Job ID = 10608886 sra ファイルのダウンロード中... Completed: 414085K bytes transferred in 18 seconds (188222K 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 15178642 spots for /home/okishinya/chipatlas/results/rn6/SRX3145025/SRR5989254.sra Written 15178642 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:58 15178642 reads; of these: 15178642 (100.00%) were unpaired; of these: 380220 (2.50%) aligned 0 times 10992523 (72.42%) aligned exactly 1 time 3805899 (25.07%) aligned >1 times 97.50% overall alignment rate Time searching: 00:11:00 Overall time: 00:11:00 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] 761326 / 14798422 = 0.0514 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 22:38:02: # Command line: callpeak -t SRX3145025.bam -f BAM -g 2.15e9 -n SRX3145025.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3145025.20 # format = BAM # ChIP-seq file = ['SRX3145025.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 22:38:02: #1 read tag files... INFO @ Thu, 03 May 2018 22:38:02: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:38:02: # Command line: callpeak -t SRX3145025.bam -f BAM -g 2.15e9 -n SRX3145025.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3145025.10 # format = BAM # ChIP-seq file = ['SRX3145025.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 22:38:02: #1 read tag files... INFO @ Thu, 03 May 2018 22:38:02: # Command line: callpeak -t SRX3145025.bam -f BAM -g 2.15e9 -n SRX3145025.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3145025.05 # format = BAM # ChIP-seq file = ['SRX3145025.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 22:38:02: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:38:02: #1 read tag files... INFO @ Thu, 03 May 2018 22:38:02: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:38:10: 1000000 INFO @ Thu, 03 May 2018 22:38:10: 1000000 INFO @ Thu, 03 May 2018 22:38:10: 1000000 INFO @ Thu, 03 May 2018 22:38:17: 2000000 INFO @ Thu, 03 May 2018 22:38:18: 2000000 INFO @ Thu, 03 May 2018 22:38:18: 2000000 INFO @ Thu, 03 May 2018 22:38:25: 3000000 INFO @ Thu, 03 May 2018 22:38:26: 3000000 INFO @ Thu, 03 May 2018 22:38:26: 3000000 INFO @ Thu, 03 May 2018 22:38:33: 4000000 INFO @ Thu, 03 May 2018 22:38:34: 4000000 INFO @ Thu, 03 May 2018 22:38:34: 4000000 INFO @ Thu, 03 May 2018 22:38:41: 5000000 INFO @ Thu, 03 May 2018 22:38:42: 5000000 INFO @ Thu, 03 May 2018 22:38:42: 5000000 INFO @ Thu, 03 May 2018 22:38:49: 6000000 INFO @ Thu, 03 May 2018 22:38:50: 6000000 INFO @ Thu, 03 May 2018 22:38:50: 6000000 INFO @ Thu, 03 May 2018 22:38:57: 7000000 INFO @ Thu, 03 May 2018 22:38:58: 7000000 INFO @ Thu, 03 May 2018 22:38:58: 7000000 INFO @ Thu, 03 May 2018 22:39:05: 8000000 INFO @ Thu, 03 May 2018 22:39:07: 8000000 INFO @ Thu, 03 May 2018 22:39:07: 8000000 INFO @ Thu, 03 May 2018 22:39:12: 9000000 INFO @ Thu, 03 May 2018 22:39:15: 9000000 INFO @ Thu, 03 May 2018 22:39:15: 9000000 INFO @ Thu, 03 May 2018 22:39:20: 10000000 INFO @ Thu, 03 May 2018 22:39:24: 10000000 INFO @ Thu, 03 May 2018 22:39:24: 10000000 INFO @ Thu, 03 May 2018 22:39:28: 11000000 INFO @ Thu, 03 May 2018 22:39:32: 11000000 INFO @ Thu, 03 May 2018 22:39:32: 11000000 INFO @ Thu, 03 May 2018 22:39:35: 12000000 INFO @ Thu, 03 May 2018 22:39:41: 12000000 INFO @ Thu, 03 May 2018 22:39:41: 12000000 INFO @ Thu, 03 May 2018 22:39:43: 13000000 INFO @ Thu, 03 May 2018 22:39:49: 13000000 INFO @ Thu, 03 May 2018 22:39:49: 13000000 INFO @ Thu, 03 May 2018 22:39:51: 14000000 INFO @ Thu, 03 May 2018 22:39:51: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:39:51: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:39:51: #1 total tags in treatment: 14037096 INFO @ Thu, 03 May 2018 22:39:51: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:39:51: #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 22:39:52: #1 tags after filtering in treatment: 14036909 INFO @ Thu, 03 May 2018 22:39:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:39:52: #1 finished! INFO @ Thu, 03 May 2018 22:39:52: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:39:54: #2 number of paired peaks: 18767 INFO @ Thu, 03 May 2018 22:39:54: start model_add_line... INFO @ Thu, 03 May 2018 22:39:54: start X-correlation... INFO @ Thu, 03 May 2018 22:39:54: end of X-cor INFO @ Thu, 03 May 2018 