Job ID = 10194896 sra ファイルのダウンロード中... Completed: 231904K bytes transferred in 14 seconds (134175K bits/sec), in 1 file. Completed: 232687K bytes transferred in 13 seconds (141771K bits/sec), in 1 file. Completed: 220211K bytes transferred in 11 seconds (156328K bits/sec), in 1 file. Completed: 217376K bytes transferred in 10 seconds (162690K bits/sec), in 1 file. Completed: 260225K bytes transferred in 12 seconds (166212K bits/sec), in 1 file. Completed: 263633K bytes transferred in 10 seconds (199600K 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 4925617 spots for /home/okishinya/chipatlas/results/rn6/SRX2202891/SRR4319893.sra Written 4925617 spots total Written 4978299 spots for /home/okishinya/chipatlas/results/rn6/SRX2202891/SRR4319892.sra Written 4978299 spots total Written 5224902 spots for /home/okishinya/chipatlas/results/rn6/SRX2202891/SRR4319891.sra Written 5224902 spots total Written 5224845 spots for /home/okishinya/chipatlas/results/rn6/SRX2202891/SRR4319890.sra Written 5224845 spots total Written 5794172 spots for /home/okishinya/chipatlas/results/rn6/SRX2202891/SRR4319895.sra Written 5794172 spots total Written 5739785 spots for /home/okishinya/chipatlas/results/rn6/SRX2202891/SRR4319894.sra Written 5739785 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: 00:23:35 31887620 reads; of these: 31887620 (100.00%) were unpaired; of these: 1366107 (4.28%) aligned 0 times 23430115 (73.48%) aligned exactly 1 time 7091398 (22.24%) aligned >1 times 95.72% overall alignment rate Time searching: 00:23:39 Overall time: 00:23:39 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] 5629839 / 30521513 = 0.1845 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 18:47:13: # Command line: callpeak -t SRX2202891.bam -f BAM -g 2.15e9 -n SRX2202891.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202891.20 # format = BAM # ChIP-seq file = ['SRX2202891.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 18:47:13: # Command line: callpeak -t SRX2202891.bam -f BAM -g 2.15e9 -n SRX2202891.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202891.05 # format = BAM # ChIP-seq file = ['SRX2202891.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 18:47:13: # Command line: callpeak -t SRX2202891.bam -f BAM -g 2.15e9 -n SRX2202891.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202891.10 # format = BAM # ChIP-seq file = ['SRX2202891.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 18:47:13: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:47:13: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:47:13: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:47:13: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:47:13: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:47:13: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:47:19: 1000000 INFO @ Fri, 10 Nov 2017 18:47:19: 1000000 INFO @ Fri, 10 Nov 2017 18:47:19: 1000000 INFO @ Fri, 10 Nov 2017 18:47:26: 2000000 INFO @ Fri, 10 Nov 2017 18:47:26: 2000000 INFO @ Fri, 10 Nov 2017 18:47:26: 2000000 INFO @ Fri, 10 Nov 2017 18:47:32: 3000000 INFO @ Fri, 10 Nov 2017 18:47:32: 3000000 INFO @ Fri, 10 Nov 2017 18:47:33: 3000000 INFO @ Fri, 10 Nov 2017 18:47:39: 4000000 INFO @ Fri, 10 Nov 2017 18:47:39: 4000000 INFO @ Fri, 10 Nov 2017 18:47:40: 4000000 INFO @ Fri, 10 Nov 2017 18:47:46: 5000000 INFO @ Fri, 10 Nov 2017 18:47:46: 5000000 INFO @ Fri, 10 Nov 2017 18:47:47: 5000000 INFO @ Fri, 10 Nov 2017 18:47:53: 6000000 INFO @ Fri, 10 Nov 2017 18:47:53: 6000000 INFO @ Fri, 10 Nov 2017 18:47:55: 6000000 INFO @ Fri, 10 Nov 2017 18:48:00: 7000000 INFO @ Fri, 10 Nov 2017 18:48:00: 7000000 INFO @ Fri, 