Job ID = 10194915 sra ファイルのダウンロード中... Completed: 115885K bytes transferred in 11 seconds (85961K bits/sec), in 1 file. Completed: 113078K bytes transferred in 7 seconds (117920K bits/sec), in 1 file. Completed: 189667K bytes transferred in 11 seconds (130694K bits/sec), in 1 file. Completed: 186391K bytes transferred in 13 seconds (111586K bits/sec), in 1 file. Completed: 186822K bytes transferred in 10 seconds (147301K bits/sec), in 1 file. Completed: 184106K bytes transferred in 10 seconds (146281K 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 2709558 spots for /home/okishinya/chipatlas/results/rn6/SRX2202910/SRR4320004.sra Written 2709558 spots total Written 2633526 spots for /home/okishinya/chipatlas/results/rn6/SRX2202910/SRR4320005.sra Written 2633526 spots total Written 4046568 spots for /home/okishinya/chipatlas/results/rn6/SRX2202910/SRR4320008.sra Written 4046568 spots total Written 3995162 spots for /home/okishinya/chipatlas/results/rn6/SRX2202910/SRR4320009.sra Written 3995162 spots total Written 4011452 spots for /home/okishinya/chipatlas/results/rn6/SRX2202910/SRR4320007.sra Written 4011452 spots total Written 4106833 spots for /home/okishinya/chipatlas/results/rn6/SRX2202910/SRR4320006.sra Written 4106833 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: 00:38:19 21503099 reads; of these: 21503099 (100.00%) were unpaired; of these: 873043 (4.06%) aligned 0 times 14298814 (66.50%) aligned exactly 1 time 6331242 (29.44%) aligned >1 times 95.94% overall alignment rate Time searching: 00:38:23 Overall time: 00:38:23 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] 7640192 / 20630056 = 0.3703 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 23:29:40: # Command line: callpeak -t SRX2202910.bam -f BAM -g 2.15e9 -n SRX2202910.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202910.10 # format = BAM # ChIP-seq file = ['SRX2202910.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 23:29:40: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:29:40: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:29:40: # Command line: callpeak -t SRX2202910.bam -f BAM -g 2.15e9 -n SRX2202910.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202910.20 # format = BAM # ChIP-seq file = ['SRX2202910.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 23:29:40: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:29:40: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:29:40: # Command line: callpeak -t SRX2202910.bam -f BAM -g 2.15e9 -n SRX2202910.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202910.05 # format = BAM # ChIP-seq file = ['SRX2202910.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 23:29:40: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:29:40: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:29:54: 1000000 INFO @ Fri, 10 Nov 2017 23:29:57: 1000000 INFO @ Fri, 10 Nov 2017 23:29:57: 1000000 INFO @ Fri, 10 Nov 2017 23:30:09: 2000000 INFO @ Fri, 10 Nov 2017 23:30:14: 2000000 INFO @ Fri, 10 Nov 2017 23:30:14: 2000000 INFO @ Fri, 10 Nov 2017 23:30:23: 3000000 INFO @ Fri, 10 Nov 2017 23:30:29: 3000000 INFO @ Fri, 10 Nov 2017 23:30:29: 3000000 INFO @ Fri, 10 Nov 2017 23:30:37: 4000000 INFO @ Fri, 10 Nov 2017 23:30:44: 4000000 INFO @ Fri, 10 Nov 2017 23:30:44: 4000000 INFO @ Fri, 10 Nov 2017 23:30:51: 5000000 INFO @ Fri, 10 Nov 2017 23:30:59: 5000000 INFO @ Fri, 10 Nov 2017 23:30:59: 5000000 INFO @ Fri, 10 Nov 2017 23:31:05: 6000000 INFO @ Fri, 10 Nov 2017 23:31:14: 6000000 INFO @ Fri, 10 Nov 2017 23:31:14: 6000000 INFO @ Fri, 10 Nov 2017 23:31:20: 7000000 INFO @ Fri, 10 Nov 2017 23:31:29: 7000000 INFO @ Fri, 10 Nov 2017 23:31:30: 7000000 INFO @ Fri, 10 Nov 2017 23:31:35: 8000000 INFO @ Fri, 10 Nov 2017 23:31:46: 8000000 INFO @ Fri, 10 Nov 2017 23:31:49: 8000000 INFO @ Fri, 10 Nov 2017 23:31:51: 9000000 INFO @ Fri, 10 Nov 2017 23:32:01: 9000000 INFO @ Fri, 10 Nov 2017 23:32:07: 10000000 INFO @ Fri, 10 Nov 2017 23:32:07: 9000000 INFO @ Fri, 10 Nov 2017 23:32:17: 10000000 INFO @ Fri, 10 Nov 2017 23:32:22: 11000000 INFO @ Fri, 10 Nov 2017 23:32:26: 10000000 INFO @ Fri, 10 Nov 2017 23:32:34: 11000000 INFO @ Fri, 10 Nov 2017 23:32:38: 12000000 INFO @ Fri, 10 Nov 2017 23:32:42: 11000000 INFO @ Fri, 10 Nov 2017 23:32:48: 12000000 INFO @ Fri, 10 Nov 2017 23:32:51: 12000000 INFO @ Fri, 10 Nov 2017 23:32:53: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:32:53: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:32:53: #1 total tags in treatment: 12989864 INFO @ Fri, 10 Nov 2017 23:32:53: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:32:53: #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 23:32:54: #1 tags after filtering in treatment: 12989695 INFO @ Fri, 10 Nov 2017 