Job ID = 1293654 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,143,797 reads read : 23,143,797 reads written : 23,143,797 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: 00:06:29 23143797 reads; of these: 23143797 (100.00%) were unpaired; of these: 880151 (3.80%) aligned 0 times 17315423 (74.82%) aligned exactly 1 time 4948223 (21.38%) aligned >1 times 96.20% overall alignment rate Time searching: 00:06:29 Overall time: 00:06:29 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_rmdupse_core] 3335623 / 22263646 = 0.1498 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 01:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.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 01:36:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:36:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.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 01:36:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:36:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.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 01:36:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:36:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:36:17: 1000000 INFO @ Mon, 03 Jun 2019 01:36:20: 1000000 INFO @ Mon, 03 Jun 2019 01:36:21: 1000000 INFO @ Mon, 03 Jun 2019 01:36:26: 2000000 INFO @ Mon, 03 Jun 2019 01:36:32: 2000000 INFO @ Mon, 03 Jun 2019 01:36:32: 2000000 INFO @ Mon, 03 Jun 2019 01:36:35: 3000000 INFO @ Mon, 03 Jun 2019 01:36:43: 3000000 INFO @ Mon, 03 Jun 2019 01:36:43: 3000000 INFO @ Mon, 03 Jun 2019 01:36:44: 4000000 INFO @ Mon, 03 Jun 2019 01:36:52: 5000000 INFO @ Mon, 03 Jun 2019 01:36:54: 4000000 INFO @ Mon, 03 Jun 2019 01:36:54: 4000000 INFO @ Mon, 03 Jun 2019 01:37:01: 6000000 INFO @ Mon, 03 Jun 2019 01:37:05: 5000000 INFO @ Mon, 03 Jun 2019 01:37:05: 5000000 INFO @ Mon, 03 Jun 2019 01:37:10: 7000000 INFO @ Mon, 03 Jun 2019 01:37:15: 6000000 INFO @ Mon, 03 Jun 2019 01:37:16: 6000000 INFO @ Mon, 03 Jun 2019 01:37:19: 8000000 INFO @ Mon, 03 Jun 2019 01:37:26: 7000000 INFO @ Mon, 03 Jun 2019 01:37:27: 9000000 INFO @ Mon, 03 Jun 2019 01:37:28: 7000000 INFO @ Mon, 03 Jun 2019 01:37:36: 8000000 INFO @ Mon, 03 Jun 2019 01:37:36: 10000000 INFO @ Mon, 03 Jun 2019 01:37:39: 8000000 INFO @ Mon, 03 Jun 2019 01:37:44: 11000000 INFO @ Mon, 03 Jun 2019 01:37:46: 9000000 INFO @ Mon, 03 Jun 2019 01:37:49: 9000000 INFO @ Mon, 03 Jun 2019 01:37:53: 12000000 INFO @ Mon, 03 Jun 2019 01:37:55: 10000000 INFO @ Mon, 03 Jun 2019 01:38:00: 10000000 INFO @ Mon, 03 Jun 2019 01:38:01: 13000000 INFO @ Mon, 03 Jun 2019 01:38:06: 11000000 INFO @ Mon, 03 Jun 2019 01:38:09: 14000000 INFO @ Mon, 03 Jun 2019 01:38:10: 11000000 INFO @ Mon, 03 Jun 2019 01:38:16: 12000000 INFO @ Mon, 03 Jun 2019 01:38:16: 15000000 INFO @ Mon, 03 Jun 2019 01:38:20: 12000000 INFO @ Mon, 03 Jun 2019 01:38:24: 16000000 INFO @ Mon, 03 Jun 2019 01:38:26: 13000000 INFO @ Mon, 03 Jun 2019 01:38:31: 13000000 INFO @ Mon, 03 Jun 2019 01:38:31: 17000000 INFO @ Mon, 03 Jun 2019 01:38:36: 14000000 INFO @ Mon, 03 Jun 2019 01:38:38: 18000000 INFO @ Mon, 03 Jun 2019 01:38:41: 14000000 INFO @ Mon, 03 Jun 2019 01:38:45: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:38:45: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:38:45: #1 total tags in treatment: 18928023 INFO @ Mon, 03 Jun 2019 01:38:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:38:45: #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 01:38:45: 15000000 INFO @ Mon, 03 Jun 2019 01:38:46: #1 tags after filtering in treatment: 18928023 INFO @ Mon, 03 Jun 2019 01:38:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:38:46: #1 finished! INFO @ Mon, 03 Jun 2019 01:38:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:38:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:38:48: #2 number of paired peaks: 893 WARNING @ Mon, 03 Jun 2019 01:38:48: Fewer paired peaks (893) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 893 pairs to build model! INFO @ Mon, 03 Jun 2019 01:38:48: start model_add_line... INFO @ Mon, 03 Jun 2019 01:38:48: start X-correlation... INFO @ Mon, 03 Jun 2019 01:38:48: end of X-cor INFO @ Mon, 03 Jun 2019 01:38:48: #2 finished! INFO @ Mon, 03 Jun 2019 01:38:48: #2 predicted fragment length is 160 bps INFO @ Mon, 03 Jun 2019 01:38:48: #2 alternative fragment length(s) may be 4,160 bps