Job ID = 10196004 sra ファイルのダウンロード中... Completed: 111582K bytes transferred in 9 seconds (91428K bits/sec), in 1 file. Completed: 108821K bytes transferred in 6 seconds (141547K bits/sec), in 1 file. Completed: 184111K bytes transferred in 13 seconds (113690K bits/sec), in 1 file. Completed: 180434K bytes transferred in 11 seconds (125842K bits/sec), in 1 file. Completed: 180860K bytes transferred in 4 seconds (302665K bits/sec), in 1 file. Completed: 177935K bytes transferred in 12 seconds (115614K 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 2548953 spots for /home/okishinya/chipatlas/results/rn6/SRX2202896/SRR4319921.sra Written 2548953 spots total Written 2625199 spots for /home/okishinya/chipatlas/results/rn6/SRX2202896/SRR4319920.sra Written 2625199 spots total Written 3882011 spots for /home/okishinya/chipatlas/results/rn6/SRX2202896/SRR4319925.sra Written 3882011 spots total Written 3904135 spots for /home/okishinya/chipatlas/results/rn6/SRX2202896/SRR4319923.sra Written 3904135 spots total Written 3940066 spots for /home/okishinya/chipatlas/results/rn6/SRX2202896/SRR4319924.sra Written 3940066 spots total Written 4010637 spots for /home/okishinya/chipatlas/results/rn6/SRX2202896/SRR4319922.sra Written 4010637 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: 00:00:03 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:45 20911001 reads; of these: 20911001 (100.00%) were unpaired; of these: 891210 (4.26%) aligned 0 times 14147380 (67.66%) aligned exactly 1 time 5872411 (28.08%) aligned >1 times 95.74% overall alignment rate Time searching: 00:15:48 Overall time: 00:15:48 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] 10387712 / 20019791 = 0.5189 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 22:18:41: # Command line: callpeak -t SRX2202896.bam -f BAM -g 2.15e9 -n SRX2202896.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202896.05 # format = BAM # ChIP-seq file = ['SRX2202896.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 22:18:41: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:18:41: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:18:41: # Command line: callpeak -t SRX2202896.bam -f BAM -g 2.15e9 -n SRX2202896.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202896.20 # format = BAM # ChIP-seq file = ['SRX2202896.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 22:18:41: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:18:41: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:18:41: # Command line: callpeak -t SRX2202896.bam -f BAM -g 2.15e9 -n SRX2202896.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202896.10 # format = BAM # ChIP-seq file = ['SRX2202896.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 22:18:41: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:18:41: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:18:48: 1000000 INFO @ Fri, 10 Nov 2017 22:18:48: 1000000 INFO @ Fri, 10 Nov 2017 22:18:48: 1000000 INFO @ Fri, 10 Nov 2017 22:18:55: 2000000 INFO @ Fri, 10 Nov 2017 22:18:56: 2000000 INFO @ Fri, 10 Nov 2017 22:18:56: 2000000 INFO @ Fri, 10 Nov 2017 22:19:02: 3000000 INFO @ Fri, 10 Nov 2017 22:19:03: 3000000 INFO @ Fri, 10 Nov 2017 22:19:03: 3000000 INFO @ Fri, 10 Nov 2017 22:19:09: 4000000 INFO @ Fri, 10 Nov 2017 22:19:10: 4000000 INFO @ Fri, 10 Nov 2017 22:19:11: 4000000 INFO @ Fri, 10 Nov 2017 22:19:16: 5000000 INFO @ Fri, 10 Nov 2017 22:19:17: 5000000 INFO @ Fri, 10 Nov 2017 22:19:18: 5000000 INFO @ Fri, 10 Nov 2017 22:19:23: 6000000 INFO @ Fri, 10 Nov 2017 22:19:24: 6000000 INFO @ Fri, 10 Nov 2017 22:19:25: 6000000 INFO @ Fri, 10 Nov 2017 22:19:31: 7000000 INFO @ Fri, 10 Nov 2017 22:19:32: 7000000 INFO @ Fri, 10 Nov 2017 22:19:33: 7000000 INFO @ Fri, 10 Nov 2017 22:19:38: 8000000 INFO @ Fri, 10 Nov 2017 22:19:39: 8000000 INFO @ Fri, 10 Nov 2017 22:19:40: 8000000 INFO @ Fri, 10 Nov 2017 22:19:45: 9000000 INFO @ Fri, 10 Nov 2017 22:19:46: 9000000 INFO @ Fri, 10 Nov 2017 22:19:48: 9000000 INFO @ Fri, 10 Nov 2017 22:19:49: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:19:49: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:19:49: #1 total tags in treatment: 9632079 INFO @ Fri, 10 Nov 2017 22:19:49: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:19:49: #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 22:19:50: #1 tags after filtering in treatment: 9631884 INFO @ Fri, 10 Nov 2017 22:19:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:19:50: #1 finished! INFO @ Fri, 10 Nov 2017 