Job ID = 1295647 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,423,883 reads read : 42,847,766 reads written : 42,847,766 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:50:36 21423883 reads; of these: 21423883 (100.00%) were paired; of these: 1559257 (7.28%) aligned concordantly 0 times 15032756 (70.17%) aligned concordantly exactly 1 time 4831870 (22.55%) aligned concordantly >1 times ---- 1559257 pairs aligned concordantly 0 times; of these: 193443 (12.41%) aligned discordantly 1 time ---- 1365814 pairs aligned 0 times concordantly or discordantly; of these: 2731628 mates make up the pairs; of these: 1440758 (52.74%) aligned 0 times 730994 (26.76%) aligned exactly 1 time 559876 (20.50%) aligned >1 times 96.64% overall alignment rate Time searching: 00:50:36 Overall time: 00:50:36 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 20 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] 12560631 / 19982269 = 0.6286 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, 03 Jun 2019 16:13:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.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, 03 Jun 2019 16:13:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:13:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:13:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.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, 03 Jun 2019 16:13:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:13:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:13:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.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, 03 Jun 2019 16:13:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:13:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:13:21: 1000000 INFO @ Mon, 03 Jun 2019 16:13:22: 1000000 INFO @ Mon, 03 Jun 2019 16:13:23: 1000000 INFO @ Mon, 03 Jun 2019 16:13:29: 2000000 INFO @ Mon, 03 Jun 2019 16:13:29: 2000000 INFO @ Mon, 03 Jun 2019 16:13:31: 2000000 INFO @ Mon, 03 Jun 2019 16:13:36: 3000000 INFO @ Mon, 03 Jun 2019 16:13:36: 3000000 INFO @ Mon, 03 Jun 2019 16:13:39: 3000000 INFO @ Mon, 03 Jun 2019 16:13:43: 4000000 INFO @ Mon, 03 Jun 2019 16:13:44: 4000000 INFO @ Mon, 03 Jun 2019 16:13:47: 4000000 INFO @ Mon, 03 Jun 2019 16:13:51: 5000000 INFO @ Mon, 03 Jun 2019 16:13:52: 5000000 INFO @ Mon, 03 Jun 2019 16:13:55: 5000000 INFO @ Mon, 03 Jun 2019 16:13:58: 6000000 INFO @ Mon, 03 Jun 2019 16:14:00: 6000000 INFO @ Mon, 03 Jun 2019 16:14:03: 6000000 INFO @ Mon, 03 Jun 2019 16:14:05: 7000000 INFO @ Mon, 03 Jun 2019 16:14:06: 7000000 INFO @ Mon, 03 Jun 2019 16:14:11: 7000000 INFO @ Mon, 03 Jun 2019 16:14:12: 8000000 INFO @ Mon, 03 Jun 2019 16:14:13: 8000000 INFO @ Mon, 03 Jun 2019 16:14:18: 8000000 INFO @ Mon, 03 Jun 2019 16:14:18: 9000000 INFO @ Mon, 03 Jun 2019 16:14:20: 9000000 INFO @ Mon, 03 Jun 2019 16:14:25: 10000000 INFO @ Mon, 03 Jun 2019 16:14:26: 9000000 INFO @ Mon, 03 Jun 2019 16:14:27: 10000000 INFO @ Mon, 03 Jun 2019 16:14:32: 11000000 INFO @ Mon, 03 Jun 2019 16:14:34: 10000000 INFO @ Mon, 03 Jun 2019 16:14:34: 11000000 INFO @ Mon, 03 Jun 2019 16:14:39: 12000000 INFO @ Mon, 03 Jun 2019 16:14:41: 12000000 INFO @ Mon, 03 Jun 2019 16:14:42: 11000000 INFO @ Mon, 03 Jun 2019 16:14:46: 13000000 INFO @ Mon, 03 Jun 2019 16:14:48: 13000000 INFO @ Mon, 03 Jun 2019 16:14:49: 12000000 INFO @ Mon, 03 Jun 2019 16:14:53: 14000000 INFO @ Mon, 03 Jun 2019 16:14:55: 14000000 INFO @ Mon, 03 Jun 2019 16:14:57: 13000000 INFO @ Mon, 03 Jun 2019 16:15:00: 15000000 INFO @ Mon, 03 Jun 2019 16:15:02: 15000000 INFO @ Mon, 03 Jun 2019 16:15:05: 14000000 INFO @ Mon, 03 Jun 2019 16:15:07: 16000000 INFO @ Mon, 03 Jun 2019 16:15:09: 16000000 INFO @ Mon, 03 Jun 2019 16:15:09: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:15:09: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:15:09: #1 total tags in treatment: 7370004 INFO @ Mon, 03 Jun 2019 16:15:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:15:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:15:09: #1 tags after filtering in treatment: 6135105 INFO @ Mon, 03 Jun 2019 16:15:09: #1 Redundant rate of treatment: 0.17 INFO @ Mon, 03 Jun 2019 16:15:09: #1 finished! INFO @ Mon, 03 Jun 2019 