Job ID = 10194885 sra ファイルのダウンロード中... Completed: 266736K bytes transferred in 8 seconds (259890K bits/sec), in 1 file. Completed: 267384K bytes transferred in 12 seconds (178710K bits/sec), in 1 file. Completed: 254630K bytes transferred in 6 seconds (324293K bits/sec), in 1 file. Completed: 251461K bytes transferred in 9 seconds (225348K bits/sec), in 1 file. Completed: 293861K bytes transferred in 9 seconds (267230K bits/sec), in 1 file. Completed: 296948K bytes transferred in 12 seconds (200899K 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 5710282 spots for /home/okishinya/chipatlas/results/rn6/SRX2202880/SRR4319827.sra Written 5710282 spots total Written 5770723 spots for /home/okishinya/chipatlas/results/rn6/SRX2202880/SRR4319826.sra Written 5770723 spots total Written 6024133 spots for /home/okishinya/chipatlas/results/rn6/SRX2202880/SRR4319825.sra Written 6024133 spots total Written 6030659 spots for /home/okishinya/chipatlas/results/rn6/SRX2202880/SRR4319824.sra Written 6030659 spots total Written 6547482 spots for /home/okishinya/chipatlas/results/rn6/SRX2202880/SRR4319829.sra Written 6547482 spots total Written 6503548 spots for /home/okishinya/chipatlas/results/rn6/SRX2202880/SRR4319828.sra Written 6503548 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: 00:00:00 Multiseed full-index search: 00:25:33 36586827 reads; of these: 36586827 (100.00%) were unpaired; of these: 4322550 (11.81%) aligned 0 times 24780535 (67.73%) aligned exactly 1 time 7483742 (20.45%) aligned >1 times 88.19% overall alignment rate Time searching: 00:25:36 Overall time: 00:25:36 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] 11631660 / 32264277 = 0.3605 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 18:14:12: # Command line: callpeak -t SRX2202880.bam -f BAM -g 2.15e9 -n SRX2202880.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202880.10 # format = BAM # ChIP-seq file = ['SRX2202880.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 18:14:12: # Command line: callpeak -t SRX2202880.bam -f BAM -g 2.15e9 -n SRX2202880.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202880.20 # format = BAM # ChIP-seq file = ['SRX2202880.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 18:14:12: # Command line: callpeak -t SRX2202880.bam -f BAM -g 2.15e9 -n SRX2202880.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202880.05 # format = BAM # ChIP-seq file = ['SRX2202880.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 18:14:12: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:14:12: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:14:12: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:14:12: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:14:12: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:14:12: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:14:20: 1000000 INFO @ Fri, 10 Nov 2017 18:14:20: 1000000 INFO @ Fri, 10 Nov 2017 18:14:21: 1000000 INFO @ Fri, 10 Nov 2017 18:14:28: 2000000 INFO @ Fri, 10 Nov 2017 18:14:28: 2000000 INFO @ Fri, 10 Nov 2017 18:14:30: 2000000 INFO @ Fri, 10 Nov 2017 18:14:36: 3000000 INFO @ Fri, 10 Nov 2017 18:14:36: 3000000 INFO @ Fri, 10 Nov 2017 18:14:38: 3000000 INFO @ Fri, 10 Nov 2017 18:14:44: 4000000 INFO @ Fri, 10 Nov 2017 18:14:44: 4000000 INFO @ Fri, 10 Nov 2017 18:14:47: 4000000 INFO @ Fri, 10 Nov 2017 18:14:51: 5000000 INFO @ Fri, 10 Nov 2017 18:14:52: 5000000 INFO @ Fri, 10 Nov 2017 18:14:56: 5000000 INFO @ Fri, 10 Nov 2017 18:14:59: 6000000 INFO @ Fri, 10 Nov 2017 18:14:59: 6000000 INFO @ Fri, 10 Nov 2017 18:15:05: 6000000 INFO @ Fri, 10 Nov 2017 18:15:07: 7000000 INFO @ Fri, 10 Nov 2017 18:15:07: 7000000 INFO @ Fri, 10 Nov 2017 18:15:13: 7000000 INFO @ Fri, 10 Nov 2017 18:15:15: 8000000 INFO @ Fri, 10 Nov 2017 18:15:15: 8000000 INFO @ Fri, 10 Nov 2017 18:15:22: 8000000 INFO @ Fri, 10 Nov 2017 18:15:23: 9000000 INFO @ Fri, 10 Nov 2017 18:15:23: 9000000 INFO @ Fri, 10 Nov 2017 18:15:30: 10000000 INFO @ Fri, 10 Nov 2017 18:15:31: 10000000 INFO @ Fri, 10 Nov 2017 18:15:31: 9000000 INFO @ Fri, 10 Nov 2017 18:15:38: 11000000 INFO @ Fri, 10 Nov 2017 18:15:39: 11000000 INFO @ Fri, 10 Nov 2017 18:15:40: 10000000 INFO @ Fri, 10 Nov 2017 18:15:46: 12000000 INFO @ Fri, 10 Nov 2017 18:15:47: 12000000 INFO @ Fri, 10 Nov 2017 18:15:48: 11000000 INFO @ Fri, 10 Nov 2017 18:15:54: 13000000 INFO @ Fri, 10 Nov 2017 18:15:54: 13000000 INFO @ Fri, 10 Nov 2017 18:15:57: 12000000 INFO @ Fri, 10 Nov 2017 18:16:01: 14000000 INFO @ Fri, 10 Nov 2017 18:16:02: 14000000 INFO @ Fri, 10 Nov 2017 18:16:06: 13000000 INFO @ Fri, 10 Nov 2017 18:16:09: 15000000 INFO @ Fri, 10 Nov 2017 18:16:10: 15000000 INFO @ Fri, 10 Nov 2017 18:16:15: 14000000 INFO @ Fri, 10 Nov 2017 18:16:17: 16000000 INFO @ Fri, 10 Nov 2017 18:16:18: 16000000 INFO @ Fri, 10 Nov 2017 18:16:24: 15000000 INFO @ Fri, 10 Nov 2017 18:16:25: 17000000 INFO @ Fri, 10 Nov 2017 18:16:26: 17000000 INFO @ Fri, 10 Nov 2017 18:16:33: 18000000 INFO @ Fri, 10 Nov 2017 18:16:33: 16000000 INFO @ Fri, 10 Nov 2017 18:16:34: 18000000 INFO @ Fri, 10 Nov 2017 18:16:41: 19000000 INFO @ Fri, 10 Nov 2017 18:16:42: 17000000 INFO @ Fri, 10 Nov 2017 18:16:42: 19000000 INFO @ Fri, 10 Nov 2017 18:16:49: 20000000 INFO @ Fri, 10 Nov 2017 18:16:50: 20000000 INFO @ Fri, 10 