10 Nov 2017 18:48:02: 7000000 INFO @ Fri, 10 Nov 2017 18:48:07: 8000000 INFO @ Fri, 10 Nov 2017 18:48:07: 8000000 INFO @ Fri, 10 Nov 2017 18:48:09: 8000000 INFO @ Fri, 10 Nov 2017 18:48:14: 9000000 INFO @ Fri, 10 Nov 2017 18:48:15: 9000000 INFO @ Fri, 10 Nov 2017 18:48:17: 9000000 INFO @ Fri, 10 Nov 2017 18:48:21: 10000000 INFO @ Fri, 10 Nov 2017 18:48:22: 10000000 INFO @ Fri, 10 Nov 2017 18:48:24: 10000000 INFO @ Fri, 10 Nov 2017 18:48:28: 11000000 INFO @ Fri, 10 Nov 2017 18:48:29: 11000000 INFO @ Fri, 10 Nov 2017 18:48:32: 11000000 INFO @ Fri, 10 Nov 2017 18:48:36: 12000000 INFO @ Fri, 10 Nov 2017 18:48:36: 12000000 INFO @ Fri, 10 Nov 2017 18:48:39: 12000000 INFO @ Fri, 10 Nov 2017 18:48:43: 13000000 INFO @ Fri, 10 Nov 2017 18:48:44: 13000000 INFO @ Fri, 10 Nov 2017 18:48:47: 13000000 INFO @ Fri, 10 Nov 2017 18:48:50: 14000000 INFO @ Fri, 10 Nov 2017 18:48:51: 14000000 INFO @ Fri, 10 Nov 2017 18:48:55: 14000000 INFO @ Fri, 10 Nov 2017 18:48:58: 15000000 INFO @ Fri, 10 Nov 2017 18:48:59: 15000000 INFO @ Fri, 10 Nov 2017 18:49:02: 15000000 INFO @ Fri, 10 Nov 2017 18:49:05: 16000000 INFO @ Fri, 10 Nov 2017 18:49:05: 16000000 INFO @ Fri, 10 Nov 2017 18:49:09: 16000000 INFO @ Fri, 10 Nov 2017 18:49:11: 17000000 INFO @ Fri, 10 Nov 2017 18:49:12: 17000000 INFO @ Fri, 10 Nov 2017 18:49:15: 17000000 INFO @ Fri, 10 Nov 2017 18:49:18: 18000000 INFO @ Fri, 10 Nov 2017 18:49:18: 18000000 INFO @ Fri, 10 Nov 2017 18:49:22: 18000000 INFO @ Fri, 10 Nov 2017 18:49:24: 19000000 INFO @ Fri, 10 Nov 2017 18:49:24: 19000000 INFO @ Fri, 10 Nov 2017 18:49:29: 19000000 INFO @ Fri, 10 Nov 2017 18:49:31: 20000000 INFO @ Fri, 10 Nov 2017 18:49:31: 20000000 INFO @ Fri, 10 Nov 2017 18:49:36: 20000000 INFO @ Fri, 10 Nov 2017 18:49:37: 21000000 INFO @ Fri, 10 Nov 2017 18:49:37: 21000000 INFO @ Fri, 10 Nov 2017 18:49:43: 21000000 INFO @ Fri, 10 Nov 2017 18:49:43: 22000000 INFO @ Fri, 10 Nov 2017 18:49:44: 22000000 INFO @ Fri, 10 Nov 2017 18:49:50: 22000000 INFO @ Fri, 10 Nov 2017 18:49:50: 23000000 INFO @ Fri, 10 Nov 2017 18:49:51: 23000000 INFO @ Fri, 10 Nov 2017 18:49:56: 24000000 INFO @ Fri, 10 Nov 2017 18:49:56: 23000000 INFO @ Fri, 10 Nov 2017 18:49:58: 24000000 INFO @ Fri, 10 Nov 2017 18:50:02: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:50:02: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:50:02: #1 total tags in treatment: 24891674 INFO @ Fri, 10 Nov 2017 18:50:02: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:50:02: #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 18:50:02: #1 tags after filtering in treatment: 24891545 INFO @ Fri, 10 Nov 2017 18:50:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:50:02: #1 finished! INFO @ Fri, 10 Nov 2017 18:50:02: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:50:03: 24000000 INFO @ Fri, 10 Nov 2017 18:50:04: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:50:04: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:50:04: #1 total tags in treatment: 24891674 INFO @ Fri, 10 Nov 2017 18:50:04: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:50:04: #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 18:50:05: #1 tags after filtering in treatment: 24891545 INFO @ Fri, 10 Nov 2017 18:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:50:05: #1 finished! INFO @ Fri, 10 Nov 2017 18:50:05: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:50:06: #2 number of paired peaks: 34805 INFO @ Fri, 10 Nov 2017 18:50:06: start model_add_line... INFO @ Fri, 10 Nov 2017 18:50:07: start X-correlation... INFO @ Fri, 10 Nov 2017 18:50:07: end of X-cor INFO @ Fri, 10 Nov 2017 18:50:07: #2 finished! INFO @ Fri, 10 Nov 2017 