Job ID = 10194913 sra ファイルのダウンロード中... Completed: 139478K bytes transferred in 9 seconds (118793K bits/sec), in 1 file. Completed: 136369K bytes transferred in 6 seconds (165769K bits/sec), in 1 file. Completed: 229079K bytes transferred in 11 seconds (162913K bits/sec), in 1 file. Completed: 225018K bytes transferred in 19 seconds (96360K bits/sec), in 1 file. Completed: 225507K bytes transferred in 14 seconds (123294K bits/sec), in 1 file. Completed: 222272K bytes transferred in 15 seconds (117402K 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 3185779 spots for /home/okishinya/chipatlas/results/rn6/SRX2202908/SRR4319993.sra Written 3185779 spots total Written 3272318 spots for /home/okishinya/chipatlas/results/rn6/SRX2202908/SRR4319992.sra Written 3272318 spots total Written 4845480 spots for /home/okishinya/chipatlas/results/rn6/SRX2202908/SRR4319997.sra Written 4845480 spots total Written 4907552 spots for /home/okishinya/chipatlas/results/rn6/SRX2202908/SRR4319996.sra Written 4907552 spots total Written 4863946 spots for /home/okishinya/chipatlas/results/rn6/SRX2202908/SRR4319995.sra Written 4863946 spots total Written 4985211 spots for /home/okishinya/chipatlas/results/rn6/SRX2202908/SRR4319994.sra Written 4985211 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:46:51 26060286 reads; of these: 26060286 (100.00%) were unpaired; of these: 800515 (3.07%) aligned 0 times 18285254 (70.17%) aligned exactly 1 time 6974517 (26.76%) aligned >1 times 96.93% overall alignment rate Time searching: 00:46:55 Overall time: 00:46:55 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] 4379433 / 25259771 = 0.1734 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 23:22:49: # Command line: callpeak -t SRX2202908.bam -f BAM -g 2.15e9 -n SRX2202908.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202908.20 # format = BAM # ChIP-seq file = ['SRX2202908.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 23:22:49: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:22:49: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:22:49: # Command line: callpeak -t SRX2202908.bam -f BAM -g 2.15e9 -n SRX2202908.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202908.05 # format = BAM # ChIP-seq file = ['SRX2202908.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 23:22:49: # Command line: callpeak -t SRX2202908.bam -f BAM -g 2.15e9 -n SRX2202908.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202908.10 # format = BAM # ChIP-seq file = ['SRX2202908.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 23:22:49: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:22:49: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:22:49: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:22:49: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:23:02: 1000000 INFO @ Fri, 10 Nov 2017 23:23:03: 1000000 INFO @ Fri, 10 Nov 2017 23:23:04: 1000000 INFO @ Fri, 10 Nov 2017 23:23:16: 2000000 INFO @ Fri, 10 Nov 2017 23:23:18: 2000000 INFO @ Fri, 10 Nov 2017 23:23:19: 2000000 INFO @ Fri, 10 Nov 2017 23:23:30: 3000000 INFO @ Fri, 10 Nov 2017 23:23:32: 3000000 INFO @ Fri, 10 Nov 2017 23:23:33: 3000000 INFO @ Fri, 10 Nov 2017 23:23:45: 4000000 INFO @ Fri, 10 Nov 2017 23:23:46: 4000000 INFO @ Fri, 10 Nov 2017 23:23:48: 4000000 INFO @ Fri, 10 Nov 2017 23:24:00: 5000000 INFO @ Fri, 10 Nov 2017 23:24:01: 5000000 INFO @ Fri, 10 Nov 2017 23:24:05: 5000000 INFO @ Fri, 10 Nov 2017 23:24:15: 6000000 INFO @ Fri, 10 Nov 2017 23:24:17: 6000000 INFO @ Fri, 10 Nov 