Nov 2017 18:16:51: 18000000 INFO @ Fri, 10 Nov 2017 18:16:54: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:16:54: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:16:54: #1 total tags in treatment: 20632617 INFO @ Fri, 10 Nov 2017 18:16:54: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:16:54: #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 18:16:55: #1 tags after filtering in treatment: 20632481 INFO @ Fri, 10 Nov 2017 18:16:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:16:55: #1 finished! INFO @ Fri, 10 Nov 2017 18:16:55: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:16:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:16:56: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:16:56: #1 total tags in treatment: 20632617 INFO @ Fri, 10 Nov 2017 18:16:56: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:16:56: #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 18:16:56: #1 tags after filtering in treatment: 20632481 INFO @ Fri, 10 Nov 2017 18:16:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:16:56: #1 finished! INFO @ Fri, 10 Nov 2017 18:16:56: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:16:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:16:58: #2 number of paired peaks: 41835 INFO @ Fri, 10 Nov 2017 18:16:58: start model_add_line... INFO @ Fri, 10 Nov 2017 18:16:58: start X-correlation... INFO @ Fri, 10 Nov 2017 18:16:58: end of X-cor INFO @ Fri, 10 Nov 2017 18:16:58: #2 finished! INFO @ Fri, 10 Nov 2017 18:16:58: #2 predicted fragment length is 147 bps INFO @ Fri, 10 Nov 2017 18:16:58: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 10 Nov 2017 18:16:58: #2.2 Generate R script for model : SRX2202880.10_model.r INFO @ Fri, 10 Nov 2017 18:16:58: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:16:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:16:59: 19000000 INFO @ Fri, 10 Nov 2017 18:17:00: #2 number of paired peaks: 41835 INFO @ Fri, 10 Nov 2017 18:17:00: start model_add_line... INFO @ Fri, 10 Nov 2017 18:17:00: start X-correlation... INFO @ Fri, 10 Nov 2017 18:17:00: end of X-cor INFO @ Fri, 10 Nov 2017 18:17:00: #2 finished! INFO @ Fri, 10 Nov 2017 18:17:00: #2 predicted fragment length is 147 bps INFO @ Fri, 10 Nov 2017 18:17:00: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 10 Nov 2017 18:17:00: #2.2 Generate R script for model : SRX2202880.05_model.r INFO @ Fri, 10 Nov 2017 18:17:00: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:17:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:17:07: 20000000 INFO @ Fri, 10 Nov 2017 18:17:12: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:17:12: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:17:12: #1 total tags in treatment: 20632617 INFO @ Fri, 10 Nov 2017 18:17:12: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:17:12: #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 18:17:12: #1 tags after filtering in treatment: 20632481 INFO @ Fri, 10 Nov 2017 18:17:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:17:12: #1 finished! INFO @ Fri, 10 Nov 2017 18:17:12: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:17:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:17:16: #2 number of paired peaks: 41835 INFO @ Fri, 10 Nov 2017 18:17:16: start model_add_line... INFO @ Fri, 10 Nov 2017 18:17:16: start X-correlation... INFO @ Fri, 10 Nov 2017 18:17:16: end of X-cor INFO @ Fri, 10 Nov 2017 18:17:16: #2 finished! INFO @ Fri, 10 Nov 2017 18:17:16: #2 predicted fragment length is 147 bps INFO @ Fri, 10 Nov 2017 18:17:16: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 10 Nov 2017 18:17:16: #2.2 Generate R script for model : SRX2202880.20_model.r INFO @ Fri, 10 Nov 2017 18:17:16: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:17:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:17:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:17:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:18:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:18:19: #4 Write output xls file... SRX2202880.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:18:19: #4 Write peak in narrowPeak format file... SRX2202880.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:18:19: #4 Write summits bed file... SRX2202880.05_summits.bed INFO @ Fri, 10 Nov 2017 18:18:19: Done! pass1 - making usageList (78 chroms): 3 millis pass2 - checking and writing primary data (11786 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:18:21: #4 Write output xls file... SRX2202880.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:18:21: #4 Write peak in narrowPeak format file... SRX2202880.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:18:21: #4 Write summits bed file... SRX2202880.10_summits.bed INFO @ Fri, 10 Nov 2017 18:18:21: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (3605 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:18:44: #4 Write output xls file... SRX2202880.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:18:44: #4 Write peak in narrowPeak format file... SRX2202880.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:18:44: #4 Write summits bed file... SRX2202880.20_summits.bed INFO @ Fri, 10 Nov 2017 18:18:44: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。