Job ID = 10480660 sra ファイルのダウンロード中... Completed: 504547K bytes transferred in 52 seconds (79324K 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 15893282 spots for /home/okishinya/chipatlas/results/dm3/SRX2832096/SRR5573760.sra Written 15893282 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:22 15893282 reads; of these: 15893282 (100.00%) were unpaired; of these: 719730 (4.53%) aligned 0 times 8209300 (51.65%) aligned exactly 1 time 6964252 (43.82%) aligned >1 times 95.47% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3902041 / 15173552 = 0.2572 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, 16 Mar 2018 07:31:51: # Command line: callpeak -t SRX2832096.bam -f BAM -g dm -n SRX2832096.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2832096.10 # format = BAM # ChIP-seq file = ['SRX2832096.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:31:51: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:31:51: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:31:51: # Command line: callpeak -t SRX2832096.bam -f BAM -g dm -n SRX2832096.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2832096.20 # format = BAM # ChIP-seq file = ['SRX2832096.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:31:51: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:31:51: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:31:51: # Command line: callpeak -t SRX2832096.bam -f BAM -g dm -n SRX2832096.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2832096.05 # format = BAM # ChIP-seq file = ['SRX2832096.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:31:51: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:31:51: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:31:57: 1000000 INFO @ Fri, 16 Mar 2018 07:31:58: 1000000 INFO @ Fri, 16 Mar 2018 07:31:58: 1000000 INFO @ Fri, 16 Mar 2018 07:32:03: 2000000 INFO @ Fri, 16 Mar 2018 07:32:04: 2000000 INFO @ Fri, 16 Mar 2018 07:32:04: 2000000 INFO @ Fri, 16 Mar 2018 07:32:09: 3000000 INFO @ Fri, 16 Mar 2018 07:32:10: 3000000 INFO @ Fri, 16 Mar 2018 07:32:10: 3000000 INFO @ Fri, 16 Mar 2018 07:32:15: 4000000 INFO @ Fri, 16 Mar 2018 07:32:16: 4000000 INFO @ Fri, 16 Mar 2018 07:32:16: 4000000 INFO @ Fri, 16 Mar 2018 07:32:21: 5000000 INFO @ Fri, 16 Mar 2018 07:32:22: 5000000 INFO @ Fri, 16 Mar 2018 07:32:23: 5000000 INFO @ Fri, 16 Mar 2018 07:32:27: 6000000 INFO @ Fri, 16 Mar 2018 07:32:29: 6000000 INFO @ Fri, 16 Mar 2018 07:32:29: 6000000 INFO @ Fri, 16 Mar 2018 07:32:33: 7000000 INFO @ Fri, 16 Mar 2018 07:32:35: 7000000 INFO @ Fri, 16 Mar 2018 07:32:35: 7000000 INFO @ Fri, 16 Mar 2018 07:32:39: 8000000 INFO @ Fri, 16 Mar 2018 07:32:41: 8000000 INFO @ Fri, 16 Mar 2018 07:32:42: 8000000 INFO @ Fri, 16 Mar 2018 07:32:45: 9000000 INFO @ Fri, 16 Mar 2018 07:32:47: 9000000 INFO @ Fri, 16 Mar 2018 07:32:48: 9000000 INFO @ Fri, 16 Mar 2018 07:32:51: 10000000 INFO @ Fri, 16 Mar 2018 07:32:54: 10000000 INFO @ Fri, 16 Mar 2018 07:32:55: 10000000 INFO @ Fri, 16 Mar 2018 07:32:57: 11000000 INFO @ Fri, 16 Mar 2018 07:32:59: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:32:59: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:32:59: #1 total tags in treatment: 11271511 INFO @ Fri, 16 Mar 2018 07:32:59: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:32:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:32:59: #1 tags after filtering in treatment: 11271511 INFO @ Fri, 16 Mar 2018 07:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:32:59: #1 finished! INFO @ Fri, 16 Mar 2018 07:32:59: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:33:00: #2 number of paired peaks: 1067 INFO @ Fri, 16 Mar 2018 07:33:00: start model_add_line... INFO @ Fri, 16 Mar 2018 07:33:00: start X-correlation... INFO @ Fri, 16 Mar 2018 07:33:00: end of X-cor INFO @ Fri, 16 Mar 2018 07:33:00: #2 finished! INFO @ Fri, 16 Mar 2018 07:33:00: #2 predicted fragment length is 130 bps INFO @ Fri, 16 Mar 2018 07:33:00: #2 alternative fragment length(s) may be 130 bps INFO @ Fri, 16 Mar 2018 07:33:00: #2.2 Generate R