2017 23:24:20: 6000000 INFO @ Fri, 10 Nov 2017 23:24:29: 7000000 INFO @ Fri, 10 Nov 2017 23:24:32: 7000000 INFO @ Fri, 10 Nov 2017 23:24:36: 7000000 INFO @ Fri, 10 Nov 2017 23:24:45: 8000000 INFO @ Fri, 10 Nov 2017 23:24:49: 8000000 INFO @ Fri, 10 Nov 2017 23:24:53: 8000000 INFO @ Fri, 10 Nov 2017 23:25:00: 9000000 INFO @ Fri, 10 Nov 2017 23:25:05: 9000000 INFO @ Fri, 10 Nov 2017 23:25:09: 9000000 INFO @ Fri, 10 Nov 2017 23:25:15: 10000000 INFO @ Fri, 10 Nov 2017 23:25:21: 10000000 INFO @ Fri, 10 Nov 2017 23:25:25: 10000000 INFO @ Fri, 10 Nov 2017 23:25:30: 11000000 INFO @ Fri, 10 Nov 2017 23:25:38: 11000000 INFO @ Fri, 10 Nov 2017 23:25:41: 11000000 INFO @ Fri, 10 Nov 2017 23:25:45: 12000000 INFO @ Fri, 10 Nov 2017 23:25:53: 12000000 INFO @ Fri, 10 Nov 2017 23:25:57: 12000000 INFO @ Fri, 10 Nov 2017 23:26:00: 13000000 INFO @ Fri, 10 Nov 2017 23:26:09: 13000000 INFO @ Fri, 10 Nov 2017 23:26:13: 13000000 INFO @ Fri, 10 Nov 2017 23:26:15: 14000000 INFO @ Fri, 10 Nov 2017 23:26:24: 14000000 INFO @ Fri, 10 Nov 2017 23:26:29: 14000000 INFO @ Fri, 10 Nov 2017 23:26:30: 15000000 INFO @ Fri, 10 Nov 2017 23:26:39: 15000000 INFO @ Fri, 10 Nov 2017 23:26:44: 15000000 INFO @ Fri, 10 Nov 2017 23:26:45: 16000000 INFO @ Fri, 10 Nov 2017 23:26:55: 16000000 INFO @ Fri, 10 Nov 2017 23:27:00: 16000000 INFO @ Fri, 10 Nov 2017 23:27:02: 17000000 INFO @ Fri, 10 Nov 2017 23:27:12: 17000000 INFO @ Fri, 10 Nov 2017 23:27:16: 17000000 INFO @ Fri, 10 Nov 2017 23:27:21: 18000000 INFO @ Fri, 10 Nov 2017 23:27:29: 18000000 INFO @ Fri, 10 Nov 2017 23:27:32: 18000000 INFO @ Fri, 10 Nov 2017 23:27:40: 19000000 INFO @ Fri, 10 Nov 2017 23:27:45: 19000000 INFO @ Fri, 10 Nov 2017 23:27:48: 19000000 INFO @ Fri, 10 Nov 2017 23:27:59: 20000000 INFO @ Fri, 10 Nov 2017 23:28:02: 20000000 INFO @ Fri, 10 Nov 2017 23:28:04: 20000000 INFO @ Fri, 10 Nov 2017 23:28:16: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:28:16: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:28:16: #1 total tags in treatment: 20880338 INFO @ Fri, 10 Nov 2017 23:28:16: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:28:16: #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 23:28:17: #1 tags after filtering in treatment: 20880222 INFO @ Fri, 10 Nov 2017 23:28:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:28:17: #1 finished! INFO @ Fri, 10 Nov 2017 23:28:17: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:28:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:28:17: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:28:17: #1 total tags in treatment: 20880338 INFO @ Fri, 10 Nov 2017 23:28:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:28:17: #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 23:28:18: #1 tags after filtering in treatment: 20880222 INFO @ Fri, 10 Nov 2017 23:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:28:18: #1 finished! INFO @ Fri, 10 Nov 2017 23:28:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:28:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:28:19: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:28:19: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:28:19: #1 total tags in treatment: 20880338 INFO @ Fri, 10 Nov 2017 23:28:19: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:28:19: #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 23:28:19: #1 tags after filtering in treatment: 20880222 INFO @ Fri, 10 Nov 2017 23:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:28:19: #1 finished! INFO @ Fri, 10 Nov 2017 