16:15:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:15:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:15:10: #2 number of paired peaks: 4844 INFO @ Mon, 03 Jun 2019 16:15:10: start model_add_line... INFO @ Mon, 03 Jun 2019 16:15:11: start X-correlation... INFO @ Mon, 03 Jun 2019 16:15:11: end of X-cor INFO @ Mon, 03 Jun 2019 16:15:11: #2 finished! INFO @ Mon, 03 Jun 2019 16:15:11: #2 predicted fragment length is 227 bps INFO @ Mon, 03 Jun 2019 16:15:11: #2 alternative fragment length(s) may be 227 bps INFO @ Mon, 03 Jun 2019 16:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.10_model.r INFO @ Mon, 03 Jun 2019 16:15:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:15:11: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:15:11: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:15:11: #1 total tags in treatment: 7370004 INFO @ Mon, 03 Jun 2019 16:15:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:15:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:15:11: #1 tags after filtering in treatment: 6135105 INFO @ Mon, 03 Jun 2019 16:15:11: #1 Redundant rate of treatment: 0.17 INFO @ Mon, 03 Jun 2019 16:15:11: #1 finished! INFO @ Mon, 03 Jun 2019 16:15:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:15:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:15:12: #2 number of paired peaks: 4844 INFO @ Mon, 03 Jun 2019 16:15:12: start model_add_line... INFO @ Mon, 03 Jun 2019 16:15:12: start X-correlation... INFO @ Mon, 03 Jun 2019 16:15:12: end of X-cor INFO @ Mon, 03 Jun 2019 16:15:12: #2 finished! INFO @ Mon, 03 Jun 2019 16:15:12: #2 predicted fragment length is 227 bps INFO @ Mon, 03 Jun 2019 16:15:12: #2 alternative fragment length(s) may be 227 bps INFO @ Mon, 03 Jun 2019 16:15:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.20_model.r INFO @ Mon, 03 Jun 2019 16:15:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:15:12: 15000000 INFO @ Mon, 03 Jun 2019 16:15:20: 16000000 INFO @ Mon, 03 Jun 2019 16:15:22: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:15:22: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:15:22: #1 total tags in treatment: 7370004 INFO @ Mon, 03 Jun 2019 16:15:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:15:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 16:15:22: #1 tags after filtering in treatment: 6135105 INFO @ Mon, 03 Jun 2019 16:15:22: #1 Redundant rate of treatment: 0.17 INFO @ Mon, 03 Jun 2019 16:15:22: #1 finished! INFO @ Mon, 03 Jun 2019 16:15:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:15:23: #2 number of paired peaks: 4844 INFO @ Mon, 03 Jun 2019 16:15:23: start model_add_line... INFO @ Mon, 03 Jun 2019 16:15:23: start X-correlation... INFO @ Mon, 03 Jun 2019 16:15:23: end of X-cor INFO @ Mon, 03 Jun 2019 16:15:23: #2 finished! INFO @ Mon, 03 Jun 2019 16:15:23: #2 predicted fragment length is 227 bps INFO @ Mon, 03 Jun 2019 16:15:23: #2 alternative fragment length(s) may be 227 bps INFO @ Mon, 03 Jun 2019 16:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.05_model.r INFO @ Mon, 03 Jun 2019 16:15:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:15:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:15:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:15:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:15:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:15:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:15:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.10_summits.bed INFO @ Mon, 03 Jun 2019 16:15:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3892 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:15:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:15:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.20_summits.bed INFO @ Mon, 03 Jun 2019 16:15:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2182 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:15:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:15:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:15:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:15:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3960604/SRX3960604.05_summits.bed INFO @ Mon, 03 Jun 2019 16:15:58: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5912 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。