Job ID = 10194891 sra ファイルのダウンロード中... Completed: 250451K bytes transferred in 10 seconds (204049K bits/sec), in 1 file. Completed: 251113K bytes transferred in 10 seconds (190404K bits/sec), in 1 file. Completed: 239325K bytes transferred in 18 seconds (108163K bits/sec), in 1 file. Completed: 236332K bytes transferred in 6 seconds (286620K bits/sec), in 1 file. Completed: 269799K bytes transferred in 8 seconds (267438K bits/sec), in 1 file. Completed: 272834K bytes transferred in 8 seconds (267322K 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 5354555 spots for /home/okishinya/chipatlas/results/rn6/SRX2202886/SRR4319863.sra Written 5354555 spots total Written 5409100 spots for /home/okishinya/chipatlas/results/rn6/SRX2202886/SRR4319862.sra Written 5409100 spots total Written 5645239 spots for /home/okishinya/chipatlas/results/rn6/SRX2202886/SRR4319861.sra Written 5645239 spots total Written 5647940 spots for /home/okishinya/chipatlas/results/rn6/SRX2202886/SRR4319860.sra Written 5647940 spots total Written 5955672 spots for /home/okishinya/chipatlas/results/rn6/SRX2202886/SRR4319864.sra Written 5955672 spots total Written 6001986 spots for /home/okishinya/chipatlas/results/rn6/SRX2202886/SRR4319865.sra Written 6001986 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:24:25 34014492 reads; of these: 34014492 (100.00%) were unpaired; of these: 1022941 (3.01%) aligned 0 times 26005487 (76.45%) aligned exactly 1 time 6986064 (20.54%) aligned >1 times 96.99% overall alignment rate Time searching: 00:24:28 Overall time: 00:24:28 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] 3081216 / 32991551 = 0.0934 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 18:31:41: # Command line: callpeak -t SRX2202886.bam -f BAM -g 2.15e9 -n SRX2202886.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202886.20 # format = BAM # ChIP-seq file = ['SRX2202886.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 18:31:41: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:31:41: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:31:41: # Command line: callpeak -t SRX2202886.bam -f BAM -g 2.15e9 -n SRX2202886.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202886.05 # format = BAM # ChIP-seq file = ['SRX2202886.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 18:31:41: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:31:41: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:31:41: # Command line: callpeak -t SRX2202886.bam -f BAM -g 2.15e9 -n SRX2202886.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202886.10 # format = BAM # ChIP-seq file = ['SRX2202886.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 18:31:41: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:31:41: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:31:48: 1000000 INFO @ Fri, 10 Nov 2017 18:31:48: 1000000 INFO @ Fri, 10 Nov 2017 18:31:48: 1000000 INFO @ Fri, 10 Nov 2017 18:31:54: 2000000 INFO @ Fri, 10 Nov 2017 18:31:56: 2000000 INFO @ Fri, 10 Nov 2017 18:31:56: 2000000 INFO @ Fri, 10 Nov 2017 18:32:01: 3000000 INFO @ Fri, 10 Nov 2017 18:32:03: 3000000 INFO @ Fri, 10 Nov 2017 18:32:03: 3000000 INFO @ Fri, 10 Nov 2017 18:32:07: 4000000 INFO @ Fri, 10 Nov 2017 18:32:10: 4000000 INFO @ Fri, 10 Nov 2017 18:32:10: 4000000 INFO @ Fri, 10 Nov 2017 18:32:14: 5000000 INFO @ Fri, 10 Nov 2017 18:32:17: 5000000 INFO @ Fri, 10 Nov 2017 18:32:18: 5000000 INFO @ Fri, 10 Nov 2017 18:32:21: 6000000 INFO @ Fri, 10 Nov 2017 18:32:25: 6000000 INFO @ Fri, 10 Nov 2017 18:32:25: 6000000 INFO @ Fri, 10 Nov 2017 18:32:28: 7000000 INFO @ Fri, 10 Nov 2017 18:32:32: 7000000 INFO @ Fri, 10 Nov 2017 18:32:32: 7000000 INFO @ Fri, 10 Nov 2017 18:32:34: 8000000 INFO @ Fri, 10 Nov 2017 18:32:39: 8000000 INFO @ Fri, 10 Nov 2017 18:32:40: 8000000 INFO @ Fri, 10 Nov 2017 18:32:41: 9000000 INFO @ Fri, 10 Nov 2017 18:32:47: 9000000 INFO @ Fri, 10 Nov 2017 