Job ID = 10608873 sra ファイルのダウンロード中... Completed: 753197K bytes transferred in 27 seconds (227927K 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 16133378 spots for /home/okishinya/chipatlas/results/rn6/SRX2727608/SRR5437671.sra Written 16133378 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 rm: cannot remove `[DSE]RR*.fastq': 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:57 16133378 reads; of these: 16133378 (100.00%) were unpaired; of these: 536854 (3.33%) aligned 0 times 13527536 (83.85%) aligned exactly 1 time 2068988 (12.82%) aligned >1 times 96.67% overall alignment rate Time searching: 00:26:59 Overall time: 00:26:59 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 8 files... [bam_rmdupse_core] 757441 / 15596524 = 0.0486 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 @ Thu, 03 May 2018 22:50:51: # Command line: callpeak -t SRX2727608.bam -f BAM -g 2.15e9 -n SRX2727608.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2727608.10 # format = BAM # ChIP-seq file = ['SRX2727608.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 @ Thu, 03 May 2018 22:50:51: #1 read tag files... INFO @ Thu, 03 May 2018 22:50:51: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:50:51: # Command line: callpeak -t SRX2727608.bam -f BAM -g 2.15e9 -n SRX2727608.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2727608.05 # format = BAM # ChIP-seq file = ['SRX2727608.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 @ Thu, 03 May 2018 22:50:51: #1 read tag files... INFO @ Thu, 03 May 2018 22:50:51: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:50:51: # Command line: callpeak -t SRX2727608.bam -f BAM -g 2.15e9 -n SRX2727608.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2727608.20 # format = BAM # ChIP-seq file = ['SRX2727608.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 @ Thu, 03 May 2018 22:50:51: #1 read tag files... INFO @ Thu, 03 May 2018 22:50:51: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:51:00: 1000000 INFO @ Thu, 03 May 2018 22:51:00: 1000000 INFO @ Thu, 03 May 2018 22:51:00: 1000000 INFO @ Thu, 03 May 2018 22:51:09: 2000000 INFO @ Thu, 03 May 2018 22:51:09: 2000000 INFO @ Thu, 03 May 2018 22:51:09: 2000000 INFO @ Thu, 03 May 2018 22:51:17: 3000000 INFO @ Thu, 03 May 2018 22:51:18: 3000000 INFO @ Thu, 03 May 2018 22:51:18: 3000000 INFO @ Thu, 03 May 2018 22:51:26: 4000000 INFO @ Thu, 03 May 2018 22:51:26: 4000000 INFO @ Thu, 03 May 2018 22:51:27: 4000000 INFO @ Thu, 03 May 2018 22:51:34: 5000000 INFO @ Thu, 03 May 2018 22:51:35: 5000000 INFO @ Thu, 03 May 2018 22:51:36: 5000000 INFO @ Thu, 03 May 2018 22:51:43: 6000000 INFO @ Thu, 03 May 2018 22:51:44: 6000000 INFO @ Thu, 03 May 2018 22:51:45: 6000000 INFO @ Thu, 03 May 2018 22:51:52: 7000000 INFO @ Thu, 03 May 2018 22:51:53: 7000000 INFO @ Thu, 03 May 2018 22:51:55: 7000000 INFO @ Thu, 03 May 2018 22:52:00: 8000000 INFO @ Thu, 03 May 2018 22:52:02: 8000000 INFO @ Thu, 03 May 2018 22:52:04: 8000000 INFO @ Thu, 03 May 2018 22:52:09: 9000000 INFO @ Thu, 03 May 2018 22:52:11: 9000000 INFO @ Thu, 03 May 2018 22:52:13: 9000000 INFO @ Thu, 03 May 2018 22:52:17: 10000000 INFO @ Thu, 03 May 2018 22:52:20: 10000000 INFO @ Thu, 03 May 2018 22:52:23: 10000000 INFO @ Thu, 03 May 2018 22:52:26: 11000000 INFO @ Thu, 03 May 2018 22:52:29: 11000000 INFO @ Thu, 03 May 2018 22:52:32: 11000000 INFO @ Thu, 03 May 2018 22:52:34: 12000000 INFO @ Thu, 03 May 2018 22:52:38: 12000000 INFO @ Thu, 03 May 2018 22:52:41: 12000000 INFO @ Thu, 03 May 2018 22:52:43: 13000000 INFO @ Thu, 03 May 2018 22:52:48: 13000000 INFO @ Thu, 03 May 2018 22:52:51: 13000000 INFO @ Thu, 03 May 2018 22:52:51: 14000000 INFO @ Thu, 03 May 2018 22:52:57: 14000000 INFO @ Thu, 03 May 2018 22:52:59: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:52:59: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:52:59: #1 total tags in treatment: 14839083 INFO @ Thu, 03 May 2018 22:52:59: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:52:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:52:59: #1 tags after filtering in treatment: 14838827 INFO @ Thu, 03 May 2018 22:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:52:59: #1 finished! INFO @ Thu, 03 May 2018 22:52:59: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:53:00: 14000000 INFO @ Thu, 03 May 2018 22:53:04: #2 number of paired peaks: 97733 INFO @ Thu, 03 May 2018 22:53:04: start model_add_line... INFO @ Thu, 03 May 2018 