22:39:54: #2 finished! INFO @ Thu, 03 May 2018 22:39:54: #2 predicted fragment length is 259 bps INFO @ Thu, 03 May 2018 22:39:54: #2 alternative fragment length(s) may be 55,259 bps INFO @ Thu, 03 May 2018 22:39:54: #2.2 Generate R script for model : SRX3145025.20_model.r INFO @ Thu, 03 May 2018 22:39:54: #3 Call peaks... INFO @ Thu, 03 May 2018 22:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:39:58: 14000000 INFO @ Thu, 03 May 2018 22:39:58: 14000000 INFO @ Thu, 03 May 2018 22:39:58: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:39:58: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:39:58: #1 total tags in treatment: 14037096 INFO @ Thu, 03 May 2018 22:39:58: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:39:58: #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 22:39:58: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:39:58: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:39:58: #1 total tags in treatment: 14037096 INFO @ Thu, 03 May 2018 22:39:58: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:39:58: #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 22:39:58: #1 tags after filtering in treatment: 14036909 INFO @ Thu, 03 May 2018 22:39:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:39:58: #1 finished! INFO @ Thu, 03 May 2018 22:39:58: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:39:58: #1 tags after filtering in treatment: 14036909 INFO @ Thu, 03 May 2018 22:39:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:39:58: #1 finished! INFO @ Thu, 03 May 2018 22:39:58: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:40:00: #2 number of paired peaks: 18767 INFO @ Thu, 03 May 2018 22:40:00: start model_add_line... INFO @ Thu, 03 May 2018 22:40:00: #2 number of paired peaks: 18767 INFO @ Thu, 03 May 2018 22:40:00: start model_add_line... INFO @ Thu, 03 May 2018 22:40:01: start X-correlation... INFO @ Thu, 03 May 2018 22:40:01: end of X-cor INFO @ Thu, 03 May 2018 22:40:01: #2 finished! INFO @ Thu, 03 May 2018 22:40:01: #2 predicted fragment length is 259 bps INFO @ Thu, 03 May 2018 22:40:01: #2 alternative fragment length(s) may be 55,259 bps INFO @ Thu, 03 May 2018 22:40:01: #2.2 Generate R script for model : SRX3145025.05_model.r INFO @ Thu, 03 May 2018 22:40:01: #3 Call peaks... INFO @ Thu, 03 May 2018 22:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:40:01: start X-correlation... INFO @ Thu, 03 May 2018 22:40:01: end of X-cor INFO @ Thu, 03 May 2018 22:40:01: #2 finished! INFO @ Thu, 03 May 2018 22:40:01: #2 predicted fragment length is 259 bps INFO @ Thu, 03 May 2018 22:40:01: #2 alternative fragment length(s) may be 55,259 bps INFO @ Thu, 03 May 2018 22:40:01: #2.2 Generate R script for model : SRX3145025.10_model.r INFO @ Thu, 03 May 2018 22:40:01: #3 Call peaks... INFO @ Thu, 03 May 2018 22:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:40:32: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:40:36: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:40:39: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:40:55: #4 Write output xls file... SRX3145025.10_peaks.xls INFO @ Thu, 03 May 2018 22:40:55: #4 Write peak in narrowPeak format file... SRX3145025.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:40:55: #4 Write summits bed file... SRX3145025.10_summits.bed INFO @ Thu, 03 May 2018 22:40:55: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:40:55: #4 Write output xls file... SRX3145025.20_peaks.xls INFO @ Thu, 03 May 2018 22:40:56: #4 Write peak in narrowPeak format file... SRX3145025.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:40:56: #4 Write summits bed file... SRX3145025.20_summits.bed INFO @ Thu, 03 May 2018 22:40:56: Done! pass1 - making usageList (26 chroms): 0 millis pass2 - checking and writing primary data (240 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:41:00: #4 Write output xls file... SRX3145025.05_peaks.xls INFO @ Thu, 03 May 2018 22:41:00: #4 Write peak in narrowPeak format file... SRX3145025.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:41:00: #4 Write summits bed file... SRX3145025.05_summits.bed INFO @ Thu, 03 May 2018 22:41:00: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (773 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。