Job ID = 9370027 sra ファイルのダウンロード中... Completed: 861792K bytes transferred in 17 seconds (401807K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 6460224 spots for /home/okishinya/chipatlas/results/ce10/SRX2035136/SRR4044260.sra Written 6460224 spots total 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: 00:22:12 6460224 reads; of these: 6460224 (100.00%) were paired; of these: 1826238 (28.27%) aligned concordantly 0 times 4047348 (62.65%) aligned concordantly exactly 1 time 586638 (9.08%) aligned concordantly >1 times ---- 1826238 pairs aligned concordantly 0 times; of these: 524361 (28.71%) aligned discordantly 1 time ---- 1301877 pairs aligned 0 times concordantly or discordantly; of these: 2603754 mates make up the pairs; of these: 2398080 (92.10%) aligned 0 times 84436 (3.24%) aligned exactly 1 time 121238 (4.66%) aligned >1 times 81.44% overall alignment rate Time searching: 00:22:12 Overall time: 00:22:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 380035 / 5153924 = 0.0737 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, 04 Aug 2017 12:23:14: # Command line: callpeak -t SRX2035136.bam -f BAM -g ce -n SRX2035136.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2035136.10 # format = BAM # ChIP-seq file = ['SRX2035136.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Aug 2017 12:23:14: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:23:14: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:23:14: # Command line: callpeak -t SRX2035136.bam -f BAM -g ce -n SRX2035136.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2035136.05 # format = BAM # ChIP-seq file = ['SRX2035136.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Aug 2017 12:23:14: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:23:14: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:23:14: # Command line: callpeak -t SRX2035136.bam -f BAM -g ce -n SRX2035136.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2035136.20 # format = BAM # ChIP-seq file = ['SRX2035136.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Aug 2017 12:23:14: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:23:14: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:23:30: 1000000 INFO @ Fri, 04 Aug 2017 12:23:30: 1000000 INFO @ Fri, 04 Aug 2017 12:23:31: 1000000 INFO @ Fri, 04 Aug 2017 12:23:45: 2000000 INFO @ Fri, 04 Aug 2017 12:23:49: 2000000 INFO @ Fri, 04 Aug 2017 12:23:50: 2000000 INFO @ Fri, 04 Aug 2017 12:24:01: 3000000 INFO @ Fri, 04 Aug 2017 12:24:08: 3000000 INFO @ Fri, 04 Aug 2017 12:24:08: 3000000 INFO @ Fri, 04 Aug 2017 12:24:16: 4000000 INFO @ Fri, 04 Aug 2017 12:24:23: 4000000 INFO @ Fri, 04 Aug 2017 12:24:25: 4000000 INFO @ Fri, 04 Aug 2017 12:24:30: 5000000 INFO @ Fri, 04 Aug 2017 12:24:37: 5000000 INFO @ Fri, 04 Aug 2017 12:24:38: 5000000 INFO @ Fri, 04 Aug 2017 12:24:45: 6000000 INFO @ Fri, 04 Aug 2017 12:24:47: 6000000 INFO @ Fri, 04 Aug 2017 12:24:48: 6000000 INFO @ Fri, 04 Aug 2017 12:25:00: 7000000 INFO @ Fri, 04 Aug 2017 12:25:00: 7000000 INFO @ Fri, 04 Aug 2017 12:25:05: 7000000 INFO @ Fri, 04 Aug 2017 12:25:11: 8000000 INFO @ Fri, 04 Aug 2017 12:25:15: 8000000 INFO @ Fri, 04 Aug 2017 12:25:22: 8000000 INFO @ Fri, 04 Aug 2017 12:25:30: 9000000 INFO @ Fri, 04 Aug 2017 12:25:31: 9000000 INFO @ Fri, 04 Aug 2017 12:25:40: 9000000 INFO @ Fri, 04 Aug 2017 12:25:43: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:25:43: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:25:43: #1 total tags in treatment: 4270386 INFO @ Fri, 04 Aug 2017 12:25:43: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:25:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:25:43: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:25:43: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:25:43: #1 total tags in treatment: 4270386 INFO @ Fri, 04 Aug 2017 12:25:43: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:25:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:25:43: #1 tags after filtering in treatment: 3947450 INFO @ Fri, 04 Aug 2017 12:25:43: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 04 Aug 2017 12:25:43: #1 finished! INFO @ Fri, 04 Aug 2017 