Job ID = 10195002 sra ファイルのダウンロード中... Completed: 667820K bytes transferred in 8 seconds (653878K 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 29579628 spots for /home/okishinya/chipatlas/results/rn6/SRX831352/SRR1743288.sra Written 29579628 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:02:54 29579628 reads; of these: 29579628 (100.00%) were unpaired; of these: 23655216 (79.97%) aligned 0 times 4449557 (15.04%) aligned exactly 1 time 1474855 (4.99%) aligned >1 times 20.03% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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_rmdupse_core] 704755 / 5924412 = 0.1190 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 19:03:01: # Command line: callpeak -t SRX831352.bam -f BAM -g 2.15e9 -n SRX831352.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX831352.10 # format = BAM # ChIP-seq file = ['SRX831352.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 19:03:01: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:03:01: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:03:01: # Command line: callpeak -t SRX831352.bam -f BAM -g 2.15e9 -n SRX831352.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX831352.05 # format = BAM # ChIP-seq file = ['SRX831352.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 19:03:01: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:03:01: # Command line: callpeak -t SRX831352.bam -f BAM -g 2.15e9 -n SRX831352.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX831352.20 # format = BAM # ChIP-seq file = ['SRX831352.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 19:03:01: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:03:01: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:03:01: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:03:07: 1000000 INFO @ Fri, 10 Nov 2017 19:03:07: 1000000 INFO @ Fri, 10 Nov 2017 19:03:08: 1000000 INFO @ Fri, 10 Nov 2017 19:03:13: 2000000 INFO @ Fri, 10 Nov 2017 19:03:14: 2000000 INFO @ Fri, 10 Nov 2017 19:03:15: 2000000 INFO @ Fri, 10 Nov 2017 19:03:19: 3000000 INFO @ Fri, 10 Nov 2017 19:03:21: 3000000 INFO @ Fri, 10 Nov 2017 19:03:22: 3000000 INFO @ Fri, 10 Nov 2017 19:03:25: 4000000 INFO @ Fri, 10 Nov 2017 19:03:27: 4000000 INFO @ Fri, 10 Nov 2017 19:03:29: 4000000 INFO @ Fri, 10 Nov 2017 19:03:31: 5000000 INFO @ Fri, 10 Nov 2017 19:03:32: #1 tag size is determined as 35 bps INFO @ Fri, 10 Nov 2017 19:03:32: #1 tag size = 35 INFO @ Fri, 10 Nov 2017 19:03:32: #1 total tags in treatment: 5219657 INFO @ Fri, 10 Nov 2017 19:03:32: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:03:32: #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 19:03:33: #1 tags after filtering in treatment: 5219400 INFO @ Fri, 10 Nov 2017 19:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:03:33: #1 finished! INFO @ Fri, 10 Nov 2017 19:03:33: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:03:34: 5000000 INFO @ Fri, 10 Nov 2017 19:03:34: #2 number of paired peaks: 15839 INFO @ Fri, 10 Nov 2017 19:03:34: start model_add_line... INFO @ Fri, 10 Nov 2017 19:03:34: start X-correlation... INFO @ Fri, 10 Nov 2017 19:03:34: end of X-cor INFO @ Fri, 10 Nov 2017 19:03:34: #2 finished! INFO @ Fri, 10 Nov 2017 19:03:34: #2 predicted fragment length is 86 bps INFO @ Fri, 10 Nov 2017 19:03:34: #2 alternative fragment length(s) may be 86 bps INFO @ Fri, 10 Nov 2017 19:03:34: #2.2 Generate R script for model : SRX831352.05_model.r INFO @ Fri, 10 Nov 2017 19:03:34: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:03:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:03:35: #1 tag size is determined as 35 bps INFO @ Fri, 10 Nov 2017 19:03:35: #1 tag size = 35 INFO @ Fri, 10 Nov 2017 19:03:35: #1 total tags in treatment: 5219657 INFO @ Fri, 10 Nov 2017 19:03:35: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:03:35: #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 19:03:35: #1 tags after filtering in treatment: 5219400 INFO @ Fri, 10 Nov 2017 19:03:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:03:35: #1 finished! INFO @ Fri, 10 Nov 2017 19:03:35: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:03:36: 5000000 INFO @ Fri, 10 Nov 2017 19:03:37: #1 tag size is determined as 35 bps INFO @ Fri, 10 Nov 2017 19:03:37: #1 tag size = 35 INFO @ Fri, 10 Nov 2017 19:03:37: #1 total tags in treatment: 5219657 INFO @ Fri, 10 Nov 2017 19:03:37: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:03:37: #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 19:03:37: #1 tags after filtering in treatment: 5219400 INFO @ Fri, 10 Nov 2017 19:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:03:37: #1 finished! INFO @ Fri, 10 Nov 2017 19:03:37: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:03:37: #2 number of paired peaks: 15839 INFO @ Fri, 10 Nov 2017 19:03:37: start model_add_line... INFO @ Fri, 10 Nov 2017 19:03:37: start X-correlation... INFO @ Fri, 10 Nov 2017 19:03:37: end of X-cor INFO @ Fri, 10 Nov 2017 19:03:37: #2 finished! INFO @ Fri, 10 Nov 2017 19:03:37: #2 predicted fragment length is 86 bps INFO @ Fri, 10 Nov 2017 19:03:37: #2 alternative fragment length(s) may be 86 bps INFO @ Fri, 10 Nov 2017 19:03:37: #2.2 Generate R script for model : SRX831352.10_model.r INFO @ Fri, 10 Nov 2017 19:03:37: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:03:39: #2 number of paired peaks: 15839 INFO @ Fri, 10 Nov 2017 19:03:39: start model_add_line... INFO @ Fri, 10 Nov 2017 19:03:39: start X-correlation... INFO @ Fri, 10 Nov 2017 19:03:39: end of X-cor INFO @ Fri, 10 Nov 2017 19:03:39: #2 finished! INFO @ Fri, 10 Nov 2017 19:03:39: #2 predicted fragment length is 86 bps INFO @ Fri, 10 Nov 2017 19:03:39: #2 alternative fragment length(s) may be 86 bps INFO @ Fri, 10 Nov 2017 19:03:39: #2.2 Generate R script for model : SRX831352.20_model.r INFO @ Fri, 10 Nov 2017 19:03:39: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:03:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:03:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:03:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:03:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:03:54: #4 Write output xls file... SRX831352.05_peaks.xls INFO @ Fri, 10 Nov 2017 19:03:54: #4 Write peak in narrowPeak format file... SRX831352.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:03:54: #4 Write summits bed file... SRX831352.05_summits.bed INFO @ Fri, 10 Nov 2017 19:03:54: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (1187 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:03:56: #4 Write output xls file... SRX831352.10_peaks.xls INFO @ Fri, 10 Nov 2017 19:03:57: #4 Write peak in narrowPeak format file... SRX831352.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:03:57: #4 Write summits bed file... SRX831352.10_summits.bed INFO @ Fri, 10 Nov 2017 19:03:57: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:03:58: #4 Write output xls file... SRX831352.20_peaks.xls INFO @ Fri, 10 Nov 2017 19:03:58: #4 Write peak in narrowPeak format file... SRX831352.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:03:58: #4 Write summits bed file... SRX831352.20_summits.bed INFO @ Fri, 10 Nov 2017 19:03:58: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。