Job ID = 11388782 sra ファイルのダウンロード中... Completed: 213911K bytes transferred in 6 seconds (270204K 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... Read 7972920 spots for /home/okishinya/chipatlas/results/rn6/SRX1453548/SRR2962624.sra Written 7972920 spots for /home/okishinya/chipatlas/results/rn6/SRX1453548/SRR2962624.sra 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:51:43 7972920 reads; of these: 7972920 (100.00%) were unpaired; of these: 1350188 (16.93%) aligned 0 times 3142958 (39.42%) aligned exactly 1 time 3479774 (43.64%) aligned >1 times 83.07% overall alignment rate Time searching: 00:51:49 Overall time: 00:51:49 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] 1774649 / 6622732 = 0.2680 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 @ Wed, 12 Dec 2018 23:07:09: # Command line: callpeak -t SRX1453548.bam -f BAM -g 2.15e9 -n SRX1453548.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1453548.20 # format = BAM # ChIP-seq file = ['SRX1453548.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 @ Wed, 12 Dec 2018 23:07:09: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:07:09: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:07:09: # Command line: callpeak -t SRX1453548.bam -f BAM -g 2.15e9 -n SRX1453548.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1453548.05 # format = BAM # ChIP-seq file = ['SRX1453548.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 @ Wed, 12 Dec 2018 23:07:09: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:07:09: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:07:09: # Command line: callpeak -t SRX1453548.bam -f BAM -g 2.15e9 -n SRX1453548.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1453548.10 # format = BAM # ChIP-seq file = ['SRX1453548.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 @ Wed, 12 Dec 2018 23:07:09: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:07:09: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:07:28: 1000000 INFO @ Wed, 12 Dec 2018 23:07:30: 1000000 INFO @ Wed, 12 Dec 2018 23:07:31: 1000000 INFO @ Wed, 12 Dec 2018 23:07:48: 2000000 INFO @ Wed, 12 Dec 2018 23:07:51: 2000000 INFO @ Wed, 12 Dec 2018 23:07:54: 2000000 INFO @ Wed, 12 Dec 2018 23:08:09: 3000000 INFO @ Wed, 12 Dec 2018 23:08:12: 3000000 INFO @ Wed, 12 Dec 2018 23:08:20: 3000000 INFO @ Wed, 12 Dec 2018 23:08:30: 4000000 INFO @ Wed, 12 Dec 2018 23:08:36: 4000000 INFO @ Wed, 12 Dec 2018 23:08:44: 4000000 INFO @ Wed, 12 Dec 2018 23:08:47: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:08:47: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:08:47: #1 total tags in treatment: 4848083 INFO @ Wed, 12 Dec 2018 23:08:47: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:08:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:08:47: #1 tags after filtering in treatment: 4847831 INFO @ Wed, 12 Dec 2018 23:08:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:08:47: #1 finished! INFO @ Wed, 12 Dec 2018 23:08:47: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:08:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:08:53: #2 number of paired peaks: 93433 INFO @ Wed, 12 Dec 2018 23:08:53: start model_add_line... INFO @ Wed, 12 Dec 2018 23:08:53: start X-correlation... INFO @ Wed, 12 Dec 2018 23:08:53: end of X-cor INFO @ Wed, 12 Dec 2018 23:08:53: #2 finished! INFO @ Wed, 12 Dec 2018 23:08:53: #2 predicted fragment length is 124 bps INFO @ Wed, 12 Dec 2018 23:08:53: #2 alternative fragment length(s) may be 124 bps INFO @ Wed, 12 Dec 2018 23:08:53: #2.2 Generate R script for model : SRX1453548.20_model.r INFO @ Wed, 12 Dec 2018 23:08:53: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:08:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:08:55: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:08:55: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:08:55: #1 total tags in treatment: 4848083 INFO @ Wed, 12 Dec 2018 23:08:55: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:08:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:08:56: #1 tags after filtering in treatment: 4847831 INFO @ Wed, 12 Dec 2018 23:08:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:08:56: #1 finished! INFO @ Wed, 12 Dec 2018 23:08:56: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:08:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:09:01: #2 number of paired peaks: 93433 INFO @ Wed, 12 Dec 2018 23:09:01: start model_add_line... INFO @ Wed, 12 Dec 2018 23:09:01: start X-correlation... INFO @ Wed, 12 Dec 2018 23:09:01: end of X-cor INFO @ Wed, 12 Dec 2018 23:09:01: #2 finished! INFO @ Wed, 12 Dec 2018 23:09:01: #2 predicted fragment length is 124 bps INFO @ Wed, 12 Dec 2018 23:09:01: #2 alternative fragment length(s) may be 124 bps INFO @ Wed, 12 Dec 2018 23:09:01: #2.2 Generate R script for model : SRX1453548.05_model.r INFO @ Wed, 12 Dec 2018 23:09:01: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:09:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:09:04: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:09:04: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:09:04: #1 total tags in treatment: 4848083 INFO @ Wed, 12 Dec 2018 23:09:04: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:09:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:09:04: #1 tags after filtering in treatment: 4847831 INFO @ Wed, 12 Dec 2018 23:09:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:09:04: #1 finished! INFO @ Wed, 12 Dec 2018 23:09:04: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:09:09: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:09:10: #2 number of paired peaks: 93433 INFO @ Wed, 12 Dec 2018 23:09:10: start model_add_line... INFO @ Wed, 12 Dec 2018 23:09:10: start X-correlation... INFO @ Wed, 12 Dec 2018 23:09:10: end of X-cor INFO @ Wed, 12 Dec 2018 23:09:10: #2 finished! INFO @ Wed, 12 Dec 2018 23:09:10: #2 predicted fragment length is 124 bps INFO @ Wed, 12 Dec 2018 23:09:10: #2 alternative fragment length(s) may be 124 bps INFO @ Wed, 12 Dec 2018 23:09:10: #2.2 Generate R script for model : SRX1453548.10_model.r INFO @ Wed, 12 Dec 2018 23:09:10: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:09:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:09:17: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:09:18: #4 Write output xls file... SRX1453548.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:09:18: #4 Write peak in narrowPeak format file... SRX1453548.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:09:18: #4 Write summits bed file... SRX1453548.20_summits.bed INFO @ Wed, 12 Dec 2018 23:09:18: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (382 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:09:26: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:09:26: #4 Write output xls file... SRX1453548.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:09:26: #4 Write peak in narrowPeak format file... SRX1453548.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:09:26: #4 Write summits bed file... SRX1453548.05_summits.bed INFO @ Wed, 12 Dec 2018 23:09:26: Done! pass1 - making usageList (72 chroms): 3 millis pass2 - checking and writing primary data (3503 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:09:35: #4 Write output xls file... SRX1453548.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:09:35: #4 Write peak in narrowPeak format file... SRX1453548.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:09:35: #4 Write summits bed file... SRX1453548.10_summits.bed INFO @ Wed, 12 Dec 2018 23:09:35: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (888 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。