Job ID = 10194882 sra ファイルのダウンロード中... Completed: 252775K bytes transferred in 11 seconds (184227K bits/sec), in 1 file. Completed: 254653K bytes transferred in 9 seconds (227274K bits/sec), in 1 file. Completed: 241060K bytes transferred in 9 seconds (203334K bits/sec), in 1 file. Completed: 237679K bytes transferred in 9 seconds (211020K bits/sec), in 1 file. Completed: 280852K bytes transferred in 10 seconds (210840K bits/sec), in 1 file. Completed: 285163K bytes transferred in 9 seconds (245518K 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 5488885 spots for /home/okishinya/chipatlas/results/rn6/SRX2202877/SRR4319808.sra Written 5488885 spots total Written 5422242 spots for /home/okishinya/chipatlas/results/rn6/SRX2202877/SRR4319809.sra Written 5422242 spots total Written 5734484 spots for /home/okishinya/chipatlas/results/rn6/SRX2202877/SRR4319806.sra Written 5734484 spots total Written 5758328 spots for /home/okishinya/chipatlas/results/rn6/SRX2202877/SRR4319807.sra Written 5758328 spots total Written 6235596 spots for /home/okishinya/chipatlas/results/rn6/SRX2202877/SRR4319810.sra Written 6235596 spots total Written 6309651 spots for /home/okishinya/chipatlas/results/rn6/SRX2202877/SRR4319811.sra Written 6309651 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 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: 00:26:54 34949186 reads; of these: 34949186 (100.00%) were unpaired; of these: 1011970 (2.90%) aligned 0 times 24395978 (69.80%) aligned exactly 1 time 9541238 (27.30%) aligned >1 times 97.10% overall alignment rate Time searching: 00:26:58 Overall time: 00:26:58 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] 1396029 / 33937216 = 0.0411 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 18:14:04: # Command line: callpeak -t SRX2202877.bam -f BAM -g 2.15e9 -n SRX2202877.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202877.10 # format = BAM # ChIP-seq file = ['SRX2202877.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 18:14:04: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:14:04: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:14:04: # Command line: callpeak -t SRX2202877.bam -f BAM -g 2.15e9 -n SRX2202877.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202877.05 # format = BAM # ChIP-seq file = ['SRX2202877.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 18:14:04: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:14:04: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:14:04: # Command line: callpeak -t SRX2202877.bam -f BAM -g 2.15e9 -n SRX2202877.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202877.20 # format = BAM # ChIP-seq file = ['SRX2202877.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 18:14:04: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:14:04: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:14:11: 1000000 INFO @ Fri, 10 Nov 2017 18:14:11: 1000000 INFO @ Fri, 10 Nov 2017 18:14:12: 1000000 INFO @ Fri, 10 Nov 2017 18:14:18: 2000000 INFO @ Fri, 10 Nov 2017 18:14:18: 2000000 INFO @ Fri, 10 Nov 2017 18:14:19: 2000000 INFO @ Fri, 10 Nov 2017 18:14:24: 3000000 INFO @ Fri, 10 Nov 2017 18:14:25: 3000000 INFO @ Fri, 10 Nov 2017 18:14:26: 3000000 INFO @ Fri, 10 Nov 2017 18:14:31: 4000000 INFO @ Fri, 10 Nov 2017 18:14:31: 4000000 INFO @ Fri, 10 Nov 2017 18:14:33: 4000000 INFO @ Fri, 10 Nov 2017 18:14:38: 5000000 INFO @ Fri, 10 Nov 2017 18:14:38: 5000000 INFO @ Fri, 10 Nov 2017 18:14:40: 5000000 INFO @ Fri, 10 Nov 2017 18:14:44: 6000000 INFO @ Fri, 10 Nov 2017 18:14:45: 6000000 INFO @ Fri, 10 Nov 2017 18:14:47: 6000000 INFO @ Fri, 10 Nov 2017 18:14:51: 7000000 INFO @ Fri, 10 Nov 2017 18:14:52: 7000000 INFO @ Fri, 10 Nov 2017 18:14:54: 7000000 INFO @ Fri, 10 Nov 2017 18:14:58: 8000000 INFO @ Fri, 10 Nov 2017 18:14:59: 8000000 INFO @ Fri, 10 Nov 2017 18:15:01: 8000000 INFO @ Fri, 10 Nov 2017 18:15:05: 9000000 INFO @ Fri, 10 Nov 2017 18:15:06: 9000000 INFO @ Fri, 10 Nov 2017 18:15:08: 9000000 INFO @ Fri, 10 Nov 2017 18:15:12: 10000000 INFO @ Fri, 10 Nov 2017 18:15:13: 10000000 INFO @ Fri, 10 Nov 2017 18:15:15: 10000000 INFO @ Fri, 10 Nov 2017 18:15:19: 11000000 INFO @ Fri, 10 Nov 2017 18:15:20: 11000000 INFO @ Fri, 10 Nov 