Job ID = 11192565 sra ファイルのダウンロード中... Completed: 616194K bytes transferred in 8 seconds (611535K 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... Read 19558967 spots for /home/okishinya/chipatlas/results/rn6/SRX2226579/SRR4374829.sra Written 19558967 spots for /home/okishinya/chipatlas/results/rn6/SRX2226579/SRR4374829.sra 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:22 19558967 reads; of these: 19558967 (100.00%) were unpaired; of these: 2258660 (11.55%) aligned 0 times 13208713 (67.53%) aligned exactly 1 time 4091594 (20.92%) aligned >1 times 88.45% overall alignment rate Time searching: 00:12:24 Overall time: 00:12:24 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] 3613405 / 17300307 = 0.2089 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 @ Sat, 15 Sep 2018 09:12:24: # Command line: callpeak -t SRX2226579.bam -f BAM -g 2.15e9 -n SRX2226579.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226579.20 # format = BAM # ChIP-seq file = ['SRX2226579.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 @ Sat, 15 Sep 2018 09:12:24: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:12:24: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:12:24: # Command line: callpeak -t SRX2226579.bam -f BAM -g 2.15e9 -n SRX2226579.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226579.05 # format = BAM # ChIP-seq file = ['SRX2226579.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 @ Sat, 15 Sep 2018 09:12:24: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:12:24: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:12:24: # Command line: callpeak -t SRX2226579.bam -f BAM -g 2.15e9 -n SRX2226579.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226579.10 # format = BAM # ChIP-seq file = ['SRX2226579.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 @ Sat, 15 Sep 2018 09:12:24: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:12:24: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:12:30: 1000000 INFO @ Sat, 15 Sep 2018 09:12:30: 1000000 INFO @ Sat, 15 Sep 2018 09:12:31: 1000000 INFO @ Sat, 15 Sep 2018 09:12:37: 2000000 INFO @ Sat, 15 Sep 2018 09:12:37: 2000000 INFO @ Sat, 15 Sep 2018 09:12:38: 2000000 INFO @ Sat, 15 Sep 2018 09:12:43: 3000000 INFO @ Sat, 15 Sep 2018 09:12:44: 3000000 INFO @ Sat, 15 Sep 2018 09:12:45: 3000000 INFO @ Sat, 15 Sep 2018 09:12:50: 4000000 INFO @ Sat, 15 Sep 2018 09:12:51: 4000000 INFO @ Sat, 15 Sep 2018 09:12:52: 4000000 INFO @ Sat, 15 Sep 2018 09:12:57: 5000000 INFO @ Sat, 15 Sep 2018 09:12:58: 5000000 INFO @ Sat, 15 Sep 2018 09:12:59: 5000000 INFO @ Sat, 15 Sep 2018 09:13:03: 6000000 INFO @ Sat, 15 Sep 2018 09:13:04: 6000000 INFO @ Sat, 15 Sep 2018 09:13:05: 6000000 INFO @ Sat, 15 Sep 2018 09:13:09: 7000000 INFO @ Sat, 15 Sep 2018 09:13:10: 7000000 INFO @ Sat, 15 Sep 2018 09:13:12: 7000000 INFO @ Sat, 15 Sep 2018 09:13:15: 8000000 INFO @ Sat, 15 Sep 2018 09:13:17: 8000000 INFO @ Sat, 15 Sep 2018 09:13:19: 8000000 INFO @ Sat, 15 Sep 2018 09:13:22: 9000000 INFO @ Sat, 15 Sep 2018 09:13:24: 9000000 INFO @ Sat, 15 Sep 2018 09:13:26: 9000000 INFO @ Sat, 15 Sep 2018 09:13:28: 10000000 INFO @ Sat, 15 Sep 2018 09:13:31: 10000000 INFO @ Sat, 15 Sep 2018 09:13:33: 10000000 INFO @ Sat, 15 Sep 2018 09:13:34: 11000000 INFO @ Sat, 15 Sep 2018 09:13:37: 11000000 INFO @ Sat, 15 Sep 2018 09:13:39: 11000000 INFO @ Sat, 15 Sep 2018 09:13:40: 12000000 INFO @ Sat, 15 Sep 2018 09:13:44: 12000000 INFO @ Sat, 15 Sep 2018 09:13:46: 12000000 INFO @ Sat, 15 Sep 2018 09:13:47: 13000000 INFO @ Sat, 15 Sep 2018 09:13:51: 13000000 INFO @ Sat, 15 Sep 2018 09:13:52: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:13:52: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:13:52: #1 total tags in treatment: 13686902 INFO @ Sat, 15 Sep 2018 09:13:52: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:13:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:13:52: #1 tags after filtering in treatment: 13686718 INFO @ Sat, 15 Sep 2018 09:13:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:13:52: #1 finished! INFO @ Sat, 15 Sep 2018 09:13:52: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:13:53: 13000000 INFO @ Sat, 15 Sep 2018 09:13:55: #2 number of paired peaks: 42775 INFO @ Sat, 15 Sep 2018 09:13:55: start model_add_line... INFO @ Sat, 15 Sep 2018 