12:25:43: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:25:43: #1 tags after filtering in treatment: 3947450 INFO @ Fri, 04 Aug 2017 12:25:43: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 04 Aug 2017 12:25:43: #1 finished! INFO @ Fri, 04 Aug 2017 12:25:43: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:25:44: #2 number of paired peaks: 3427 INFO @ Fri, 04 Aug 2017 12:25:44: start model_add_line... INFO @ Fri, 04 Aug 2017 12:25:44: #2 number of paired peaks: 3427 INFO @ Fri, 04 Aug 2017 12:25:44: start model_add_line... INFO @ Fri, 04 Aug 2017 12:25:44: start X-correlation... INFO @ Fri, 04 Aug 2017 12:25:44: end of X-cor INFO @ Fri, 04 Aug 2017 12:25:44: #2 finished! INFO @ Fri, 04 Aug 2017 12:25:44: #2 predicted fragment length is 282 bps INFO @ Fri, 04 Aug 2017 12:25:44: #2 alternative fragment length(s) may be 282 bps INFO @ Fri, 04 Aug 2017 12:25:44: #2.2 Generate R script for model : SRX2035136.20_model.r INFO @ Fri, 04 Aug 2017 12:25:44: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:25:44: start X-correlation... INFO @ Fri, 04 Aug 2017 12:25:44: end of X-cor INFO @ Fri, 04 Aug 2017 12:25:44: #2 finished! INFO @ Fri, 04 Aug 2017 12:25:44: #2 predicted fragment length is 282 bps INFO @ Fri, 04 Aug 2017 12:25:44: #2 alternative fragment length(s) may be 282 bps INFO @ Fri, 04 Aug 2017 12:25:44: #2.2 Generate R script for model : SRX2035136.10_model.r INFO @ Fri, 04 Aug 2017 12:25:44: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:25:50: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:25:50: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:25:50: #1 total tags in treatment: 4270386 INFO @ Fri, 04 Aug 2017 12:25:50: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:25:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:25:50: #1 tags after filtering in treatment: 3947450 INFO @ Fri, 04 Aug 2017 12:25:50: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 04 Aug 2017 12:25:50: #1 finished! INFO @ Fri, 04 Aug 2017 12:25:50: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:25:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:25:51: #2 number of paired peaks: 3427 INFO @ Fri, 04 Aug 2017 12:25:51: start model_add_line... INFO @ Fri, 04 Aug 2017 12:25:51: start X-correlation... INFO @ Fri, 04 Aug 2017 12:25:51: end of X-cor INFO @ Fri, 04 Aug 2017 12:25:51: #2 finished! INFO @ Fri, 04 Aug 2017 12:25:51: #2 predicted fragment length is 282 bps INFO @ Fri, 04 Aug 2017 12:25:51: #2 alternative fragment length(s) may be 282 bps INFO @ Fri, 04 Aug 2017 12:25:51: #2.2 Generate R script for model : SRX2035136.05_model.r INFO @ Fri, 04 Aug 2017 12:25:51: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:25:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:26:02: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:26:02: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:26:10: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:26:11: #4 Write output xls file... SRX2035136.20_peaks.xls INFO @ Fri, 04 Aug 2017 12:26:11: #4 Write peak in narrowPeak format file... SRX2035136.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:26:11: #4 Write summits bed file... SRX2035136.20_summits.bed INFO @ Fri, 04 Aug 2017 12:26:11: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2021 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:26:13: #4 Write output xls file... SRX2035136.10_peaks.xls INFO @ Fri, 04 Aug 2017 12:26:13: #4 Write peak in narrowPeak format file... SRX2035136.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:26:13: #4 Write summits bed file... SRX2035136.10_summits.bed INFO @ Fri, 04 Aug 2017 12:26:13: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2572 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:26:20: #4 Write output xls file... SRX2035136.05_peaks.xls INFO @ Fri, 04 Aug 2017 12:26:20: #4 Write peak in narrowPeak format file... SRX2035136.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:26:20: #4 Write summits bed file... SRX2035136.05_summits.bed INFO @ Fri, 04 Aug 2017 12:26:20: Done! pass1 - making usageList (6 chroms): 7 millis pass2 - checking and writing primary data (3132 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。