23:28:19: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:28:22: #2 number of paired peaks: 42098 INFO @ Fri, 10 Nov 2017 23:28:22: start model_add_line... INFO @ Fri, 10 Nov 2017 23:28:22: start X-correlation... INFO @ Fri, 10 Nov 2017 23:28:22: end of X-cor INFO @ Fri, 10 Nov 2017 23:28:22: #2 finished! INFO @ Fri, 10 Nov 2017 23:28:22: #2 predicted fragment length is 133 bps INFO @ Fri, 10 Nov 2017 23:28:22: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 10 Nov 2017 23:28:22: #2.2 Generate R script for model : SRX2202908.20_model.r INFO @ Fri, 10 Nov 2017 23:28:22: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:28:23: #2 number of paired peaks: 42098 INFO @ Fri, 10 Nov 2017 23:28:23: start model_add_line... INFO @ Fri, 10 Nov 2017 23:28:23: start X-correlation... INFO @ Fri, 10 Nov 2017 23:28:24: end of X-cor INFO @ Fri, 10 Nov 2017 23:28:24: #2 finished! INFO @ Fri, 10 Nov 2017 23:28:24: #2 predicted fragment length is 133 bps INFO @ Fri, 10 Nov 2017 23:28:24: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 10 Nov 2017 23:28:24: #2.2 Generate R script for model : SRX2202908.10_model.r INFO @ Fri, 10 Nov 2017 23:28:24: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:28:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:28:24: #2 number of paired peaks: 42098 INFO @ Fri, 10 Nov 2017 23:28:24: start model_add_line... INFO @ Fri, 10 Nov 2017 23:28:25: start X-correlation... INFO @ Fri, 10 Nov 2017 23:28:25: end of X-cor INFO @ Fri, 10 Nov 2017 23:28:25: #2 finished! INFO @ Fri, 10 Nov 2017 23:28:25: #2 predicted fragment length is 133 bps INFO @ Fri, 10 Nov 2017 23:28:25: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 10 Nov 2017 23:28:25: #2.2 Generate R script for model : SRX2202908.05_model.r INFO @ Fri, 10 Nov 2017 23:28:25: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:28:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:29:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:29:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:29:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:30:14: #4 Write output xls file... SRX2202908.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:30:15: #4 Write peak in narrowPeak format file... SRX2202908.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:30:15: #4 Write summits bed file... SRX2202908.05_summits.bed INFO @ Fri, 10 Nov 2017 23:30:15: Done! INFO @ Fri, 10 Nov 2017 23:30:15: #4 Write output xls file... SRX2202908.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:30:15: #4 Write peak in narrowPeak format file... SRX2202908.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:30:15: #4 Write summits bed file... SRX2202908.10_summits.bed INFO @ Fri, 10 Nov 2017 23:30:16: Done! pass1 - making usageList (103 chroms): 7 millis pass2 - checking and writing primary data (24981 records, 4 fields): 49 millis CompletedMACS2peakCalling pass1 - making usageList (85 chroms): 6 millis pass2 - checking and writing primary data (17332 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:30:28: #4 Write output xls file... SRX2202908.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:30:28: #4 Write peak in narrowPeak format file... SRX2202908.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:30:28: #4 Write summits bed file... SRX2202908.20_summits.bed INFO @ Fri, 10 Nov 2017 23:30:28: Done! pass1 - making usageList (51 chroms): 3 millis pass2 - checking and writing primary data (8595 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。