18:32:47: 9000000 INFO @ Fri, 10 Nov 2017 18:32:48: 10000000 INFO @ Fri, 10 Nov 2017 18:32:54: 10000000 INFO @ Fri, 10 Nov 2017 18:32:54: 11000000 INFO @ Fri, 10 Nov 2017 18:32:55: 10000000 INFO @ Fri, 10 Nov 2017 18:33:01: 12000000 INFO @ Fri, 10 Nov 2017 18:33:02: 11000000 INFO @ Fri, 10 Nov 2017 18:33:02: 11000000 INFO @ Fri, 10 Nov 2017 18:33:07: 13000000 INFO @ Fri, 10 Nov 2017 18:33:09: 12000000 INFO @ Fri, 10 Nov 2017 18:33:10: 12000000 INFO @ Fri, 10 Nov 2017 18:33:14: 14000000 INFO @ Fri, 10 Nov 2017 18:33:16: 13000000 INFO @ Fri, 10 Nov 2017 18:33:17: 13000000 INFO @ Fri, 10 Nov 2017 18:33:21: 15000000 INFO @ Fri, 10 Nov 2017 18:33:24: 14000000 INFO @ Fri, 10 Nov 2017 18:33:25: 14000000 INFO @ Fri, 10 Nov 2017 18:33:27: 16000000 INFO @ Fri, 10 Nov 2017 18:33:31: 15000000 INFO @ Fri, 10 Nov 2017 18:33:32: 15000000 INFO @ Fri, 10 Nov 2017 18:33:34: 17000000 INFO @ Fri, 10 Nov 2017 18:33:39: 16000000 INFO @ Fri, 10 Nov 2017 18:33:40: 16000000 INFO @ Fri, 10 Nov 2017 18:33:40: 18000000 INFO @ Fri, 10 Nov 2017 18:33:47: 17000000 INFO @ Fri, 10 Nov 2017 18:33:47: 19000000 INFO @ Fri, 10 Nov 2017 18:33:48: 17000000 INFO @ Fri, 10 Nov 2017 18:33:54: 20000000 INFO @ Fri, 10 Nov 2017 18:33:55: 18000000 INFO @ Fri, 10 Nov 2017 18:33:56: 18000000 INFO @ Fri, 10 Nov 2017 18:34:00: 21000000 INFO @ Fri, 10 Nov 2017 18:34:03: 19000000 INFO @ Fri, 10 Nov 2017 18:34:04: 19000000 INFO @ Fri, 10 Nov 2017 18:34:07: 22000000 INFO @ Fri, 10 Nov 2017 18:34:11: 20000000 INFO @ Fri, 10 Nov 2017 18:34:12: 20000000 INFO @ Fri, 10 Nov 2017 18:34:14: 23000000 INFO @ Fri, 10 Nov 2017 18:34:19: 21000000 INFO @ Fri, 10 Nov 2017 18:34:20: 21000000 INFO @ Fri, 10 Nov 2017 18:34:21: 24000000 INFO @ Fri, 10 Nov 2017 18:34:27: 22000000 INFO @ Fri, 10 Nov 2017 18:34:27: 25000000 INFO @ Fri, 10 Nov 2017 18:34:29: 22000000 INFO @ Fri, 10 Nov 2017 18:34:34: 26000000 INFO @ Fri, 10 Nov 2017 18:34:35: 23000000 INFO @ Fri, 10 Nov 2017 18:34:37: 23000000 INFO @ Fri, 10 Nov 2017 18:34:41: 27000000 INFO @ Fri, 10 Nov 2017 18:34:43: 24000000 INFO @ Fri, 10 Nov 2017 18:34:45: 24000000 INFO @ Fri, 10 Nov 2017 18:34:48: 28000000 INFO @ Fri, 10 Nov 2017 18:34:51: 25000000 INFO @ Fri, 10 Nov 2017 18:34:53: 25000000 INFO @ Fri, 10 Nov 2017 18:34:55: 29000000 INFO @ Fri, 10 Nov 2017 18:34:59: 26000000 INFO @ Fri, 10 Nov 2017 18:35:01: 26000000 INFO @ Fri, 10 Nov 2017 18:35:01: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:35:01: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:35:01: #1 total tags in treatment: 29910335 INFO @ Fri, 10 Nov 2017 18:35:01: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:35:01: #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 18:35:02: #1 tags after filtering in treatment: 29910207 INFO @ Fri, 10 Nov 2017 18:35:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:35:02: #1 finished! INFO @ Fri, 10 Nov 2017 18:35:02: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:35:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:35:07: #2 number of paired peaks: 55373 INFO @ Fri, 10 Nov 2017 18:35:07: start model_add_line... INFO @ Fri, 10 Nov 2017 18:35:07: start X-correlation... INFO @ Fri, 10 Nov 2017 18:35:07: end of X-cor INFO @ Fri, 10 Nov 2017 18:35:07: #2 finished! INFO @ Fri, 10 Nov 2017 18:35:07: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Nov 2017 18:35:07: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Nov 2017 18:35:07: #2.2 Generate R script for model : SRX2202886.10_model.r INFO @ Fri, 10 Nov 2017 18:35:07: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:35:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:35:08: 27000000 INFO @ Fri, 10 Nov 2017 18:35:10: 27000000 INFO @ Fri, 10 Nov 2017 18:35:16: 28000000 INFO @ Fri, 10 Nov 2017 18:35:18: 28000000 INFO @ Fri, 10 Nov 2017 18:35:24: 29000000 INFO @ Fri, 10 Nov 2017 18:35:26: 29000000 INFO @ Fri, 10 Nov 2017 