Job ID = 10194893 sra ファイルのダウンロード中... Completed: 189116K bytes transferred in 8 seconds (191386K bits/sec), in 1 file. Completed: 188792K bytes transferred in 7 seconds (199132K bits/sec), in 1 file. Completed: 180246K bytes transferred in 6 seconds (223821K bits/sec), in 1 file. Completed: 177947K bytes transferred in 7 seconds (199686K bits/sec), in 1 file. Completed: 214892K bytes transferred in 17 seconds (103222K bits/sec), in 1 file. Completed: 216011K bytes transferred in 13 seconds (134334K 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 4007299 spots for /home/okishinya/chipatlas/results/rn6/SRX2202888/SRR4319875.sra Written 4007299 spots total Written 4050044 spots for /home/okishinya/chipatlas/results/rn6/SRX2202888/SRR4319874.sra Written 4050044 spots total Written 4216576 spots for /home/okishinya/chipatlas/results/rn6/SRX2202888/SRR4319873.sra Written 4216576 spots total Written 4238370 spots for /home/okishinya/chipatlas/results/rn6/SRX2202888/SRR4319872.sra Written 4238370 spots total Written 4717820 spots for /home/okishinya/chipatlas/results/rn6/SRX2202888/SRR4319877.sra Written 4717820 spots total Written 4710605 spots for /home/okishinya/chipatlas/results/rn6/SRX2202888/SRR4319876.sra Written 4710605 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: 00:19:39 25940714 reads; of these: 25940714 (100.00%) were unpaired; of these: 833242 (3.21%) aligned 0 times 19045992 (73.42%) aligned exactly 1 time 6061480 (23.37%) aligned >1 times 96.79% overall alignment rate Time searching: 00:19:42 Overall time: 00:19:42 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] 1867116 / 25107472 = 0.0744 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 18:39:06: # Command line: callpeak -t SRX2202888.bam -f BAM -g 2.15e9 -n SRX2202888.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202888.10 # format = BAM # ChIP-seq file = ['SRX2202888.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 18:39:06: # Command line: callpeak -t SRX2202888.bam -f BAM -g 2.15e9 -n SRX2202888.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202888.05 # format = BAM # ChIP-seq file = ['SRX2202888.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 18:39:06: # Command line: callpeak -t SRX2202888.bam -f BAM -g 2.15e9 -n SRX2202888.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202888.20 # format = BAM # ChIP-seq file = ['SRX2202888.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 18:39:06: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:39:06: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:39:06: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:39:06: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:39:06: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:39:06: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:39:13: 1000000 INFO @ Fri, 10 Nov 2017 18:39:14: 1000000 INFO @ Fri, 10 Nov 2017 18:39:14: 1000000 INFO @ Fri, 10 Nov 2017 18:39:21: 2000000 INFO @ Fri, 10 Nov 2017 18:39:21: 2000000 INFO @ Fri, 10 Nov 2017 18:39:21: 2000000 INFO @ Fri, 10 Nov 2017 18:39:28: 3000000 INFO @ Fri, 10 Nov 2017 18:39:29: 3000000 INFO @ Fri, 10 Nov 2017 18:39:29: 3000000 INFO @ Fri, 10 Nov 2017 18:39:35: 4000000 INFO @ Fri, 10 Nov 2017 18:39:36: 4000000 INFO @ Fri, 10 Nov 2017 18:39:36: 4000000 INFO @ Fri, 10 Nov 2017 18:39:42: 5000000 INFO @ Fri, 10 Nov 2017 18:39:44: 5000000 INFO @ Fri, 10 Nov 2017 18:39:44: 5000000 INFO @ Fri, 10 Nov 2017 18:39:51: 6000000 INFO @ Fri, 10 Nov 2017 18:39:53: 6000000 INFO @ Fri, 10 Nov 2017 18:39:53: 6000000 INFO @ Fri, 10 Nov 2017 18:39:59: 7000000 INFO @ Fri, 10 Nov 2017 18:40:02: 7000000 INFO @ Fri, 10 