Job ID = 2589107 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,237,636 reads read : 24,237,636 reads written : 24,237,636 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:58 24237636 reads; of these: 24237636 (100.00%) were unpaired; of these: 635810 (2.62%) aligned 0 times 18011918 (74.31%) aligned exactly 1 time 5589908 (23.06%) aligned >1 times 97.38% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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_rmdupse_core] 10608958 / 23601826 = 0.4495 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 17:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.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 @ Mon, 12 Aug 2019 17:13:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:13:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.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 @ Mon, 12 Aug 2019 17:13:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:13:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.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 @ Mon, 12 Aug 2019 17:13:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:13:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:13:57: 1000000 INFO @ Mon, 12 Aug 2019 17:13:57: 1000000 INFO @ Mon, 12 Aug 2019 17:13:59: 1000000 INFO @ Mon, 12 Aug 2019 17:14:04: 2000000 INFO @ Mon, 12 Aug 2019 17:14:06: 2000000 INFO @ Mon, 12 Aug 2019 17:14:08: 2000000 INFO @ Mon, 12 Aug 2019 17:14:11: 3000000 INFO @ Mon, 12 Aug 2019 17:14:15: 3000000 INFO @ Mon, 12 Aug 2019 17:14:17: 3000000 INFO @ Mon, 12 Aug 2019 17:14:18: 4000000 INFO @ Mon, 12 Aug 2019 17:14:24: 4000000 INFO @ Mon, 12 Aug 2019 17:14:25: 5000000 INFO @ Mon, 12 Aug 2019 17:14:26: 4000000 INFO @ Mon, 12 Aug 2019 17:14:31: 6000000 INFO @ Mon, 12 Aug 2019 17:14:32: 5000000 INFO @ Mon, 12 Aug 2019 17:14:34: 5000000 INFO @ Mon, 12 Aug 2019 17:14:38: 7000000 INFO @ Mon, 12 Aug 2019 17:14:41: 6000000 INFO @ Mon, 12 Aug 2019 17:14:43: 6000000 INFO @ Mon, 12 Aug 2019 17:14:45: 8000000 INFO @ Mon, 12 Aug 2019 17:14:49: 7000000 INFO @ Mon, 12 Aug 2019 17:14:51: 7000000 INFO @ Mon, 12 Aug 2019 17:14:52: 9000000 INFO @ Mon, 12 Aug 2019 17:14:58: 8000000 INFO @ Mon, 12 Aug 2019 17:14:59: 10000000 INFO @ Mon, 12 Aug 2019 17:15:00: 8000000 INFO @ Mon, 12 Aug 2019 17:15:05: 11000000 INFO @ Mon, 12 Aug 2019 17:15:06: 9000000 INFO @ Mon, 12 Aug 2019 17:15:08: 9000000 INFO @ Mon, 12 Aug 2019 17:15:12: 12000000 INFO @ Mon, 12 Aug 2019 17:15:15: 10000000 INFO @ Mon, 12 Aug 2019 17:15:17: 10000000 INFO @ Mon, 12 Aug 2019 17:15:19: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:15:19: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:15:19: #1 total tags in treatment: 12992868 INFO @ Mon, 12 Aug 2019 17:15:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:15:19: #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 17:15:19: #1 tags after filtering in treatment: 12992868 INFO @ Mon, 12 Aug 2019 17:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:15:19: #1 finished! INFO @ Mon, 12 Aug 2019 17:15:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:15:20: #2 number of paired peaks: 177 WARNING @ Mon, 12 Aug 2019 17:15:20: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Mon, 12 Aug 2019 17:15:20: start model_add_line... INFO @ Mon, 12 Aug 2019 17:15:21: start X-correlation... INFO @ Mon, 12 Aug 2019 17:15:21: end of X-cor INFO @ Mon, 12 Aug 2019 17:15:21: #2 finished! INFO @ Mon, 12 Aug 2019 17:15:21: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 17:15:21: #2 alternative fragment length(s) may be 2,32,52,473 bps INFO @ Mon, 12 Aug 2019 17:15:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.10_model.r WARNING @ Mon, 12 Aug 2019 17:15:21: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:15:21: #2 You may need to consider one of the other alternative d(s): 2,32,52,473 WARNING @ Mon, 12 Aug 2019 17:15:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:15:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:15:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:15:23: 11000000 INFO @ Mon, 12 Aug 2019 17:15:25: 11000000 INFO @ Mon, 12 Aug 2019 17:15:32: 12000000 INFO @ Mon, 12 Aug 2019 17:15:34: 12000000 INFO @ Mon, 12 Aug 2019 17:15:40: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:15:40: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:15:40: #1 total tags in treatment: 12992868 INFO @ Mon, 12 Aug 2019 17:15:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:15:40: #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 17:15:41: #1 tags after filtering in treatment: 12992868 INFO @ Mon, 12 Aug 2019 17:15:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:15:41: #1 finished! INFO @ Mon, 12 Aug 2019 17:15:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:15:42: #2 number of paired peaks: 177 WARNING @ Mon, 12 Aug 2019 17:15:42: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Mon, 12 Aug 2019 17:15:42: start model_add_line... INFO @ Mon, 12 Aug 2019 17:15:42: start X-correlation... INFO @ Mon, 12 Aug 2019 17:15:42: end of X-cor INFO @ Mon, 12 Aug 2019 17:15:42: #2 finished! INFO @ Mon, 12 Aug 2019 17:15:42: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 17:15:42: #2 alternative fragment length(s) may be 2,32,52,473 bps INFO @ Mon, 12 Aug 2019 17:15:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.05_model.r WARNING @ Mon, 12 Aug 2019 17:15:42: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:15:42: #2 You may need to consider one of the other alternative d(s): 2,32,52,473 WARNING @ Mon, 12 Aug 2019 17:15:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:15:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:15:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:15:42: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:15:42: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:15:42: #1 total tags in treatment: 12992868 INFO @ Mon, 12 Aug 2019 17:15:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:15:42: #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 17:15:42: #1 tags after filtering in treatment: 12992868 INFO @ Mon, 12 Aug 2019 17:15:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:15:42: #1 finished! INFO @ Mon, 12 Aug 2019 17:15:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:15:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:15:44: #2 number of paired peaks: 177 WARNING @ Mon, 12 Aug 2019 17:15:44: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Mon, 12 Aug 2019 17:15:44: start model_add_line... INFO @ Mon, 12 Aug 2019 17:15:44: start X-correlation... INFO @ Mon, 12 Aug 2019 17:15:44: end of X-cor INFO @ Mon, 12 Aug 2019 17:15:44: #2 finished! INFO @ Mon, 12 Aug 2019 17:15:44: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 17:15:44: #2 alternative fragment length(s) may be 2,32,52,473 bps INFO @ Mon, 12 Aug 2019 17:15:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.20_model.r WARNING @ Mon, 12 Aug 2019 17:15:44: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:15:44: #2 You may need to consider one of the other alternative d(s): 2,32,52,473 WARNING @ Mon, 12 Aug 2019 17:15:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:15:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:15:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:15:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.10_summits.bed INFO @ Mon, 12 Aug 2019 17:16:05: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:16:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:16:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:16:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:16:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:16:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.05_summits.bed INFO @ Mon, 12 Aug 2019 17:16:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:16:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:16:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:16:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999206/ERX1999206.20_summits.bed INFO @ Mon, 12 Aug 2019 17:16:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。