18:35:31: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:35:31: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:35:31: #1 total tags in treatment: 29910335 INFO @ Fri, 10 Nov 2017 18:35:31: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:35:31: #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 18:35:31: #1 tags after filtering in treatment: 29910207 INFO @ Fri, 10 Nov 2017 18:35:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:35:31: #1 finished! INFO @ Fri, 10 Nov 2017 18:35:31: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:35:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:35:33: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:35:33: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:35:33: #1 total tags in treatment: 29910335 INFO @ Fri, 10 Nov 2017 18:35:33: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:35:33: #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 18:35:34: #1 tags after filtering in treatment: 29910207 INFO @ Fri, 10 Nov 2017 18:35:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:35:34: #1 finished! INFO @ Fri, 10 Nov 2017 18:35:34: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:35:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:35:37: #2 number of paired peaks: 55373 INFO @ Fri, 10 Nov 2017 18:35:37: start model_add_line... INFO @ Fri, 10 Nov 2017 18:35:37: start X-correlation... INFO @ Fri, 10 Nov 2017 18:35:37: end of X-cor INFO @ Fri, 10 Nov 2017 18:35:37: #2 finished! INFO @ Fri, 10 Nov 2017 18:35:37: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Nov 2017 18:35:37: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Nov 2017 18:35:37: #2.2 Generate R script for model : SRX2202886.20_model.r INFO @ Fri, 10 Nov 2017 18:35:37: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:35:39: #2 number of paired peaks: 55373 INFO @ Fri, 10 Nov 2017 18:35:39: start model_add_line... INFO @ Fri, 10 Nov 2017 18:35:39: start X-correlation... INFO @ Fri, 10 Nov 2017 18:35:39: end of X-cor INFO @ Fri, 10 Nov 2017 18:35:39: #2 finished! INFO @ Fri, 10 Nov 2017 18:35:39: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Nov 2017 18:35:39: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Nov 2017 18:35:39: #2.2 Generate R script for model : SRX2202886.05_model.r INFO @ Fri, 10 Nov 2017 18:35:39: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:36:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:36:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:36:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:37:03: #4 Write output xls file... SRX2202886.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:37:03: #4 Write peak in narrowPeak format file... SRX2202886.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:37:03: #4 Write summits bed file... SRX2202886.10_summits.bed INFO @ Fri, 10 Nov 2017 18:37:03: Done! pass1 - making usageList (75 chroms): 4 millis pass2 - checking and writing primary data (13755 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:37:32: #4 Write output xls file... SRX2202886.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:37:32: #4 Write peak in narrowPeak format file... SRX2202886.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:37:32: #4 Write summits bed file... SRX2202886.20_summits.bed INFO @ Fri, 10 Nov 2017 18:37:33: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (4600 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:37:43: #4 Write output xls file... SRX2202886.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:37:43: #4 Write peak in narrowPeak format file... SRX2202886.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:37:43: #4 Write summits bed file... SRX2202886.05_summits.bed INFO @ Fri, 10 Nov 2017 18:37:43: Done! pass1 - making usageList (99 chroms): 5 millis pass2 - checking and writing primary data (24427 records, 4 fields): 32 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。