Job ID = 2590562 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,156,385 reads read : 12,312,770 reads written : 12,312,770 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: 00:18:04 6156385 reads; of these: 6156385 (100.00%) were paired; of these: 1243351 (20.20%) aligned concordantly 0 times 3355427 (54.50%) aligned concordantly exactly 1 time 1557607 (25.30%) aligned concordantly >1 times ---- 1243351 pairs aligned concordantly 0 times; of these: 104172 (8.38%) aligned discordantly 1 time ---- 1139179 pairs aligned 0 times concordantly or discordantly; of these: 2278358 mates make up the pairs; of these: 1770651 (77.72%) aligned 0 times 275985 (12.11%) aligned exactly 1 time 231722 (10.17%) aligned >1 times 85.62% overall alignment rate Time searching: 00:18:04 Overall time: 00:18:04 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] 1021674 / 5005193 = 0.2041 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 22:50:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.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 22:50:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:50:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.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 22:50:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:50:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:50:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.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 22:50:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:50:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:50:51: 1000000 INFO @ Mon, 12 Aug 2019 22:50:52: 1000000 INFO @ Mon, 12 Aug 2019 22:50:53: 1000000 INFO @ Mon, 12 Aug 2019 22:50:57: 2000000 INFO @ Mon, 12 Aug 2019 22:50:58: 2000000 INFO @ Mon, 12 Aug 2019 22:51:01: 2000000 INFO @ Mon, 12 Aug 2019 22:51:04: 3000000 INFO @ Mon, 12 Aug 2019 22:51:05: 3000000 INFO @ Mon, 12 Aug 2019 22:51:08: 3000000 INFO @ Mon, 12 Aug 2019 22:51:11: 4000000 INFO @ Mon, 12 Aug 2019 22:51:12: 4000000 INFO @ Mon, 12 Aug 2019 22:51:16: 4000000 INFO @ Mon, 12 Aug 2019 22:51:18: 5000000 INFO @ Mon, 12 Aug 2019 22:51:19: 5000000 INFO @ Mon, 12 Aug 2019 22:51:24: 5000000 INFO @ Mon, 12 Aug 2019 22:51:25: 6000000 INFO @ Mon, 12 Aug 2019 22:51:26: 6000000 INFO @ Mon, 12 Aug 2019 22:51:31: 6000000 INFO @ Mon, 12 Aug 2019 22:51:31: 7000000 INFO @ Mon, 12 Aug 2019 22:51:32: 7000000 INFO @ Mon, 12 Aug 2019 22:51:38: 8000000 INFO @ Mon, 12 Aug 2019 22:51:39: 7000000 INFO @ Mon, 12 Aug 2019 22:51:39: 8000000 INFO @ Mon, 12 Aug 2019 22:51:42: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:51:42: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:51:42: #1 total tags in treatment: 3902368 INFO @ Mon, 12 Aug 2019 22:51:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:51:42: #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 22:51:42: #1 tags after filtering in treatment: 3314534 INFO @ Mon, 12 Aug 2019 22:51:42: #1 Redundant rate of treatment: 0.15 INFO @ Mon, 12 Aug 2019 22:51:42: #1 finished! INFO @ Mon, 12 Aug 2019 22:51:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:51:42: #2 number of paired peaks: 4353 INFO @ Mon, 12 Aug 2019 22:51:42: start model_add_line... INFO @ Mon, 12 Aug 2019 22:51:42: start X-correlation... INFO @ Mon, 12 Aug 2019 22:51:42: end of X-cor INFO @ Mon, 12 Aug 2019 22:51:42: #2 finished! INFO @ Mon, 12 Aug 2019 22:51:42: #2 predicted fragment length is 185 bps INFO @ Mon, 12 Aug 2019 22:51:42: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 12 Aug 2019 22:51:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.05_model.r INFO @ Mon, 12 Aug 2019 22:51:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:51:42: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:51:42: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:51:42: #1 total tags in treatment: 3902368 INFO @ Mon, 12 Aug 2019 22:51:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:51:42: #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 22:51:43: #1 tags after filtering in treatment: 3314534 INFO @ Mon, 12 Aug 2019 22:51:43: #1 Redundant rate of treatment: 0.15 INFO @ Mon, 12 Aug 2019 22:51:43: #1 finished! INFO @ Mon, 12 Aug 2019 22:51:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:51:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:51:43: #2 number of paired peaks: 4353 INFO @ Mon, 12 Aug 2019 22:51:43: start model_add_line... INFO @ Mon, 12 Aug 2019 22:51:43: start X-correlation... INFO @ Mon, 12 Aug 2019 22:51:43: end of X-cor INFO @ Mon, 12 Aug 2019 22:51:43: #2 finished! INFO @ Mon, 12 Aug 2019 22:51:43: #2 predicted fragment length is 185 bps INFO @ Mon, 12 Aug 2019 22:51:43: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 12 Aug 2019 22:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.10_model.r INFO @ Mon, 12 Aug 2019 22:51:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:51:46: 8000000 INFO @ Mon, 12 Aug 2019 22:51:50: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:51:50: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:51:50: #1 total tags in treatment: 3902368 INFO @ Mon, 12 Aug 2019 22:51:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:51:50: #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 22:51:50: #1 tags after filtering in treatment: 3314534 INFO @ Mon, 12 Aug 2019 22:51:50: #1 Redundant rate of treatment: 0.15 INFO @ Mon, 12 Aug 2019 22:51:50: #1 finished! INFO @ Mon, 12 Aug 2019 22:51:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:51:50: #2 number of paired peaks: 4353 INFO @ Mon, 12 Aug 2019 22:51:50: start model_add_line... INFO @ Mon, 12 Aug 2019 22:51:50: start X-correlation... INFO @ Mon, 12 Aug 2019 22:51:50: end of X-cor INFO @ Mon, 12 Aug 2019 22:51:50: #2 finished! INFO @ Mon, 12 Aug 2019 22:51:50: #2 predicted fragment length is 185 bps INFO @ Mon, 12 Aug 2019 22:51:50: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 12 Aug 2019 22:51:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.20_model.r INFO @ Mon, 12 Aug 2019 22:51:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:51:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:51:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:52:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:52:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:52:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.05_summits.bed INFO @ Mon, 12 Aug 2019 22:52:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7269 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:52:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:52:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:52:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.10_summits.bed INFO @ Mon, 12 Aug 2019 22:52:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4394 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:52:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501952/SRX4501952.20_summits.bed INFO @ Mon, 12 Aug 2019 22:52:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2458 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。