22:19:50: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:19:51: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:19:51: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:19:51: #1 total tags in treatment: 9632079 INFO @ Fri, 10 Nov 2017 22:19:51: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:19:51: #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 22:19:51: #1 tags after filtering in treatment: 9631884 INFO @ Fri, 10 Nov 2017 22:19:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:19:51: #1 finished! INFO @ Fri, 10 Nov 2017 22:19:51: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:19:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:19:52: #2 number of paired peaks: 36071 INFO @ Fri, 10 Nov 2017 22:19:52: start model_add_line... INFO @ Fri, 10 Nov 2017 22:19:52: start X-correlation... INFO @ Fri, 10 Nov 2017 22:19:52: end of X-cor INFO @ Fri, 10 Nov 2017 22:19:52: #2 finished! INFO @ Fri, 10 Nov 2017 22:19:52: #2 predicted fragment length is 134 bps INFO @ Fri, 10 Nov 2017 22:19:52: #2 alternative fragment length(s) may be 134 bps INFO @ Fri, 10 Nov 2017 22:19:52: #2.2 Generate R script for model : SRX2202896.20_model.r INFO @ Fri, 10 Nov 2017 22:19:52: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:19:53: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:19:53: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:19:53: #1 total tags in treatment: 9632079 INFO @ Fri, 10 Nov 2017 22:19:53: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:19:53: #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 22:19:53: #1 tags after filtering in treatment: 9631884 INFO @ Fri, 10 Nov 2017 22:19:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:19:53: #1 finished! INFO @ Fri, 10 Nov 2017 22:19:53: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:19:54: #2 number of paired peaks: 36071 INFO @ Fri, 10 Nov 2017 22:19:54: start model_add_line... INFO @ Fri, 10 Nov 2017 22:19:54: start X-correlation... INFO @ Fri, 10 Nov 2017 22:19:54: end of X-cor INFO @ Fri, 10 Nov 2017 22:19:54: #2 finished! INFO @ Fri, 10 Nov 2017 22:19:54: #2 predicted fragment length is 134 bps INFO @ Fri, 10 Nov 2017 22:19:54: #2 alternative fragment length(s) may be 134 bps INFO @ Fri, 10 Nov 2017 22:19:54: #2.2 Generate R script for model : SRX2202896.10_model.r INFO @ Fri, 10 Nov 2017 22:19:54: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:19:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:19:55: #2 number of paired peaks: 36071 INFO @ Fri, 10 Nov 2017 22:19:55: start model_add_line... INFO @ Fri, 10 Nov 2017 22:19:55: start X-correlation... INFO @ Fri, 10 Nov 2017 22:19:55: end of X-cor INFO @ Fri, 10 Nov 2017 22:19:55: #2 finished! INFO @ Fri, 10 Nov 2017 22:19:55: #2 predicted fragment length is 134 bps INFO @ Fri, 10 Nov 2017 22:19:55: #2 alternative fragment length(s) may be 134 bps INFO @ Fri, 10 Nov 2017 22:19:55: #2.2 Generate R script for model : SRX2202896.05_model.r INFO @ Fri, 10 Nov 2017 22:19:55: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:20:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:20:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:20:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:20:30: #4 Write output xls file... SRX2202896.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:20:30: #4 Write peak in narrowPeak format file... SRX2202896.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:20:30: #4 Write summits bed file... SRX2202896.20_summits.bed INFO @ Fri, 10 Nov 2017 22:20:30: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (398 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:20:33: #4 Write output xls file... SRX2202896.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:20:33: #4 Write peak in narrowPeak format file... SRX2202896.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:20:33: #4 Write summits bed file... SRX2202896.10_summits.bed INFO @ Fri, 10 Nov 2017 22:20:33: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (2182 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:20:37: #4 Write output xls file... SRX2202896.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:20:37: #4 Write peak in narrowPeak format file... SRX2202896.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:20:37: #4 Write summits bed file... SRX2202896.05_summits.bed INFO @ Fri, 10 Nov 2017 22:20:37: Done! pass1 - making usageList (66 chroms): 2 millis pass2 - checking and writing primary data (8696 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。