Job ID = 4178410 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 27,099,673 reads read : 54,199,346 reads written : 54,199,346 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: 00:00:01 Multiseed full-index search: 00:18:30 27099673 reads; of these: 27099673 (100.00%) were paired; of these: 14840443 (54.76%) aligned concordantly 0 times 10627273 (39.22%) aligned concordantly exactly 1 time 1631957 (6.02%) aligned concordantly >1 times ---- 14840443 pairs aligned concordantly 0 times; of these: 825157 (5.56%) aligned discordantly 1 time ---- 14015286 pairs aligned 0 times concordantly or discordantly; of these: 28030572 mates make up the pairs; of these: 26986485 (96.28%) aligned 0 times 693817 (2.48%) aligned exactly 1 time 350270 (1.25%) aligned >1 times 50.21% overall alignment rate Time searching: 00:18:32 Overall time: 00:18:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 2278279 / 13070332 = 0.1743 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:07:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 05 Dec 2019 13:07:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:07:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:07:33: 1000000 INFO @ Thu, 05 Dec 2019 13:07:48: 2000000 INFO @ Thu, 05 Dec 2019 13:07:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 05 Dec 2019 13:07:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:07:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:07:59: 3000000 INFO @ Thu, 05 Dec 2019 13:08:03: 1000000 INFO @ Thu, 05 Dec 2019 13:08:08: 4000000 INFO @ Thu, 05 Dec 2019 13:08:10: 2000000 INFO @ Thu, 05 Dec 2019 13:08:17: 5000000 INFO @ Thu, 05 Dec 2019 13:08:18: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:08:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 05 Dec 2019 13:08:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:08:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:08:25: 4000000 INFO @ Thu, 05 Dec 2019 13:08:27: 6000000 INFO @ Thu, 05 Dec 2019 13:08:33: 5000000 INFO @ Thu, 05 Dec 2019 13:08:34: 1000000 INFO @ Thu, 05 Dec 2019 13:08:36: 7000000 INFO @ Thu, 05 Dec 2019 13:08:41: 6000000 INFO @ Thu, 05 Dec 2019 13:08:43: 2000000 INFO @ Thu, 05 Dec 2019 13:08:46: 8000000 INFO @ Thu, 05 Dec 2019 13:08:48: 7000000 INFO @ Thu, 05 Dec 2019 13:08:53: 3000000 INFO @ Thu, 05 Dec 2019 13:08:56: 9000000 INFO @ Thu, 05 Dec 2019 13:08:56: 8000000 INFO @ Thu, 05 Dec 2019 13:09:03: 4000000 INFO @ Thu, 05 Dec 2019 13:09:04: 9000000 INFO @ Thu, 05 Dec 2019 13:09:07: 10000000 INFO @ Thu, 05 Dec 2019 13:09:12: 10000000 INFO @ Thu, 05 Dec 2019 13:09:18: 5000000 INFO @ Thu, 05 Dec 2019 13:09:22: 11000000 INFO @ Thu, 05 Dec 2019 13:09:23: 11000000 INFO @ Thu, 05 Dec 2019 13:09:28: 6000000 INFO @ Thu, 05 Dec 2019 13:09:30: 12000000 INFO @ Thu, 05 Dec 2019 13:09:34: 12000000 INFO @ Thu, 05 Dec 2019 13:09:38: 13000000 INFO @ Thu, 05 Dec 2019 13:09:39: 7000000 INFO @ Thu, 05 Dec 2019 13:09:45: 13000000 INFO @ Thu, 05 Dec 2019 13:09:45: 14000000 INFO @ Thu, 05 Dec 2019 13:09:49: 8000000 INFO @ Thu, 05 Dec 2019 13:09:53: 15000000 INFO @ Thu, 05 Dec 2019 13:09:56: 14000000 INFO @ Thu, 05 Dec 2019 13:09:58: 9000000 INFO @ Thu, 05 Dec 2019 13:10:01: 16000000 INFO @ Thu, 05 Dec 2019 13:10:07: 15000000 INFO @ Thu, 05 Dec 2019 13:10:08: 10000000 INFO @ Thu, 05 Dec 2019 13:10:09: 17000000 INFO @ Thu, 05 Dec 2019 13:10:17: 18000000 INFO @ Thu, 05 Dec 2019 13:10:18: 11000000 INFO @ Thu, 05 Dec 2019 13:10:18: 16000000 INFO @ Thu, 05 Dec 2019 13:10:25: 19000000 INFO @ Thu, 05 Dec 2019 13:10:27: 12000000 INFO @ Thu, 05 Dec 2019 13:10:29: 17000000 INFO @ Thu, 05 Dec 2019 13:10:33: 20000000 INFO @ Thu, 05 Dec 2019 13:10:37: 13000000 INFO @ Thu, 05 Dec 2019 13:10:38: 18000000 INFO @ Thu, 05 Dec 2019 13:10:42: 21000000 INFO @ Thu, 05 Dec 2019 13:10:48: 14000000 INFO @ Thu, 05 Dec 2019 13:10:52: 19000000 INFO @ Thu, 05 Dec 2019 13:10:53: 22000000 INFO @ Thu, 05 Dec 2019 13:10:58: 15000000 INFO @ Thu, 05 Dec 2019 13:11:00: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:11:00: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:11:00: #1 total tags in treatment: 10076073 INFO @ Thu, 05 Dec 2019 13:11:00: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:11:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:11:00: #1 tags after filtering in treatment: 9342448 INFO @ Thu, 05 Dec 2019 13:11:00: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Dec 2019 13:11:00: #1 finished! INFO @ Thu, 05 Dec 2019 13:11:00: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:11:01: #2 number of paired peaks: 405 WARNING @ Thu, 05 Dec 2019 13:11:01: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Thu, 05 Dec 2019 13:11:01: start model_add_line... INFO @ Thu, 05 Dec 2019 13:11:01: start X-correlation... INFO @ Thu, 05 Dec 2019 13:11:01: end of X-cor INFO @ Thu, 05 Dec 2019 13:11:01: #2 finished! INFO @ Thu, 05 Dec 2019 13:11:01: #2 predicted fragment length is 147 bps INFO @ Thu, 05 Dec 2019 13:11:01: #2 alternative fragment length(s) may be 4,147 bps INFO @ Thu, 05 Dec 2019 13:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.10_model.r INFO @ Thu, 05 Dec 2019 13:11:01: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:11:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:11:04: 20000000 INFO @ Thu, 05 Dec 2019 13:11:07: 16000000 INFO @ Thu, 05 Dec 2019 13:11:13: 21000000 INFO @ Thu, 05 Dec 2019 13:11:16: 17000000 INFO @ Thu, 05 Dec 2019 13:11:23: 22000000 INFO @ Thu, 05 Dec 2019 13:11:26: 18000000 INFO @ Thu, 05 Dec 2019 13:11:28: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:11:31: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:11:31: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:11:31: #1 total tags in treatment: 10076073 INFO @ Thu, 05 Dec 2019 13:11:31: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:11:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:11:31: #1 tags after filtering in treatment: 9342448 INFO @ Thu, 05 Dec 2019 13:11:31: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Dec 2019 13:11:31: #1 finished! INFO @ Thu, 05 Dec 2019 13:11:31: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:11:32: #2 number of paired peaks: 405 WARNING @ Thu, 05 Dec 2019 13:11:32: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Thu, 05 Dec 2019 13:11:32: start model_add_line... INFO @ Thu, 05 Dec 2019 13:11:32: start X-correlation... INFO @ Thu, 05 Dec 2019 13:11:32: end of X-cor INFO @ Thu, 05 Dec 2019 13:11:32: #2 finished! INFO @ Thu, 05 Dec 2019 13:11:32: #2 predicted fragment length is 147 bps INFO @ Thu, 05 Dec 2019 13:11:32: #2 alternative fragment length(s) may be 4,147 bps INFO @ Thu, 05 Dec 2019 13:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.05_model.r INFO @ Thu, 05 Dec 2019 13:11:32: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:11:36: 19000000 INFO @ Thu, 05 Dec 2019 13:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.10_summits.bed INFO @ Thu, 05 Dec 2019 13:11:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (269 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:11:46: 20000000 INFO @ Thu, 05 Dec 2019 13:11:56: 21000000 INFO @ Thu, 05 Dec 2019 13:11:59: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:12:05: 22000000 INFO @ Thu, 05 Dec 2019 13:12:11: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:12:11: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:12:11: #1 total tags in treatment: 10076073 INFO @ Thu, 05 Dec 2019 13:12:11: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:12:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:12:12: #1 tags after filtering in treatment: 9342448 INFO @ Thu, 05 Dec 2019 13:12:12: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Dec 2019 13:12:12: #1 finished! INFO @ Thu, 05 Dec 2019 13:12:12: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:12:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:12:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.05_summits.bed INFO @ Thu, 05 Dec 2019 13:12:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (377 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:12:12: #2 number of paired peaks: 405 WARNING @ Thu, 05 Dec 2019 13:12:12: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Thu, 05 Dec 2019 13:12:12: start model_add_line... INFO @ Thu, 05 Dec 2019 13:12:13: start X-correlation... INFO @ Thu, 05 Dec 2019 13:12:13: end of X-cor INFO @ Thu, 05 Dec 2019 13:12:13: #2 finished! INFO @ Thu, 05 Dec 2019 13:12:13: #2 predicted fragment length is 147 bps INFO @ Thu, 05 Dec 2019 13:12:13: #2 alternative fragment length(s) may be 4,147 bps INFO @ Thu, 05 Dec 2019 13:12:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.20_model.r INFO @ Thu, 05 Dec 2019 13:12:13: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:12:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:12:46: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7175089/SRX7175089.20_summits.bed INFO @ Thu, 05 Dec 2019 13:12:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (194 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。