script for model : SRX2832096.05_model.r INFO @ Fri, 16 Mar 2018 07:33:00: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:33:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:33:00: 11000000 INFO @ Fri, 16 Mar 2018 07:33:01: 11000000 INFO @ Fri, 16 Mar 2018 07:33:02: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:33:02: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:33:02: #1 total tags in treatment: 11271511 INFO @ Fri, 16 Mar 2018 07:33:02: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:33:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:33:02: #1 tags after filtering in treatment: 11271511 INFO @ Fri, 16 Mar 2018 07:33:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:33:02: #1 finished! INFO @ Fri, 16 Mar 2018 07:33:02: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:33:03: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:33:03: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:33:03: #1 total tags in treatment: 11271511 INFO @ Fri, 16 Mar 2018 07:33:03: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:33:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:33:03: #1 tags after filtering in treatment: 11271511 INFO @ Fri, 16 Mar 2018 07:33:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:33:03: #1 finished! INFO @ Fri, 16 Mar 2018 07:33:03: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:33:03: #2 number of paired peaks: 1067 INFO @ Fri, 16 Mar 2018 07:33:03: start model_add_line... INFO @ Fri, 16 Mar 2018 07:33:03: start X-correlation... INFO @ Fri, 16 Mar 2018 07:33:03: end of X-cor INFO @ Fri, 16 Mar 2018 07:33:03: #2 finished! INFO @ Fri, 16 Mar 2018 07:33:03: #2 predicted fragment length is 130 bps INFO @ Fri, 16 Mar 2018 07:33:03: #2 alternative fragment length(s) may be 130 bps INFO @ Fri, 16 Mar 2018 07:33:03: #2.2 Generate R script for model : SRX2832096.20_model.r INFO @ Fri, 16 Mar 2018 07:33:03: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:33:04: #2 number of paired peaks: 1067 INFO @ Fri, 16 Mar 2018 07:33:04: start model_add_line... INFO @ Fri, 16 Mar 2018 07:33:04: start X-correlation... INFO @ Fri, 16 Mar 2018 07:33:04: end of X-cor INFO @ Fri, 16 Mar 2018 07:33:04: #2 finished! INFO @ Fri, 16 Mar 2018 07:33:04: #2 predicted fragment length is 130 bps INFO @ Fri, 16 Mar 2018 07:33:04: #2 alternative fragment length(s) may be 130 bps INFO @ Fri, 16 Mar 2018 07:33:04: #2.2 Generate R script for model : SRX2832096.10_model.r INFO @ Fri, 16 Mar 2018 07:33:04: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:33:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:33:27: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:33:30: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:33:32: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:33:42: #4 Write output xls file... SRX2832096.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:33:42: #4 Write peak in narrowPeak format file... SRX2832096.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:33:42: #4 Write summits bed file... SRX2832096.05_summits.bed INFO @ Fri, 16 Mar 2018 07:33:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6208 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:33:46: #4 Write output xls file... SRX2832096.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:33:46: #4 Write peak in narrowPeak format file... SRX2832096.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:33:46: #4 Write summits bed file... SRX2832096.20_summits.bed INFO @ Fri, 16 Mar 2018 07:33:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1737 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:33:47: #4 Write output xls file... SRX2832096.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:33:47: #4 Write peak in narrowPeak format file... SRX2832096.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:33:47: #4 Write summits bed file... SRX2832096.10_summits.bed INFO @ Fri, 16 Mar 2018 07:33:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3564 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。