Nov 2017 18:40:02: 7000000 INFO @ Fri, 10 Nov 2017 18:40:06: 8000000 INFO @ Fri, 10 Nov 2017 18:40:10: 8000000 INFO @ Fri, 10 Nov 2017 18:40:10: 8000000 INFO @ Fri, 10 Nov 2017 18:40:14: 9000000 INFO @ Fri, 10 Nov 2017 18:40:18: 9000000 INFO @ Fri, 10 Nov 2017 18:40:18: 9000000 INFO @ Fri, 10 Nov 2017 18:40:21: 10000000 INFO @ Fri, 10 Nov 2017 18:40:25: 10000000 INFO @ Fri, 10 Nov 2017 18:40:25: 10000000 INFO @ Fri, 10 Nov 2017 18:40:28: 11000000 INFO @ Fri, 10 Nov 2017 18:40:34: 11000000 INFO @ Fri, 10 Nov 2017 18:40:34: 11000000 INFO @ Fri, 10 Nov 2017 18:40:35: 12000000 INFO @ Fri, 10 Nov 2017 18:40:41: 12000000 INFO @ Fri, 10 Nov 2017 18:40:41: 12000000 INFO @ Fri, 10 Nov 2017 18:40:42: 13000000 INFO @ Fri, 10 Nov 2017 18:40:49: 14000000 INFO @ Fri, 10 Nov 2017 18:40:49: 13000000 INFO @ Fri, 10 Nov 2017 18:40:49: 13000000 INFO @ Fri, 10 Nov 2017 18:40:56: 15000000 INFO @ Fri, 10 Nov 2017 18:40:57: 14000000 INFO @ Fri, 10 Nov 2017 18:40:57: 14000000 INFO @ Fri, 10 Nov 2017 18:41:03: 16000000 INFO @ Fri, 10 Nov 2017 18:41:05: 15000000 INFO @ Fri, 10 Nov 2017 18:41:05: 15000000 INFO @ Fri, 10 Nov 2017 18:41:10: 17000000 INFO @ Fri, 10 Nov 2017 18:41:13: 16000000 INFO @ Fri, 10 Nov 2017 18:41:13: 16000000 INFO @ Fri, 10 Nov 2017 18:41:17: 18000000 INFO @ Fri, 10 Nov 2017 18:41:21: 17000000 INFO @ Fri, 10 Nov 2017 18:41:21: 17000000 INFO @ Fri, 10 Nov 2017 18:41:24: 19000000 INFO @ Fri, 10 Nov 2017 18:41:29: 18000000 INFO @ Fri, 10 Nov 2017 18:41:29: 18000000 INFO @ Fri, 10 Nov 2017 18:41:31: 20000000 INFO @ Fri, 10 Nov 2017 18:41:37: 19000000 INFO @ Fri, 10 Nov 2017 18:41:37: 19000000 INFO @ Fri, 10 Nov 2017 18:41:38: 21000000 INFO @ Fri, 10 Nov 2017 18:41:45: 20000000 INFO @ Fri, 10 Nov 2017 18:41:45: 20000000 INFO @ Fri, 10 Nov 2017 18:41:45: 22000000 INFO @ Fri, 10 Nov 2017 18:41:52: 23000000 INFO @ Fri, 10 Nov 2017 18:41:53: 21000000 INFO @ Fri, 10 Nov 2017 18:41:53: 21000000 INFO @ Fri, 10 Nov 2017 18:41:54: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:41:54: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:41:54: #1 total tags in treatment: 23240356 INFO @ Fri, 10 Nov 2017 18:41:54: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:41:54: #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 18:41:55: #1 tags after filtering in treatment: 23240210 INFO @ Fri, 10 Nov 2017 18:41:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:41:55: #1 finished! INFO @ Fri, 10 Nov 2017 18:41:55: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:41:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:41:58: #2 number of paired peaks: 31509 INFO @ Fri, 10 Nov 2017 18:41:58: start model_add_line... INFO @ Fri, 10 Nov 2017 18:41:58: start X-correlation... INFO @ Fri, 10 Nov 2017 18:41:58: end of X-cor INFO @ Fri, 10 Nov 2017 18:41:58: #2 finished! INFO @ Fri, 10 Nov 2017 18:41:58: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Nov 2017 18:41:58: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Nov 2017 18:41:58: #2.2 Generate R script for model : SRX2202888.10_model.r INFO @ Fri, 10 Nov 2017 18:41:58: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:41:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:42:01: 22000000 INFO @ Fri, 10 Nov 2017 18:42:01: 22000000 INFO @ Fri, 10 Nov 2017 18:42:10: 23000000 INFO @ Fri, 10 Nov 2017 18:42:10: 23000000 INFO @ Fri, 10 Nov 2017 18:42:12: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:42:12: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:42:12: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:42:12: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:42:12: #1 total tags in treatment: 23240356 