Job ID = 10194895 sra ファイルのダウンロード中... Completed: 261159K bytes transferred in 15 seconds (141364K bits/sec), in 1 file. Completed: 262469K bytes transferred in 15 seconds (141042K bits/sec), in 1 file. Completed: 248102K bytes transferred in 10 seconds (192107K bits/sec), in 1 file. Completed: 244885K bytes transferred in 14 seconds (138187K bits/sec), in 1 file. Completed: 298460K bytes transferred in 15 seconds (153960K bits/sec), in 1 file. Completed: 301672K bytes transferred in 17 seconds (142845K 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 5544070 spots for /home/okishinya/chipatlas/results/rn6/SRX2202890/SRR4319887.sra Written 5544070 spots total Written 5606205 spots for /home/okishinya/chipatlas/results/rn6/SRX2202890/SRR4319886.sra Written 5606205 spots total Written 5896362 spots for /home/okishinya/chipatlas/results/rn6/SRX2202890/SRR4319885.sra Written 5896362 spots total Written 5887988 spots for /home/okishinya/chipatlas/results/rn6/SRX2202890/SRR4319884.sra Written 5887988 spots total Written 6644676 spots for /home/okishinya/chipatlas/results/rn6/SRX2202890/SRR4319889.sra Written 6644676 spots total Written 6599572 spots for /home/okishinya/chipatlas/results/rn6/SRX2202890/SRR4319888.sra Written 6599572 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: 00:26:03 36178873 reads; of these: 36178873 (100.00%) were unpaired; of these: 1214215 (3.36%) aligned 0 times 26846633 (74.21%) aligned exactly 1 time 8118025 (22.44%) aligned >1 times 96.64% overall alignment rate Time searching: 00:26:06 Overall time: 00:26:06 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] 4973974 / 34964658 = 0.1423 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 18:49:36: # Command line: callpeak -t SRX2202890.bam -f BAM -g 2.15e9 -n SRX2202890.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202890.20 # format = BAM # ChIP-seq file = ['SRX2202890.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 18:49:36: # Command line: callpeak -t SRX2202890.bam -f BAM -g 2.15e9 -n SRX2202890.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202890.05 # format = BAM # ChIP-seq file = ['SRX2202890.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 18:49:36: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:49:36: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:49:36: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:49:36: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:49:36: # Command line: callpeak -t SRX2202890.bam -f BAM -g 2.15e9 -n SRX2202890.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202890.10 # format = BAM # ChIP-seq file = ['SRX2202890.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 18:49:36: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:49:36: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:49:44: 1000000 INFO @ Fri, 10 Nov 2017 18:49:44: 1000000 INFO @ Fri, 10 Nov 2017 18:49:44: 1000000 INFO @ Fri, 10 Nov 2017 18:49:52: 2000000 INFO @ Fri, 10 Nov 2017 18:49:52: 2000000 INFO @ Fri, 10 Nov 2017 18:49:52: 2000000 INFO @ Fri, 10 Nov 2017 18:50:00: 3000000 INFO @ Fri, 10 Nov 2017 18:50:00: 3000000 INFO @ Fri, 10 Nov 2017 18:50:00: 3000000 INFO @ Fri, 10 Nov 2017 18:50:08: 4000000 INFO @ Fri, 10 Nov 2017 18:50:08: 4000000 INFO @ Fri, 10 Nov 2017 18:50:08: 4000000 INFO @ Fri, 10 Nov 2017 18:50:15: 5000000 INFO @ Fri, 10 Nov 2017 18:50:15: 5000000 INFO @ Fri, 10 Nov 2017 18:50:15: 5000000 INFO @ Fri, 10 Nov 2017 18:50:23: 6000000 INFO @ Fri, 10 Nov 2017 18:50:23: 6000000 INFO @ Fri, 10 Nov 2017 18:50:23: 6000000 INFO @ Fri, 10 Nov 2017 18:50:31: 7000000 INFO @ Fri, 10 Nov 2017 18:50:31: 7000000 INFO @ Fri, 10 Nov 2017 18:50:31: 7000000 INFO @ Fri, 10 Nov 2017 18:50:39: 8000000 INFO @ Fri, 10 Nov 2017 18:50:39: 8000000 INFO @ Fri, 10 Nov 2017 18:50:39: 8000000 INFO @ Fri, 10 Nov 2017 18:50:46: 9000000 