22:53:04: start X-correlation... INFO @ Thu, 03 May 2018 22:53:04: end of X-cor INFO @ Thu, 03 May 2018 22:53:04: #2 finished! INFO @ Thu, 03 May 2018 22:53:04: #2 predicted fragment length is 215 bps INFO @ Thu, 03 May 2018 22:53:04: #2 alternative fragment length(s) may be 215 bps INFO @ Thu, 03 May 2018 22:53:04: #2.2 Generate R script for model : SRX2727608.10_model.r INFO @ Thu, 03 May 2018 22:53:04: #3 Call peaks... INFO @ Thu, 03 May 2018 22:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:53:04: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:53:04: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:53:04: #1 total tags in treatment: 14839083 INFO @ Thu, 03 May 2018 22:53:04: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:53:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:53:05: #1 tags after filtering in treatment: 14838827 INFO @ Thu, 03 May 2018 22:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:53:05: #1 finished! INFO @ Thu, 03 May 2018 22:53:05: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:53:07: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:53:07: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:53:07: #1 total tags in treatment: 14839083 INFO @ Thu, 03 May 2018 22:53:07: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:53:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:53:08: #1 tags after filtering in treatment: 14838827 INFO @ Thu, 03 May 2018 22:53:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:53:08: #1 finished! INFO @ Thu, 03 May 2018 22:53:08: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:53:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:53:10: #2 number of paired peaks: 97733 INFO @ Thu, 03 May 2018 22:53:10: start model_add_line... INFO @ Thu, 03 May 2018 22:53:10: start X-correlation... INFO @ Thu, 03 May 2018 22:53:10: end of X-cor INFO @ Thu, 03 May 2018 22:53:10: #2 finished! INFO @ Thu, 03 May 2018 22:53:10: #2 predicted fragment length is 215 bps INFO @ Thu, 03 May 2018 22:53:10: #2 alternative fragment length(s) may be 215 bps INFO @ Thu, 03 May 2018 22:53:10: #2.2 Generate R script for model : SRX2727608.20_model.r INFO @ Thu, 03 May 2018 22:53:10: #3 Call peaks... INFO @ Thu, 03 May 2018 22:53:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:53:13: #2 number of paired peaks: 97733 INFO @ Thu, 03 May 2018 22:53:13: start model_add_line... INFO @ Thu, 03 May 2018 22:53:13: start X-correlation... INFO @ Thu, 03 May 2018 22:53:13: end of X-cor INFO @ Thu, 03 May 2018 22:53:13: #2 finished! INFO @ Thu, 03 May 2018 22:53:13: #2 predicted fragment length is 215 bps INFO @ Thu, 03 May 2018 22:53:13: #2 alternative fragment length(s) may be 215 bps INFO @ Thu, 03 May 2018 22:53:13: #2.2 Generate R script for model : SRX2727608.05_model.r INFO @ Thu, 03 May 2018 22:53:13: #3 Call peaks... INFO @ Thu, 03 May 2018 22:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:53:43: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:53:47: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:53:50: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:54:06: #4 Write output xls file... SRX2727608.10_peaks.xls INFO @ Thu, 03 May 2018 22:54:07: #4 Write peak in narrowPeak format file... SRX2727608.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:54:07: #4 Write summits bed file... SRX2727608.10_summits.bed INFO @ Thu, 03 May 2018 22:54:07: Done! pass1 - making usageList (73 chroms): 3 millis pass2 - checking and writing primary data (17278 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:54:09: #4 Write output xls file... SRX2727608.20_peaks.xls INFO @ Thu, 03 May 2018 22:54:09: #4 Write peak in narrowPeak format file... SRX2727608.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:54:09: #4 Write summits bed file... SRX2727608.20_summits.bed INFO @ Thu, 03 May 2018 22:54:09: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (5595 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:54:14: #4 Write output xls file... SRX2727608.05_peaks.xls INFO @ Thu, 03 May 2018 22:54:14: #4 Write peak in narrowPeak format file... SRX2727608.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:54:14: #4 Write summits bed file... SRX2727608.05_summits.bed INFO @ Thu, 03 May 2018 22:54:14: Done! pass1 - making usageList (106 chroms): 7 millis pass2 - checking and writing primary data (31632 records, 4 fields): 40 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。