2017 18:15:22: 11000000 INFO @ Fri, 10 Nov 2017 18:15:26: 12000000 INFO @ Fri, 10 Nov 2017 18:15:27: 12000000 INFO @ Fri, 10 Nov 2017 18:15:29: 12000000 INFO @ Fri, 10 Nov 2017 18:15:33: 13000000 INFO @ Fri, 10 Nov 2017 18:15:34: 13000000 INFO @ Fri, 10 Nov 2017 18:15:36: 13000000 INFO @ Fri, 10 Nov 2017 18:15:39: 14000000 INFO @ Fri, 10 Nov 2017 18:15:41: 14000000 INFO @ Fri, 10 Nov 2017 18:15:43: 14000000 INFO @ Fri, 10 Nov 2017 18:15:46: 15000000 INFO @ Fri, 10 Nov 2017 18:15:48: 15000000 INFO @ Fri, 10 Nov 2017 18:15:50: 15000000 INFO @ Fri, 10 Nov 2017 18:15:53: 16000000 INFO @ Fri, 10 Nov 2017 18:15:55: 16000000 INFO @ Fri, 10 Nov 2017 18:15:57: 16000000 INFO @ Fri, 10 Nov 2017 18:16:00: 17000000 INFO @ Fri, 10 Nov 2017 18:16:02: 17000000 INFO @ Fri, 10 Nov 2017 18:16:03: 17000000 INFO @ Fri, 10 Nov 2017 18:16:07: 18000000 INFO @ Fri, 10 Nov 2017 18:16:09: 18000000 INFO @ Fri, 10 Nov 2017 18:16:10: 18000000 INFO @ Fri, 10 Nov 2017 18:16:14: 19000000 INFO @ Fri, 10 Nov 2017 18:16:16: 19000000 INFO @ Fri, 10 Nov 2017 18:16:18: 19000000 INFO @ Fri, 10 Nov 2017 18:16:20: 20000000 INFO @ Fri, 10 Nov 2017 18:16:23: 20000000 INFO @ Fri, 10 Nov 2017 18:16:24: 20000000 INFO @ Fri, 10 Nov 2017 18:16:27: 21000000 INFO @ Fri, 10 Nov 2017 18:16:30: 21000000 INFO @ Fri, 10 Nov 2017 18:16:32: 21000000 INFO @ Fri, 10 Nov 2017 18:16:34: 22000000 INFO @ Fri, 10 Nov 2017 18:16:37: 22000000 INFO @ Fri, 10 Nov 2017 18:16:39: 22000000 INFO @ Fri, 10 Nov 2017 18:16:41: 23000000 INFO @ Fri, 10 Nov 2017 18:16:45: 23000000 INFO @ Fri, 10 Nov 2017 18:16:45: 23000000 INFO @ Fri, 10 Nov 2017 18:16:48: 24000000 INFO @ Fri, 10 Nov 2017 18:16:52: 24000000 INFO @ Fri, 10 Nov 2017 18:16:52: 24000000 INFO @ Fri, 10 Nov 2017 18:16:54: 25000000 INFO @ Fri, 10 Nov 2017 18:16:59: 25000000 INFO @ Fri, 10 Nov 2017 18:16:59: 25000000 INFO @ Fri, 10 Nov 2017 18:17:01: 26000000 INFO @ Fri, 10 Nov 2017 18:17:06: 26000000 INFO @ Fri, 10 Nov 2017 18:17:06: 26000000 INFO @ Fri, 10 Nov 2017 18:17:08: 27000000 INFO @ Fri, 10 Nov 2017 18:17:13: 27000000 INFO @ Fri, 10 Nov 2017 18:17:14: 27000000 INFO @ Fri, 10 Nov 2017 18:17:15: 28000000 INFO @ Fri, 10 Nov 2017 18:17:20: 28000000 INFO @ Fri, 10 Nov 2017 18:17:21: 28000000 INFO @ Fri, 10 Nov 2017 18:17:22: 29000000 INFO @ Fri, 10 Nov 2017 18:17:28: 29000000 INFO @ Fri, 10 Nov 2017 18:17:29: 29000000 INFO @ Fri, 10 Nov 2017 18:17:29: 30000000 INFO @ Fri, 10 Nov 2017 18:17:36: 30000000 INFO @ Fri, 10 Nov 2017 18:17:36: 30000000 INFO @ Fri, 10 Nov 2017 18:17:37: 31000000 INFO @ Fri, 10 Nov 2017 18:17:44: 31000000 INFO @ Fri, 10 Nov 2017 18:17:44: 32000000 INFO @ Fri, 10 Nov 2017 18:17:44: 31000000 INFO @ Fri, 10 Nov 2017 18:17:48: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:17:48: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:17:48: #1 total tags in treatment: 32541187 INFO @ Fri, 10 Nov 2017 18:17:48: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:17:48: #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 18:17:49: #1 tags after filtering in treatment: 32541099 INFO @ Fri, 10 Nov 2017 18:17:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:17:49: #1 finished! INFO @ Fri, 10 Nov 2017 18:17:49: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:17:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:17:51: 32000000 INFO @ Fri, 10 Nov 2017 18:17:52: 32000000 INFO @ Fri, 10 Nov 2017 18:17:52: #2 number of paired peaks: 10680 INFO @ Fri, 10 Nov 2017 18:17:52: start model_add_line... INFO @ Fri, 10 Nov 2017 18:17:53: start X-correlation... INFO @ Fri, 10 Nov 2017 18:17:53: end of X-cor INFO @ Fri, 10 Nov 2017 18:17:53: #2 finished! INFO @ Fri, 10 Nov 2017 18:17:53: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Nov 2017 18:17:53: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Nov 2017 18:17:53: #2.2 Generate R script for model : SRX2202877.10_model.r WARNING @ Fri, 10 Nov 2017 18:17:53: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 18:17:53: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Nov 2017 18:17:53: #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 