09:13:55: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:13:55: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:13:55: #1 total tags in treatment: 13686902 INFO @ Sat, 15 Sep 2018 09:13:55: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:13:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:13:55: start X-correlation... INFO @ Sat, 15 Sep 2018 09:13:55: end of X-cor INFO @ Sat, 15 Sep 2018 09:13:55: #2 finished! INFO @ Sat, 15 Sep 2018 09:13:55: #2 predicted fragment length is 203 bps INFO @ Sat, 15 Sep 2018 09:13:55: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 15 Sep 2018 09:13:55: #2.2 Generate R script for model : SRX2226579.10_model.r INFO @ Sat, 15 Sep 2018 09:13:55: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:13:56: #1 tags after filtering in treatment: 13686718 INFO @ Sat, 15 Sep 2018 09:13:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:13:56: #1 finished! INFO @ Sat, 15 Sep 2018 09:13:56: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:13:58: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:13:58: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:13:58: #1 total tags in treatment: 13686902 INFO @ Sat, 15 Sep 2018 09:13:58: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:13:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:13:58: #1 tags after filtering in treatment: 13686718 INFO @ Sat, 15 Sep 2018 09:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:13:58: #1 finished! INFO @ Sat, 15 Sep 2018 09:13:58: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:13:58: #2 number of paired peaks: 42775 INFO @ Sat, 15 Sep 2018 09:13:58: start model_add_line... INFO @ Sat, 15 Sep 2018 09:13:59: start X-correlation... INFO @ Sat, 15 Sep 2018 09:13:59: end of X-cor INFO @ Sat, 15 Sep 2018 09:13:59: #2 finished! INFO @ Sat, 15 Sep 2018 09:13:59: #2 predicted fragment length is 203 bps INFO @ Sat, 15 Sep 2018 09:13:59: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 15 Sep 2018 09:13:59: #2.2 Generate R script for model : SRX2226579.05_model.r INFO @ Sat, 15 Sep 2018 09:13:59: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:14:01: #2 number of paired peaks: 42775 INFO @ Sat, 15 Sep 2018 09:14:01: start model_add_line... INFO @ Sat, 15 Sep 2018 09:14:01: start X-correlation... INFO @ Sat, 15 Sep 2018 09:14:01: end of X-cor INFO @ Sat, 15 Sep 2018 09:14:01: #2 finished! INFO @ Sat, 15 Sep 2018 09:14:01: #2 predicted fragment length is 203 bps INFO @ Sat, 15 Sep 2018 09:14:01: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 15 Sep 2018 09:14:01: #2.2 Generate R script for model : SRX2226579.20_model.r INFO @ Sat, 15 Sep 2018 09:14:01: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:14:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:14:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:14:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:14:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:14:49: #4 Write output xls file... SRX2226579.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:14:50: #4 Write peak in narrowPeak format file... SRX2226579.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:14:50: #4 Write summits bed file... SRX2226579.10_summits.bed INFO @ Sat, 15 Sep 2018 09:14:50: Done! pass1 - making usageList (65 chroms): 3 millis pass2 - checking and writing primary data (10509 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:14:58: #4 Write output xls file... SRX2226579.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:14:58: #4 Write peak in narrowPeak format file... SRX2226579.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:14:58: #4 Write summits bed file... SRX2226579.20_summits.bed INFO @ Sat, 15 Sep 2018 09:14:58: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (4368 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:14:58: #4 Write output xls file... SRX2226579.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:14:58: #4 Write peak in narrowPeak format file... SRX2226579.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:14:58: #4 Write summits bed file... SRX2226579.05_summits.bed INFO @ Sat, 15 Sep 2018 09:14:58: Done! pass1 - making usageList (94 chroms): 4 millis pass2 - checking and writing primary data (20379 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。