Job ID = 4303139 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 17,551,502 reads read : 35,103,004 reads written : 35,103,004 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1554222.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: 00:05:11 17551502 reads; of these: 17551502 (100.00%) were paired; of these: 15472769 (88.16%) aligned concordantly 0 times 1658018 (9.45%) aligned concordantly exactly 1 time 420715 (2.40%) aligned concordantly >1 times ---- 15472769 pairs aligned concordantly 0 times; of these: 253663 (1.64%) aligned discordantly 1 time ---- 15219106 pairs aligned 0 times concordantly or discordantly; of these: 30438212 mates make up the pairs; of these: 30158601 (99.08%) aligned 0 times 188620 (0.62%) aligned exactly 1 time 90991 (0.30%) aligned >1 times 14.09% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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_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] 1766463 / 2330291 = 0.7580 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:57:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.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 00:57:04: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:57:04: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:57:08: 1000000 INFO @ Thu, 12 Dec 2019 00:57:09: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 00:57:09: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 00:57:09: #1 total tags in treatment: 479142 INFO @ Thu, 12 Dec 2019 00:57:09: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:57:09: #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 00:57:09: #1 tags after filtering in treatment: 459187 INFO @ Thu, 12 Dec 2019 00:57:09: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 12 Dec 2019 00:57:09: #1 finished! INFO @ Thu, 12 Dec 2019 00:57:09: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:57:09: #2 number of paired peaks: 2737 INFO @ Thu, 12 Dec 2019 00:57:09: start model_add_line... INFO @ Thu, 12 Dec 2019 00:57:09: start X-correlation... INFO @ Thu, 12 Dec 2019 00:57:09: end of X-cor INFO @ Thu, 12 Dec 2019 00:57:09: #2 finished! INFO @ Thu, 12 Dec 2019 00:57:09: #2 predicted fragment length is 174 bps INFO @ Thu, 12 Dec 2019 00:57:09: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 12 Dec 2019 00:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.05_model.r INFO @ Thu, 12 Dec 2019 00:57:09: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:57:10: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.05_summits.bed INFO @ Thu, 12 Dec 2019 00:57:10: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1015 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:57:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.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 00:57:34: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:57:34: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:57:38: 1000000 INFO @ Thu, 12 Dec 2019 00:57:39: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 00:57:39: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 00:57:39: #1 total tags in treatment: 479142 INFO @ Thu, 12 Dec 2019 00:57:39: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:57:39: #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 00:57:39: #1 tags after filtering in treatment: 459187 INFO @ Thu, 12 Dec 2019 00:57:39: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 12 Dec 2019 00:57:39: #1 finished! INFO @ Thu, 12 Dec 2019 00:57:39: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:57:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:57:39: #2 number of paired peaks: 2737 INFO @ Thu, 12 Dec 2019 00:57:39: start model_add_line... INFO @ Thu, 12 Dec 2019 00:57:39: start X-correlation... INFO @ Thu, 12 Dec 2019 00:57:39: end of X-cor INFO @ Thu, 12 Dec 2019 00:57:39: #2 finished! INFO @ Thu, 12 Dec 2019 00:57:39: #2 predicted fragment length is 174 bps INFO @ Thu, 12 Dec 2019 00:57:39: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 12 Dec 2019 00:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.10_model.r INFO @ Thu, 12 Dec 2019 00:57:39: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:57:40: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:57:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:57:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:57:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.10_summits.bed INFO @ Thu, 12 Dec 2019 00:57:40: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (506 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.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 00:58:04: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:58:04: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:58:08: 1000000 INFO @ Thu, 12 Dec 2019 00:58:09: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 00:58:09: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 00:58:09: #1 total tags in treatment: 479142 INFO @ Thu, 12 Dec 2019 00:58:09: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:58:09: #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 00:58:09: #1 tags after filtering in treatment: 459187 INFO @ Thu, 12 Dec 2019 00:58:09: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 12 Dec 2019 00:58:09: #1 finished! INFO @ Thu, 12 Dec 2019 00:58:09: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:58:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:58:10: #2 number of paired peaks: 2737 INFO @ Thu, 12 Dec 2019 00:58:10: start model_add_line... INFO @ Thu, 12 Dec 2019 00:58:10: start X-correlation... INFO @ Thu, 12 Dec 2019 00:58:10: end of X-cor INFO @ Thu, 12 Dec 2019 00:58:10: #2 finished! INFO @ Thu, 12 Dec 2019 00:58:10: #2 predicted fragment length is 174 bps INFO @ Thu, 12 Dec 2019 00:58:10: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 12 Dec 2019 00:58:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.20_model.r INFO @ Thu, 12 Dec 2019 00:58:10: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:58:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:58:10: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:58:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:58:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:58:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX683496/SRX683496.20_summits.bed INFO @ Thu, 12 Dec 2019 00:58:11: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。