Job ID = 1292373 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 27,439,278 reads read : 54,878,556 reads written : 54,878,556 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: 00:42:21 27439278 reads; of these: 27439278 (100.00%) were paired; of these: 1752051 (6.39%) aligned concordantly 0 times 22939082 (83.60%) aligned concordantly exactly 1 time 2748145 (10.02%) aligned concordantly >1 times ---- 1752051 pairs aligned concordantly 0 times; of these: 346661 (19.79%) aligned discordantly 1 time ---- 1405390 pairs aligned 0 times concordantly or discordantly; of these: 2810780 mates make up the pairs; of these: 2182419 (77.64%) aligned 0 times 409613 (14.57%) aligned exactly 1 time 218748 (7.78%) aligned >1 times 96.02% overall alignment rate Time searching: 00:42:21 Overall time: 00:42:21 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 24 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] 16624672 / 25998332 = 0.6395 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 @ Sun, 02 Jun 2019 19:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.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 @ Sun, 02 Jun 2019 19:30:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:30:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.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 @ Sun, 02 Jun 2019 19:30:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:30:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.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 @ Sun, 02 Jun 2019 19:30:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:30:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:30:15: 1000000 INFO @ Sun, 02 Jun 2019 19:30:16: 1000000 INFO @ Sun, 02 Jun 2019 19:30:17: 1000000 INFO @ Sun, 02 Jun 2019 19:30:23: 2000000 INFO @ Sun, 02 Jun 2019 19:30:25: 2000000 INFO @ Sun, 02 Jun 2019 19:30:27: 2000000 INFO @ Sun, 02 Jun 2019 19:30:31: 3000000 INFO @ Sun, 02 Jun 2019 19:30:34: 3000000 INFO @ Sun, 02 Jun 2019 19:30:36: 3000000 INFO @ Sun, 02 Jun 2019 19:30:39: 4000000 INFO @ Sun, 02 Jun 2019 19:30:43: 4000000 INFO @ Sun, 02 Jun 2019 19:30:45: 4000000 INFO @ Sun, 02 Jun 2019 19:30:47: 5000000 INFO @ Sun, 02 Jun 2019 19:30:53: 5000000 INFO @ Sun, 02 Jun 2019 19:30:55: 5000000 INFO @ Sun, 02 Jun 2019 19:30:55: 6000000 INFO @ Sun, 02 Jun 2019 19:31:02: 6000000 INFO @ Sun, 02 Jun 2019 19:31:03: 7000000 INFO @ Sun, 02 Jun 2019 19:31:05: 6000000 INFO @ Sun, 02 Jun 2019 19:31:11: 7000000 INFO @ Sun, 02 Jun 2019 19:31:11: 8000000 INFO @ Sun, 02 Jun 2019 19:31:15: 7000000 INFO @ Sun, 02 Jun 2019 19:31:19: 9000000 INFO @ Sun, 02 Jun 2019 19:31:20: 8000000 INFO @ Sun, 02 Jun 2019 19:31:24: 8000000 INFO @ Sun, 02 Jun 2019 19:31:27: 10000000 INFO @ Sun, 02 Jun 2019 19:31:29: 9000000 INFO @ Sun, 02 Jun 2019 19:31:34: 9000000 INFO @ Sun, 02 Jun 2019 19:31:35: 11000000 INFO @ Sun, 02 Jun 2019 19:31:38: 10000000 INFO @ Sun, 02 Jun 2019 19:31:43: 10000000 INFO @ Sun, 02 Jun 2019 19:31:43: 12000000 INFO @ Sun, 02 Jun 2019 19:31:47: 11000000 INFO @ Sun, 02 Jun 2019 19:31:51: 13000000 INFO @ Sun, 02 Jun 2019 19:31:52: 11000000 INFO @ Sun, 02 Jun 2019 19:31:56: 12000000 INFO @ Sun, 02 Jun 2019 19:31:59: 14000000 INFO @ Sun, 02 Jun 2019 19:32:01: 12000000 INFO @ Sun, 02 Jun 2019 19:32:05: 13000000 INFO @ Sun, 02 Jun 2019 19:32:07: 15000000 INFO @ Sun, 02 Jun 2019 19:32:11: 13000000 INFO @ Sun, 02 Jun 2019 19:32:14: 14000000 INFO @ Sun, 02 Jun 2019 19:32:15: 16000000 INFO @ Sun, 02 Jun 2019 19:32:20: 14000000 INFO @ Sun, 02 Jun 2019 19:32:23: 15000000 INFO @ Sun, 02 Jun 2019 19:32:23: 17000000 INFO @ Sun, 02 Jun 2019 19:32:30: 15000000 INFO @ Sun, 02 Jun 2019 19:32:31: 18000000 INFO @ Sun, 02 Jun 2019 19:32:32: 16000000 INFO @ Sun, 02 Jun 2019 19:32:39: 19000000 INFO @ Sun, 02 Jun 2019 19:32:39: 16000000 INFO @ Sun, 02 Jun 2019 19:32:41: 17000000 INFO @ Sun, 02 Jun 2019 19:32:43: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:32:43: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:32:43: #1 total tags in treatment: 9189135 INFO @ Sun, 02 Jun 2019 19:32:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:32:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:32:43: #1 tags after filtering in treatment: 7670211 INFO @ Sun, 02 Jun 2019 19:32:43: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 19:32:43: #1 finished! INFO @ Sun, 02 Jun 2019 19:32:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:32:44: #2 number of paired peaks: 538 WARNING @ Sun, 02 Jun 2019 19:32:44: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sun, 02 Jun 2019 19:32:44: start model_add_line... INFO @ Sun, 02 Jun 2019 19:32:44: start X-correlation... INFO @ Sun, 02 Jun 2019 19:32:44: end of X-cor INFO @ Sun, 02 Jun 2019 19:32:44: #2 finished! INFO @ Sun, 02 Jun 2019 19:32:44: #2 predicted fragment length is 165 bps INFO @ Sun, 02 Jun 2019 19:32:44: #2 alternative fragment length(s) may be 4,165 bps INFO @ Sun, 02 Jun 2019 19:32:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.05_model.r INFO @ Sun, 02 Jun 2019 19:32:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:32:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:32:49: 17000000 INFO @ Sun, 02 Jun 2019 19:32:50: 18000000 INFO @ Sun, 02 Jun 2019 19:32:58: 18000000 INFO @ Sun, 02 Jun 2019 19:32:58: 19000000 INFO @ Sun, 02 Jun 2019 19:33:02: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:33:02: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:33:02: #1 total tags in treatment: 9189135 INFO @ Sun, 02 Jun 2019 19:33:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:33:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:33:02: #1 tags after filtering in treatment: 7670211 INFO @ Sun, 02 Jun 2019 19:33:02: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 19:33:02: #1 finished! INFO @ Sun, 02 Jun 2019 19:33:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:33:03: #2 number of paired peaks: 538 WARNING @ Sun, 02 Jun 2019 19:33:03: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sun, 02 Jun 2019 19:33:03: start model_add_line... INFO @ Sun, 02 Jun 2019 19:33:03: start X-correlation... INFO @ Sun, 02 Jun 2019 19:33:03: end of X-cor INFO @ Sun, 02 Jun 2019 19:33:03: #2 finished! INFO @ Sun, 02 Jun 2019 19:33:03: #2 predicted fragment length is 165 bps INFO @ Sun, 02 Jun 2019 19:33:03: #2 alternative fragment length(s) may be 4,165 bps INFO @ Sun, 02 Jun 2019 19:33:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.20_model.r INFO @ Sun, 02 Jun 2019 19:33:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:33:07: 19000000 INFO @ Sun, 02 Jun 2019 19:33:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:33:10: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:33:10: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:33:10: #1 total tags in treatment: 9189135 INFO @ Sun, 02 Jun 2019 19:33:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:33:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:33:11: #1 tags after filtering in treatment: 7670211 INFO @ Sun, 02 Jun 2019 19:33:11: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 19:33:11: #1 finished! INFO @ Sun, 02 Jun 2019 19:33:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:33:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:33:11: #2 number of paired peaks: 538 WARNING @ Sun, 02 Jun 2019 19:33:11: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sun, 02 Jun 2019 19:33:11: start model_add_line... INFO @ Sun, 02 Jun 2019 19:33:12: start X-correlation... INFO @ Sun, 02 Jun 2019 19:33:12: end of X-cor INFO @ Sun, 02 Jun 2019 19:33:12: #2 finished! INFO @ Sun, 02 Jun 2019 19:33:12: #2 predicted fragment length is 165 bps INFO @ Sun, 02 Jun 2019 19:33:12: #2 alternative fragment length(s) may be 4,165 bps INFO @ Sun, 02 Jun 2019 19:33:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.10_model.r INFO @ Sun, 02 Jun 2019 19:33:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:33:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.05_summits.bed INFO @ Sun, 02 Jun 2019 19:33:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:33:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:33:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:33:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:33:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:33:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.20_summits.bed INFO @ Sun, 02 Jun 2019 19:33:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:33:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733160/SRX3733160.10_summits.bed INFO @ Sun, 02 Jun 2019 19:33:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (348 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。