INFO @ Mon, 03 Jun 2019 01:38:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.20_model.r INFO @ Mon, 03 Jun 2019 01:38:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:38:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:38:51: 15000000 INFO @ Mon, 03 Jun 2019 01:38:55: 16000000 INFO @ Mon, 03 Jun 2019 01:39:01: 16000000 INFO @ Mon, 03 Jun 2019 01:39:05: 17000000 INFO @ Mon, 03 Jun 2019 01:39:12: 17000000 INFO @ Mon, 03 Jun 2019 01:39:14: 18000000 INFO @ Mon, 03 Jun 2019 01:39:22: 18000000 INFO @ Mon, 03 Jun 2019 01:39:23: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:39:23: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:39:23: #1 total tags in treatment: 18928023 INFO @ Mon, 03 Jun 2019 01:39:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:39:23: #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 01:39:23: #1 tags after filtering in treatment: 18928023 INFO @ Mon, 03 Jun 2019 01:39:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:39:23: #1 finished! INFO @ Mon, 03 Jun 2019 01:39:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:39:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:39:25: #2 number of paired peaks: 893 WARNING @ Mon, 03 Jun 2019 01:39:25: Fewer paired peaks (893) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 893 pairs to build model! INFO @ Mon, 03 Jun 2019 01:39:25: start model_add_line... INFO @ Mon, 03 Jun 2019 01:39:25: start X-correlation... INFO @ Mon, 03 Jun 2019 01:39:25: end of X-cor INFO @ Mon, 03 Jun 2019 01:39:25: #2 finished! INFO @ Mon, 03 Jun 2019 01:39:25: #2 predicted fragment length is 160 bps INFO @ Mon, 03 Jun 2019 01:39:25: #2 alternative fragment length(s) may be 4,160 bps INFO @ Mon, 03 Jun 2019 01:39:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.10_model.r INFO @ Mon, 03 Jun 2019 01:39:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:39:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:39:31: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:39:31: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:39:31: #1 total tags in treatment: 18928023 INFO @ Mon, 03 Jun 2019 01:39:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:39:31: #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 01:39:31: #1 tags after filtering in treatment: 18928023 INFO @ Mon, 03 Jun 2019 01:39:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:39:31: #1 finished! INFO @ Mon, 03 Jun 2019 01:39:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:39:33: #2 number of paired peaks: 893 WARNING @ Mon, 03 Jun 2019 01:39:33: Fewer paired peaks (893) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 893 pairs to build model! INFO @ Mon, 03 Jun 2019 01:39:33: start model_add_line... INFO @ Mon, 03 Jun 2019 01:39:33: start X-correlation... INFO @ Mon, 03 Jun 2019 01:39:33: end of X-cor INFO @ Mon, 03 Jun 2019 01:39:33: #2 finished! INFO @ Mon, 03 Jun 2019 01:39:33: #2 predicted fragment length is 160 bps INFO @ Mon, 03 Jun 2019 01:39:33: #2 alternative fragment length(s) may be 4,160 bps INFO @ Mon, 03 Jun 2019 01:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.05_model.r INFO @ Mon, 03 Jun 2019 01:39:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:39:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:40:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:40:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:40:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.20_summits.bed INFO @ Mon, 03 Jun 2019 01:40:06: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (219 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:40:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:40:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:40:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:40:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:40:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.10_summits.bed INFO @ Mon, 03 Jun 2019 01:40:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:40:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:40:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:40:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104967/SRX104967.05_summits.bed INFO @ Mon, 03 Jun 2019 01:40:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2548 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。