INFO @ Fri, 10 Nov 2017 18:42:12: #1 total tags in treatment: 23240356 INFO @ Fri, 10 Nov 2017 18:42:12: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:42:12: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:42:12: #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 18:42:12: #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 18:42:13: #1 tags after filtering in treatment: 23240210 INFO @ Fri, 10 Nov 2017 18:42:13: #1 tags after filtering in treatment: 23240210 INFO @ Fri, 10 Nov 2017 18:42:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:42:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:42:13: #1 finished! INFO @ Fri, 10 Nov 2017 18:42:13: #1 finished! INFO @ Fri, 10 Nov 2017 18:42:13: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:42:13: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:42:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:42:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:42:16: #2 number of paired peaks: 31509 INFO @ Fri, 10 Nov 2017 18:42:16: start model_add_line... INFO @ Fri, 10 Nov 2017 18:42:16: #2 number of paired peaks: 31509 INFO @ Fri, 10 Nov 2017 18:42:16: start model_add_line... INFO @ Fri, 10 Nov 2017 18:42:16: start X-correlation... INFO @ Fri, 10 Nov 2017 18:42:16: end of X-cor INFO @ Fri, 10 Nov 2017 18:42:16: #2 finished! INFO @ Fri, 10 Nov 2017 18:42:16: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Nov 2017 18:42:16: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Nov 2017 18:42:16: #2.2 Generate R script for model : SRX2202888.05_model.r INFO @ Fri, 10 Nov 2017 18:42:16: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:42:17: start X-correlation... INFO @ Fri, 10 Nov 2017 18:42:17: end of X-cor INFO @ Fri, 10 Nov 2017 18:42:17: #2 finished! INFO @ Fri, 10 Nov 2017 18:42:17: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Nov 2017 18:42:17: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Nov 2017 18:42:17: #2.2 Generate R script for model : SRX2202888.20_model.r INFO @ Fri, 10 Nov 2017 18:42:17: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:42:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:42:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:43:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:43:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:43:28: #4 Write output xls file... SRX2202888.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:43:28: #4 Write peak in narrowPeak format file... SRX2202888.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:43:28: #4 Write summits bed file... SRX2202888.10_summits.bed INFO @ Fri, 10 Nov 2017 18:43:28: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (3236 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:43:44: #4 Write output xls file... SRX2202888.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:43:44: #4 Write peak in narrowPeak format file... SRX2202888.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:43:44: #4 Write summits bed file... SRX2202888.20_summits.bed INFO @ Fri, 10 Nov 2017 18:43:44: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (437 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:43:54: #4 Write output xls file... SRX2202888.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:43:54: #4 Write peak in narrowPeak format file... SRX2202888.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:43:54: #4 Write summits bed file... SRX2202888.05_summits.bed INFO @ Fri, 10 Nov 2017 18:43:54: Done! pass1 - making usageList (67 chroms): 3 millis pass2 - checking and writing primary data (10539 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。