Job ID = 4303116 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 53,639,490 reads read : 107,278,980 reads written : 107,278,980 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1538976.sra.cache’: No such file or directory 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: 01:02:55 53639490 reads; of these: 53639490 (100.00%) were paired; of these: 15897716 (29.64%) aligned concordantly 0 times 32439746 (60.48%) aligned concordantly exactly 1 time 5302028 (9.88%) aligned concordantly >1 times ---- 15897716 pairs aligned concordantly 0 times; of these: 1336470 (8.41%) aligned discordantly 1 time ---- 14561246 pairs aligned 0 times concordantly or discordantly; of these: 29122492 mates make up the pairs; of these: 27841412 (95.60%) aligned 0 times 846906 (2.91%) aligned exactly 1 time 434174 (1.49%) aligned >1 times 74.05% overall alignment rate Time searching: 01:02:55 Overall time: 01:02:55 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 36 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 35277844 / 39059638 = 0.9032 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 02:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.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 @ Thu, 12 Dec 2019 02:06:23: #1 read tag files... INFO @ Thu, 12 Dec 2019 02:06:23: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 02:06:28: 1000000 INFO @ Thu, 12 Dec 2019 02:06:32: 2000000 INFO @ Thu, 12 Dec 2019 02:06:37: 3000000 INFO @ Thu, 12 Dec 2019 02:06:41: 4000000 INFO @ Thu, 12 Dec 2019 02:06:46: 5000000 INFO @ Thu, 12 Dec 2019 02:06:50: 6000000 INFO @ Thu, 12 Dec 2019 02:06:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.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 @ Thu, 12 Dec 2019 02:06:52: #1 read tag files... INFO @ Thu, 12 Dec 2019 02:06:52: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 02:06:55: 7000000 INFO @ Thu, 12 Dec 2019 02:06:57: 1000000 INFO @ Thu, 12 Dec 2019 02:07:00: 8000000 INFO @ Thu, 12 Dec 2019 02:07:02: 2000000 INFO @ Thu, 12 Dec 2019 02:07:05: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 02:07:05: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 02:07:05: #1 total tags in treatment: 3537067 INFO @ Thu, 12 Dec 2019 02:07:05: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 02:07:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 02:07:05: #1 tags after filtering in treatment: 3347461 INFO @ Thu, 12 Dec 2019 02:07:05: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 12 Dec 2019 02:07:05: #1 finished! INFO @ Thu, 12 Dec 2019 02:07:05: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 02:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 02:07:05: #2 number of paired peaks: 2876 INFO @ Thu, 12 Dec 2019 02:07:05: start model_add_line... INFO @ Thu, 12 Dec 2019 02:07:05: start X-correlation... INFO @ Thu, 12 Dec 2019 02:07:05: end of X-cor INFO @ Thu, 12 Dec 2019 02:07:05: #2 finished! INFO @ Thu, 12 Dec 2019 02:07:05: #2 predicted fragment length is 175 bps INFO @ Thu, 12 Dec 2019 02:07:05: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 12 Dec 2019 02:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.05_model.r INFO @ Thu, 12 Dec 2019 02:07:05: #3 Call peaks... INFO @ Thu, 12 Dec 2019 02:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 02:07:07: 3000000 INFO @ Thu, 12 Dec 2019 02:07:11: 4000000 INFO @ Thu, 12 Dec 2019 02:07:13: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 02:07:16: 5000000 INFO @ Thu, 12 Dec 2019 02:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.05_peaks.xls INFO @ Thu, 12 Dec 2019 02:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 02:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.05_summits.bed INFO @ Thu, 12 Dec 2019 02:07:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6342 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 12 Dec 2019 02:07:21: 6000000 INFO @ Thu, 12 Dec 2019 02:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.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 @ Thu, 12 Dec 2019 02:07:22: #1 read tag files... INFO @ Thu, 12 Dec 2019 02:07:22: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 02:07:25: 7000000 INFO @ Thu, 12 Dec 2019 02:07:27: 1000000 INFO @ Thu, 12 Dec 2019 02:07:30: 8000000 INFO @ Thu, 12 Dec 2019 02:07:32: 2000000 INFO @ Thu, 12 Dec 2019 02:07:34: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 02:07:34: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 02:07:34: #1 total tags in treatment: 3537067 INFO @ Thu, 12 Dec 2019 02:07:34: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 02:07:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 02:07:34: #1 tags after filtering in treatment: 3347461 INFO @ Thu, 12 Dec 2019 02:07:34: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 12 Dec 2019 02:07:34: #1 finished! INFO @ Thu, 12 Dec 2019 02:07:34: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 02:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 02:07:34: #2 number of paired peaks: 2876 INFO @ Thu, 12 Dec 2019 02:07:34: start model_add_line... INFO @ Thu, 12 Dec 2019 02:07:34: start X-correlation... INFO @ Thu, 12 Dec 2019 02:07:34: end of X-cor INFO @ Thu, 12 Dec 2019 02:07:34: #2 finished! INFO @ Thu, 12 Dec 2019 02:07:34: #2 predicted fragment length is 175 bps INFO @ Thu, 12 Dec 2019 02:07:34: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 12 Dec 2019 02:07:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.10_model.r INFO @ Thu, 12 Dec 2019 02:07:34: #3 Call peaks... INFO @ Thu, 12 Dec 2019 02:07:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 02:07:37: 3000000 INFO @ Thu, 12 Dec 2019 02:07:41: 4000000 INFO @ Thu, 12 Dec 2019 02:07:42: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 02:07:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.10_peaks.xls INFO @ Thu, 12 Dec 2019 02:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 02:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.10_summits.bed INFO @ Thu, 12 Dec 2019 02:07:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3580 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 02:07:46: 5000000 INFO @ Thu, 12 Dec 2019 02:07:51: 6000000 INFO @ Thu, 12 Dec 2019 02:07:55: 7000000 INFO @ Thu, 12 Dec 2019 02:08:00: 8000000 INFO @ Thu, 12 Dec 2019 02:08:04: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 02:08:04: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 02:08:04: #1 total tags in treatment: 3537067 INFO @ Thu, 12 Dec 2019 02:08:04: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 02:08:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 02:08:04: #1 tags after filtering in treatment: 3347461 INFO @ Thu, 12 Dec 2019 02:08:04: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 12 Dec 2019 02:08:04: #1 finished! INFO @ Thu, 12 Dec 2019 02:08:04: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 02:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 02:08:05: #2 number of paired peaks: 2876 INFO @ Thu, 12 Dec 2019 02:08:05: start model_add_line... INFO @ Thu, 12 Dec 2019 02:08:05: start X-correlation... INFO @ Thu, 12 Dec 2019 02:08:05: end of X-cor INFO @ Thu, 12 Dec 2019 02:08:05: #2 finished! INFO @ Thu, 12 Dec 2019 02:08:05: #2 predicted fragment length is 175 bps INFO @ Thu, 12 Dec 2019 02:08:05: #2 alternative fragment length(s) may be 175 bps INFO @ Thu, 12 Dec 2019 02:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.20_model.r INFO @ Thu, 12 Dec 2019 02:08:05: #3 Call peaks... INFO @ Thu, 12 Dec 2019 02:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 02:08:12: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 02:08:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.20_peaks.xls INFO @ Thu, 12 Dec 2019 02:08:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 02:08:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX671942/SRX671942.20_summits.bed INFO @ Thu, 12 Dec 2019 02:08:16: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1581 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。