000000 INFO @ Fri, 15 Feb 2019 07:07:54: 36000000 INFO @ Fri, 15 Feb 2019 07:07:55: 35000000 INFO @ Fri, 15 Feb 2019 07:07:57: 35000000 INFO @ Fri, 15 Feb 2019 07:08:01: 37000000 INFO @ Fri, 15 Feb 2019 07:08:02: 36000000 INFO @ Fri, 15 Feb 2019 07:08:05: 36000000 INFO @ Fri, 15 Feb 2019 07:08:09: 38000000 INFO @ Fri, 15 Feb 2019 07:08:10: 37000000 INFO @ Fri, 15 Feb 2019 07:08:12: 37000000 INFO @ Fri, 15 Feb 2019 07:08:17: 39000000 INFO @ Fri, 15 Feb 2019 07:08:17: 38000000 INFO @ Fri, 15 Feb 2019 07:08:20: 38000000 INFO @ Fri, 15 Feb 2019 07:08:24: 40000000 INFO @ Fri, 15 Feb 2019 07:08:25: 39000000 INFO @ Fri, 15 Feb 2019 07:08:27: 39000000 INFO @ Fri, 15 Feb 2019 07:08:32: 41000000 INFO @ Fri, 15 Feb 2019 07:08:32: 40000000 INFO @ Fri, 15 Feb 2019 07:08:33: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:08:33: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:08:33: #1 total tags in treatment: 41045175 INFO @ Fri, 15 Feb 2019 07:08:33: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:08:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:08:34: #1 tags after filtering in treatment: 41045084 INFO @ Fri, 15 Feb 2019 07:08:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:08:34: #1 finished! INFO @ Fri, 15 Feb 2019 07:08:34: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:08:35: 40000000 INFO @ Fri, 15 Feb 2019 07:08:38: #2 number of paired peaks: 3542 INFO @ Fri, 15 Feb 2019 07:08:38: start model_add_line... INFO @ Fri, 15 Feb 2019 07:08:38: start X-correlation... INFO @ Fri, 15 Feb 2019 07:08:38: end of X-cor INFO @ Fri, 15 Feb 2019 07:08:38: #2 finished! INFO @ Fri, 15 Feb 2019 07:08:38: #2 predicted fragment length is 40 bps INFO @ Fri, 15 Feb 2019 07:08:38: #2 alternative fragment length(s) may be 40,114,216,404,511 bps INFO @ Fri, 15 Feb 2019 07:08:38: #2.2 Generate R script for model : SRX3782475.05_model.r WARNING @ Fri, 15 Feb 2019 07:08:38: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:08:38: #2 You may need to consider one of the other alternative d(s): 40,114,216,404,511 WARNING @ Fri, 15 Feb 2019 07:08:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:08:38: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:08:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:08:40: 41000000 INFO @ Fri, 15 Feb 2019 07:08:40: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:08:40: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:08:40: #1 total tags in treatment: 41045175 INFO @ Fri, 15 Feb 2019 07:08:40: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:08:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:08:41: #1 tags after filtering in treatment: 41045084 INFO @ Fri, 15 Feb 2019 07:08:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:08:41: #1 finished! INFO @ Fri, 15 Feb 2019 07:08:41: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:08:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:08:42: 41000000 INFO @ Fri, 15 Feb 2019 07:08:43: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:08:43: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:08:43: #1 total tags in treatment: 41045175 INFO @ Fri, 15 Feb 2019 07:08:43: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:08:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:08:44: #1 tags after filtering in treatment: 41045084 INFO @ Fri, 15 Feb 2019 07:08:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:08:44: #1 finished! INFO @ Fri, 15 Feb 2019 07:08:44: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:08:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:08:45: #2 number of paired peaks: 3542 INFO @ Fri, 15 Feb 2019 07:08:45: start model_add_line... INFO @ Fri, 15 Feb 2019 07:08:45: start X-correlation... INFO @ Fri, 15 Feb 2019 07:08:45: end of X-cor INFO @ Fri, 15 Feb 2019 07:08:45: #2 finished! INFO @ Fri, 15 Feb 2019 07:08:45: #2 predicted fragment length is 40 bps INFO @ Fri, 15 Feb 2019 07:08:45: #2 alternative fragment length(s) may be 40,114,216,404,511 bps INFO @ Fri, 15 Feb 2019 07:08:45: #2.2 Generate R script for model : SRX3782475.20_model.r WARNING @ Fri, 15 Feb 2019 07:08:45: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:08:45: #2 You may need to consider one of the other alternative d(s): 40,114,216,404,511 WARNING @ Fri, 15 Feb 2019 07:08:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:08:45: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:08:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:08:47: #2 number of paired peaks: 3542 INFO @ Fri, 15 Feb 2019 07:08:47: start model_add_line... INFO @ Fri, 15 Feb 2019 07:08:48: start X-correlation... INFO @ Fri, 15 Feb 2019 07:08:48: end of X-cor INFO @ Fri, 15 Feb 2019 07:08:48: #2 finished! INFO @ Fri, 15 Feb 2019 07:08:48: #2 predicted fragment length is 40 bps INFO @ Fri, 15 Feb 2019 07:08:48: #2 alternative fragment length(s) may be 40,114,216,404,511 bps INFO @ Fri, 15 Feb 2019 07:08:48: #2.2 Generate R script for model : SRX3782475.10_model.r WARNING @ Fri, 15 Feb 2019 07:08:48: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:08:48: #2 You may need to consider one of the other alternative d(s): 40,114,216,404,511 WARNING @ Fri, 15 Feb 2019 07:08:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:08:48: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:08:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:10:15: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:10:18: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:10:25: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:11:09: #4 Write output xls file... SRX3782475.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:11:09: #4 Write peak in narrowPeak format file... SRX3782475.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:11:09: #4 Write summits bed file... SRX3782475.05_summits.bed INFO @ Fri, 15 Feb 2019 07:11:09: Done! pass1 - making usageList (45 chroms): 3 millis pass2 - checking and writing primary data (1802 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:11:14: #4 Write output xls file... SRX3782475.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:11:14: #4 Write peak in narrowPeak format file... SRX3782475.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:11:14: #4 Write summits bed file... SRX3782475.20_summits.bed INFO @ Fri, 15 Feb 2019 07:11:14: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (490 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:11:24: #4 Write output xls file... SRX3782475.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:11:24: #4 Write peak in narrowPeak format file... SRX3782475.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:11:24: #4 Write summits bed file... SRX3782475.10_summits.bed INFO @ Fri, 15 Feb 2019 07:11:24: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (1062 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。