Job ID = 2590557 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,754,870 reads read : 21,509,740 reads written : 21,509,740 rm: cannot remove ‘[DSE]RR*’: 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: 00:13:35 10754870 reads; of these: 10754870 (100.00%) were paired; of these: 5652740 (52.56%) aligned concordantly 0 times 3770116 (35.05%) aligned concordantly exactly 1 time 1332014 (12.39%) aligned concordantly >1 times ---- 5652740 pairs aligned concordantly 0 times; of these: 20023 (0.35%) aligned discordantly 1 time ---- 5632717 pairs aligned 0 times concordantly or discordantly; of these: 11265434 mates make up the pairs; of these: 10988428 (97.54%) aligned 0 times 186898 (1.66%) aligned exactly 1 time 90108 (0.80%) aligned >1 times 48.91% overall alignment rate Time searching: 00:13:35 Overall time: 00:13:35 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 8 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] 2761432 / 5119181 = 0.5394 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 @ Mon, 12 Aug 2019 22:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.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 @ Mon, 12 Aug 2019 22:41:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:41:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.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 @ Mon, 12 Aug 2019 22:41:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:41:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.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 @ Mon, 12 Aug 2019 22:41:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:41:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:41:39: 1000000 INFO @ Mon, 12 Aug 2019 22:41:40: 1000000 INFO @ Mon, 12 Aug 2019 22:41:42: 1000000 INFO @ Mon, 12 Aug 2019 22:41:48: 2000000 INFO @ Mon, 12 Aug 2019 22:41:48: 2000000 INFO @ Mon, 12 Aug 2019 22:41:53: 2000000 INFO @ Mon, 12 Aug 2019 22:41:56: 3000000 INFO @ Mon, 12 Aug 2019 22:41:57: 3000000 INFO @ Mon, 12 Aug 2019 22:42:04: 4000000 INFO @ Mon, 12 Aug 2019 22:42:04: 3000000 INFO @ Mon, 12 Aug 2019 22:42:06: 4000000 INFO @ Mon, 12 Aug 2019 22:42:11: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:42:11: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:42:11: #1 total tags in treatment: 2346509 INFO @ Mon, 12 Aug 2019 22:42:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:42:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:42:12: #1 tags after filtering in treatment: 2277728 INFO @ Mon, 12 Aug 2019 22:42:12: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 12 Aug 2019 22:42:12: #1 finished! INFO @ Mon, 12 Aug 2019 22:42:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:42:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:42:12: #2 number of paired peaks: 1946 INFO @ Mon, 12 Aug 2019 22:42:12: start model_add_line... INFO @ Mon, 12 Aug 2019 22:42:12: start X-correlation... INFO @ Mon, 12 Aug 2019 22:42:12: end of X-cor INFO @ Mon, 12 Aug 2019 22:42:12: #2 finished! INFO @ Mon, 12 Aug 2019 22:42:12: #2 predicted fragment length is 159 bps INFO @ Mon, 12 Aug 2019 22:42:12: #2 alternative fragment length(s) may be 159 bps INFO @ Mon, 12 Aug 2019 22:42:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.20_model.r INFO @ Mon, 12 Aug 2019 22:42:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:42:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:42:15: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:42:15: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:42:15: #1 total tags in treatment: 2346509 INFO @ Mon, 12 Aug 2019 22:42:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:42:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:42:15: #1 tags after filtering in treatment: 2277728 INFO @ Mon, 12 Aug 2019 22:42:15: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 12 Aug 2019 22:42:15: #1 finished! INFO @ Mon, 12 Aug 2019 22:42:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:42:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:42:15: #2 number of paired peaks: 1946 INFO @ Mon, 12 Aug 2019 22:42:15: start model_add_line... INFO @ Mon, 12 Aug 2019 22:42:15: start X-correlation... INFO @ Mon, 12 Aug 2019 22:42:15: end of X-cor INFO @ Mon, 12 Aug 2019 22:42:15: #2 finished! INFO @ Mon, 12 Aug 2019 22:42:15: #2 predicted fragment length is 159 bps INFO @ Mon, 12 Aug 2019 22:42:15: #2 alternative fragment length(s) may be 159 bps INFO @ Mon, 12 Aug 2019 22:42:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.05_model.r INFO @ Mon, 12 Aug 2019 22:42:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:42:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:42:15: 4000000 INFO @ Mon, 12 Aug 2019 22:42:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:42:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:42:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:42:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.20_summits.bed INFO @ Mon, 12 Aug 2019 22:42:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:42:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:42:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:42:25: #1 total tags in treatment: 2346509 INFO @ Mon, 12 Aug 2019 22:42:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:42:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:42:25: #1 tags after filtering in treatment: 2277728 INFO @ Mon, 12 Aug 2019 22:42:25: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 12 Aug 2019 22:42:25: #1 finished! INFO @ Mon, 12 Aug 2019 22:42:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:42:26: #2 number of paired peaks: 1946 INFO @ Mon, 12 Aug 2019 22:42:26: start model_add_line... INFO @ Mon, 12 Aug 2019 22:42:26: start X-correlation... INFO @ Mon, 12 Aug 2019 22:42:26: end of X-cor INFO @ Mon, 12 Aug 2019 22:42:26: #2 finished! INFO @ Mon, 12 Aug 2019 22:42:26: #2 predicted fragment length is 159 bps INFO @ Mon, 12 Aug 2019 22:42:26: #2 alternative fragment length(s) may be 159 bps INFO @ Mon, 12 Aug 2019 22:42:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.10_model.r INFO @ Mon, 12 Aug 2019 22:42:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:42:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:42:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:42:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:42:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.05_summits.bed INFO @ Mon, 12 Aug 2019 22:42:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1367 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:42:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:42:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:42:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:42:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501949/SRX4501949.10_summits.bed INFO @ Mon, 12 Aug 2019 22:42:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (746 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。