18:17:53: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:17:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:17:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:17:56: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:17:56: #1 total tags in treatment: 32541187 INFO @ Fri, 10 Nov 2017 18:17:56: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:17:56: #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 18:17:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:17:56: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:17:56: #1 total tags in treatment: 32541187 INFO @ Fri, 10 Nov 2017 18:17:56: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:17:56: #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 18:17:57: #1 tags after filtering in treatment: 32541099 INFO @ Fri, 10 Nov 2017 18:17:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:17:57: #1 finished! INFO @ Fri, 10 Nov 2017 18:17:57: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:17:57: #1 tags after filtering in treatment: 32541099 INFO @ Fri, 10 Nov 2017 18:17:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:17:57: #1 finished! INFO @ Fri, 10 Nov 2017 18:17:57: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:18:00: #2 number of paired peaks: 10680 INFO @ Fri, 10 Nov 2017 18:18:00: start model_add_line... INFO @ Fri, 10 Nov 2017 18:18:00: start X-correlation... INFO @ Fri, 10 Nov 2017 18:18:00: end of X-cor INFO @ Fri, 10 Nov 2017 18:18:00: #2 finished! INFO @ Fri, 10 Nov 2017 18:18:00: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Nov 2017 18:18:00: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Nov 2017 18:18:00: #2.2 Generate R script for model : SRX2202877.20_model.r WARNING @ Fri, 10 Nov 2017 18:18:00: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 18:18:00: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Nov 2017 18:18:00: #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 18:18:00: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:18:01: #2 number of paired peaks: 10680 INFO @ Fri, 10 Nov 2017 18:18:01: start model_add_line... INFO @ Fri, 10 Nov 2017 18:18:01: start X-correlation... INFO @ Fri, 10 Nov 2017 18:18:01: end of X-cor INFO @ Fri, 10 Nov 2017 18:18:01: #2 finished! INFO @ Fri, 10 Nov 2017 18:18:01: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Nov 2017 18:18:01: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Nov 2017 18:18:01: #2.2 Generate R script for model : SRX2202877.05_model.r WARNING @ Fri, 10 Nov 2017 18:18:01: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 18:18:01: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Nov 2017 18:18:01: #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 18:18:01: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:18:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:19:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:19:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:19:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:19:55: #4 Write output xls file... SRX2202877.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:19:55: #4 Write peak in narrowPeak format file... SRX2202877.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:19:55: #4 Write summits bed file... SRX2202877.10_summits.bed INFO @ Fri, 10 Nov 2017 18:19:55: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (1131 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:20:10: #4 Write output xls file... SRX2202877.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:20:10: #4 Write peak in narrowPeak format file... SRX2202877.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:20:10: #4 Write summits bed file... SRX2202877.05_summits.bed INFO @ Fri, 10 Nov 2017 18:20:10: Done! INFO @ Fri, 10 Nov 2017 18:20:10: #4 Write output xls file... SRX2202877.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:20:10: #4 Write peak in narrowPeak format file... SRX2202877.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:20:10: #4 Write summits bed file... SRX2202877.20_summits.bed INFO @ Fri, 10 Nov 2017 18:20:10: Done! pass1 - making usageList (57 chroms): 1 millis pass2 - checking and writing primary data (2275 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (555 records, 4 fields): 53 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。