18:50:07: #2 predicted fragment length is 135 bps INFO @ Fri, 10 Nov 2017 18:50:07: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 10 Nov 2017 18:50:07: #2.2 Generate R script for model : SRX2202891.05_model.r INFO @ Fri, 10 Nov 2017 18:50:07: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:50:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:50:08: #2 number of paired peaks: 34805 INFO @ Fri, 10 Nov 2017 18:50:08: start model_add_line... INFO @ Fri, 10 Nov 2017 18:50:09: start X-correlation... INFO @ Fri, 10 Nov 2017 18:50:09: end of X-cor INFO @ Fri, 10 Nov 2017 18:50:09: #2 finished! INFO @ Fri, 10 Nov 2017 18:50:09: #2 predicted fragment length is 135 bps INFO @ Fri, 10 Nov 2017 18:50:09: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 10 Nov 2017 18:50:09: #2.2 Generate R script for model : SRX2202891.20_model.r INFO @ Fri, 10 Nov 2017 18:50:09: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:50:09: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:50:09: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:50:09: #1 total tags in treatment: 24891674 INFO @ Fri, 10 Nov 2017 18:50:09: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:50:09: #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 18:50:10: #1 tags after filtering in treatment: 24891545 INFO @ Fri, 10 Nov 2017 18:50:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:50:10: #1 finished! INFO @ Fri, 10 Nov 2017 18:50:10: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:50:13: #2 number of paired peaks: 34805 INFO @ Fri, 10 Nov 2017 18:50:13: start model_add_line... INFO @ Fri, 10 Nov 2017 18:50:14: start X-correlation... INFO @ Fri, 10 Nov 2017 18:50:14: end of X-cor INFO @ Fri, 10 Nov 2017 18:50:14: #2 finished! INFO @ Fri, 10 Nov 2017 18:50:14: #2 predicted fragment length is 135 bps INFO @ Fri, 10 Nov 2017 18:50:14: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 10 Nov 2017 18:50:14: #2.2 Generate R script for model : SRX2202891.10_model.r INFO @ Fri, 10 Nov 2017 18:50:14: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:50:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:51:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:51:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:51:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:51:46: #4 Write output xls file... SRX2202891.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:51:46: #4 Write peak in narrowPeak format file... SRX2202891.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:51:46: #4 Write summits bed file... SRX2202891.20_summits.bed INFO @ Fri, 10 Nov 2017 18:51:46: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (408 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:51:48: #4 Write output xls file... SRX2202891.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:51:48: #4 Write peak in narrowPeak format file... SRX2202891.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:51:48: #4 Write summits bed file... SRX2202891.05_summits.bed INFO @ Fri, 10 Nov 2017 18:51:48: Done! pass1 - making usageList (68 chroms): 3 millis pass2 - checking and writing primary data (10777 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:51:52: #4 Write output xls file... SRX2202891.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:51:52: #4 Write peak in narrowPeak format file... SRX2202891.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:51:52: #4 Write summits bed file... SRX2202891.10_summits.bed INFO @ Fri, 10 Nov 2017 18:51:52: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (2892 records, 4 fields): 84 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。