23:32:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:32:54: #1 finished! INFO @ Fri, 10 Nov 2017 23:32:54: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:32:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:32:57: #2 number of paired peaks: 43058 INFO @ Fri, 10 Nov 2017 23:32:57: start model_add_line... INFO @ Fri, 10 Nov 2017 23:32:58: start X-correlation... INFO @ Fri, 10 Nov 2017 23:32:58: end of X-cor INFO @ Fri, 10 Nov 2017 23:32:58: #2 finished! INFO @ Fri, 10 Nov 2017 23:32:58: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 23:32:58: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 23:32:58: #2.2 Generate R script for model : SRX2202910.20_model.r INFO @ Fri, 10 Nov 2017 23:32:58: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:32:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:33:00: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:33:00: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:33:00: #1 total tags in treatment: 12989864 INFO @ Fri, 10 Nov 2017 23:33:00: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:33:00: #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 23:33:01: #1 tags after filtering in treatment: 12989695 INFO @ Fri, 10 Nov 2017 23:33:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:33:01: #1 finished! INFO @ Fri, 10 Nov 2017 23:33:01: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:33:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:33:04: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:33:04: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:33:04: #1 total tags in treatment: 12989864 INFO @ Fri, 10 Nov 2017 23:33:04: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:33:04: #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 23:33:05: #1 tags after filtering in treatment: 12989695 INFO @ Fri, 10 Nov 2017 23:33:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:33:05: #1 finished! INFO @ Fri, 10 Nov 2017 23:33:05: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:33:05: #2 number of paired peaks: 43058 INFO @ Fri, 10 Nov 2017 23:33:05: start model_add_line... INFO @ Fri, 10 Nov 2017 23:33:05: start X-correlation... INFO @ Fri, 10 Nov 2017 23:33:05: end of X-cor INFO @ Fri, 10 Nov 2017 23:33:05: #2 finished! INFO @ Fri, 10 Nov 2017 23:33:05: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 23:33:05: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 23:33:05: #2.2 Generate R script for model : SRX2202910.05_model.r INFO @ Fri, 10 Nov 2017 23:33:05: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:33:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:33:09: #2 number of paired peaks: 43058 INFO @ Fri, 10 Nov 2017 23:33:09: start model_add_line... INFO @ Fri, 10 Nov 2017 23:33:09: start X-correlation... INFO @ Fri, 10 Nov 2017 23:33:09: end of X-cor INFO @ Fri, 10 Nov 2017 23:33:09: #2 finished! INFO @ Fri, 10 Nov 2017 23:33:09: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 23:33:09: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 23:33:09: #2.2 Generate R script for model : SRX2202910.10_model.r INFO @ Fri, 10 Nov 2017 23:33:09: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:33:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:33:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:33:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:33:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:34:05: #4 Write output xls file... SRX2202910.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:34:05: #4 Write peak in narrowPeak format file... SRX2202910.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:34:05: #4 Write summits bed file... SRX2202910.20_summits.bed INFO @ Fri, 10 Nov 2017 23:34:05: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (1732 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:34:17: #4 Write output xls file... SRX2202910.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:34:17: #4 Write peak in narrowPeak format file... SRX2202910.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:34:18: #4 Write summits bed file... SRX2202910.10_summits.bed INFO @ Fri, 10 Nov 2017 23:34:18: Done! pass1 - making usageList (63 chroms): 4 millis INFO @ Fri, 10 Nov 2017 23:34:18: #4 Write output xls file... SRX2202910.05_peaks.xls pass2 - checking and writing primary data (9771 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:34:18: #4 Write peak in narrowPeak format file... SRX2202910.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:34:18: #4 Write summits bed file... SRX2202910.05_summits.bed INFO @ Fri, 10 Nov 2017 23:34:19: Done! pass1 - making usageList (95 chroms): 6 millis pass2 - checking and writing primary data (19238 records, 4 fields): 38 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。