INFO @ Fri, 10 Nov 2017 18:50:46: 9000000 INFO @ Fri, 10 Nov 2017 18:50:46: 9000000 INFO @ Fri, 10 Nov 2017 18:50:54: 10000000 INFO @ Fri, 10 Nov 2017 18:50:54: 10000000 INFO @ Fri, 10 Nov 2017 18:50:54: 10000000 INFO @ Fri, 10 Nov 2017 18:51:02: 11000000 INFO @ Fri, 10 Nov 2017 18:51:02: 11000000 INFO @ Fri, 10 Nov 2017 18:51:02: 11000000 INFO @ Fri, 10 Nov 2017 18:51:09: 12000000 INFO @ Fri, 10 Nov 2017 18:51:09: 12000000 INFO @ Fri, 10 Nov 2017 18:51:09: 12000000 INFO @ Fri, 10 Nov 2017 18:51:16: 13000000 INFO @ Fri, 10 Nov 2017 18:51:16: 13000000 INFO @ Fri, 10 Nov 2017 18:51:16: 13000000 INFO @ Fri, 10 Nov 2017 18:51:23: 14000000 INFO @ Fri, 10 Nov 2017 18:51:23: 14000000 INFO @ Fri, 10 Nov 2017 18:51:24: 14000000 INFO @ Fri, 10 Nov 2017 18:51:30: 15000000 INFO @ Fri, 10 Nov 2017 18:51:30: 15000000 INFO @ Fri, 10 Nov 2017 18:51:31: 15000000 INFO @ Fri, 10 Nov 2017 18:51:37: 16000000 INFO @ Fri, 10 Nov 2017 18:51:37: 16000000 INFO @ Fri, 10 Nov 2017 18:51:38: 16000000 INFO @ Fri, 10 Nov 2017 18:51:44: 17000000 INFO @ Fri, 10 Nov 2017 18:51:44: 17000000 INFO @ Fri, 10 Nov 2017 18:51:45: 17000000 INFO @ Fri, 10 Nov 2017 18:51:52: 18000000 INFO @ Fri, 10 Nov 2017 18:51:52: 18000000 INFO @ Fri, 10 Nov 2017 18:51:52: 18000000 INFO @ Fri, 10 Nov 2017 18:51:59: 19000000 INFO @ Fri, 10 Nov 2017 18:51:59: 19000000 INFO @ Fri, 10 Nov 2017 18:51:59: 19000000 INFO @ Fri, 10 Nov 2017 18:52:06: 20000000 INFO @ Fri, 10 Nov 2017 18:52:06: 20000000 INFO @ Fri, 10 Nov 2017 18:52:07: 20000000 INFO @ Fri, 10 Nov 2017 18:52:13: 21000000 INFO @ Fri, 10 Nov 2017 18:52:13: 21000000 INFO @ Fri, 10 Nov 2017 18:52:14: 21000000 INFO @ Fri, 10 Nov 2017 18:52:20: 22000000 INFO @ Fri, 10 Nov 2017 18:52:20: 22000000 INFO @ Fri, 10 Nov 2017 18:52:21: 22000000 INFO @ Fri, 10 Nov 2017 18:52:27: 23000000 INFO @ Fri, 10 Nov 2017 18:52:27: 23000000 INFO @ Fri, 10 Nov 2017 18:52:29: 23000000 INFO @ Fri, 10 Nov 2017 18:52:34: 24000000 INFO @ Fri, 10 Nov 2017 18:52:34: 24000000 INFO @ Fri, 10 Nov 2017 18:52:36: 24000000 INFO @ Fri, 10 Nov 2017 18:52:42: 25000000 INFO @ Fri, 10 Nov 2017 18:52:42: 25000000 INFO @ Fri, 10 Nov 2017 18:52:44: 25000000 INFO @ Fri, 10 Nov 2017 18:52:51: 26000000 INFO @ Fri, 10 Nov 2017 18:52:51: 26000000 INFO @ Fri, 10 Nov 2017 18:52:53: 26000000 INFO @ Fri, 10 Nov 2017 18:52:59: 27000000 INFO @ Fri, 10 Nov 2017 18:52:59: 27000000 INFO @ Fri, 10 Nov 2017 18:53:01: 27000000 INFO @ Fri, 10 Nov 2017 18:53:07: 28000000 INFO @ Fri, 10 Nov 2017 18:53:07: 28000000 INFO @ Fri, 10 Nov 2017 18:53:09: 28000000 INFO @ Fri, 10 Nov 2017 18:53:15: 29000000 INFO @ Fri, 10 Nov 2017 18:53:15: 29000000 INFO @ Fri, 10 Nov 2017 18:53:17: 29000000 INFO @ Fri, 10 Nov 2017 18:53:23: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:53:23: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:53:23: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:53:23: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:53:23: #1 total tags in treatment: 29990684 INFO @ Fri, 10 Nov 2017 18:53:23: #1 total tags in treatment: 29990684 INFO @ Fri, 10 Nov 2017 18:53:23: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:53:23: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:53:23: #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 18:53:23: #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 18:53:24: #1 tags after filtering in treatment: 29990563 INFO @ Fri, 10 Nov 2017 18:53:24: #1 tags after filtering in treatment: 29990563 INFO @ Fri, 10 Nov 2017 18:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:53:24: #1 finished! INFO @ Fri, 10 Nov 2017 18:53:24: #1 finished! INFO @ Fri, 10 Nov 2017 18:53:24: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:53:24: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:53:25: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:53:25: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:53:25: #1 total tags in treatment: 29990684 INFO @ Fri, 10 Nov 2017 18:53:25: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:53:25: #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 18:53:26: #1 tags after filtering in treatment: 29990563 INFO @ Fri, 10 Nov 2017 18:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:53:26: #1 finished! INFO @ Fri, 10 Nov 2017 18:53:26: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:53:28: #2 number of paired peaks: 42838 INFO @ Fri, 10 Nov 2017 18:53:28: start model_add_line... INFO @ Fri, 10 Nov 2017 18:53:29: #2 number of paired peaks: 42838 INFO @ Fri, 10 Nov 2017 18:53:29: start model_add_line... INFO @ Fri, 10 Nov 2017 18:53:29: start X-correlation... INFO @ Fri, 10 Nov 2017 18:53:29: end of X-cor INFO @ Fri, 10 Nov 2017 18:53:29: #2 finished! INFO @ Fri, 10 Nov 2017 18:53:29: #2 predicted fragment length is 142 bps INFO @ Fri, 10 Nov 2017 18:53:29: #2 alternative fragment length(s) may be 142 bps INFO @ Fri, 10 Nov 2017 18:53:29: #2.2 Generate R script for model : SRX2202890.20_model.r INFO @ Fri, 10 Nov 2017 18:53:29: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:53:29: start X-correlation... INFO @ Fri, 10 Nov 2017 18:53:29: end of X-cor INFO @ Fri, 10 Nov 2017 18:53:29: #2 finished! INFO @ Fri, 10 Nov 2017 18:53:29: #2 predicted fragment length is 142 bps INFO @ Fri, 10 Nov 2017 18:53:29: #2 alternative fragment length(s) may be 142 bps INFO @ Fri, 10 Nov 2017 18:53:29: #2.2 Generate R script for model : SRX2202890.05_model.r INFO @ Fri, 10 Nov 2017 18:53:29: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:53:30: #2 number of paired peaks: 42838 INFO @ Fri, 10 Nov 2017 18:53:30: start model_add_line... INFO @ Fri, 10 Nov 2017 18:53:31: start X-correlation... INFO @ Fri, 10 Nov 2017 18:53:31: end of X-cor INFO @ Fri, 10 Nov 2017 18:53:31: #2 finished! INFO @ Fri, 10 Nov 2017 18:53:31: #2 predicted fragment length is 142 bps INFO @ Fri, 10 Nov 2017 18:53:31: #2 alternative fragment length(s) may be 142 bps INFO @ Fri, 10 Nov 2017 18:53:31: #2.2 Generate R script for model : SRX2202890.10_model.r INFO @ Fri, 10 Nov 2017 18:53:31: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:53:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:54:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:54:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:54:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:55:23: #4 Write output xls file... SRX2202890.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:55:23: #4 Write peak in narrowPeak format file... SRX2202890.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:55:23: #4 Write summits bed file... SRX2202890.20_summits.bed INFO @ Fri, 10 Nov 2017 18:55:23: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (4418 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:55:28: #4 Write output xls file... SRX2202890.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:55:28: #4 Write peak in narrowPeak format file... SRX2202890.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:55:28: #4 Write summits bed file... SRX2202890.10_summits.bed INFO @ Fri, 10 Nov 2017 18:55:28: Done! pass1 - making usageList (77 chroms): 3 millis pass2 - checking and writing primary data (12506 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:55:29: #4 Write output xls file... SRX2202890.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:55:30: #4 Write peak in narrowPeak format file... SRX2202890.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:55:30: #4 Write summits bed file... SRX2202890.05_summits.bed INFO @ Fri, 10 Nov 2017 18:55:30: Done! pass1 - making usageList (105 chroms): 5 millis pass2 - checking and writing primary data (21967 records, 4 fields): 29 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。