Job ID = 4303049 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,970,231 reads read : 22,970,231 reads written : 22,970,231 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198446.sra.cache’: 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: 00:06:06 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517609 (10.96%) aligned 0 times 16805751 (73.16%) aligned exactly 1 time 3646871 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 2297432 / 20452622 = 0.1123 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:50:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.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, 12 Dec 2019 00:50:06: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:50:06: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:50:14: 1000000 INFO @ Thu, 12 Dec 2019 00:50:21: 2000000 INFO @ Thu, 12 Dec 2019 00:50:29: 3000000 INFO @ Thu, 12 Dec 2019 00:50:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.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, 12 Dec 2019 00:50:36: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:50:36: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:50:37: 4000000 INFO @ Thu, 12 Dec 2019 00:50:43: 1000000 INFO @ Thu, 12 Dec 2019 00:50:44: 5000000 INFO @ Thu, 12 Dec 2019 00:50:50: 2000000 INFO @ Thu, 12 Dec 2019 00:50:52: 6000000 INFO @ Thu, 12 Dec 2019 00:50:57: 3000000 INFO @ Thu, 12 Dec 2019 00:51:00: 7000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:51:04: 4000000 INFO @ Thu, 12 Dec 2019 00:51:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.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, 12 Dec 2019 00:51:06: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:51:06: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:51:08: 8000000 INFO @ Thu, 12 Dec 2019 00:51:12: 5000000 INFO @ Thu, 12 Dec 2019 00:51:15: 1000000 INFO @ Thu, 12 Dec 2019 00:51:16: 9000000 INFO @ Thu, 12 Dec 2019 00:51:19: 6000000 INFO @ Thu, 12 Dec 2019 00:51:24: 2000000 INFO @ Thu, 12 Dec 2019 00:51:24: 10000000 INFO @ Thu, 12 Dec 2019 00:51:26: 7000000 INFO @ Thu, 12 Dec 2019 00:51:32: 11000000 INFO @ Thu, 12 Dec 2019 00:51:32: 3000000 INFO @ Thu, 12 Dec 2019 00:51:32: 8000000 INFO @ Thu, 12 Dec 2019 00:51:40: 9000000 INFO @ Thu, 12 Dec 2019 00:51:40: 12000000 INFO @ Thu, 12 Dec 2019 00:51:41: 4000000 INFO @ Thu, 12 Dec 2019 00:51:46: 10000000 INFO @ Thu, 12 Dec 2019 00:51:48: 13000000 INFO @ Thu, 12 Dec 2019 00:51:49: 5000000 INFO @ Thu, 12 Dec 2019 00:51:53: 11000000 INFO @ Thu, 12 Dec 2019 00:51:56: 14000000 INFO @ Thu, 12 Dec 2019 00:51:58: 6000000 INFO @ Thu, 12 Dec 2019 00:52:00: 12000000 INFO @ Thu, 12 Dec 2019 00:52:04: 15000000 INFO @ Thu, 12 Dec 2019 00:52:06: 7000000 INFO @ Thu, 12 Dec 2019 00:52:08: 13000000 INFO @ Thu, 12 Dec 2019 00:52:12: 16000000 INFO @ Thu, 12 Dec 2019 00:52:15: 14000000 INFO @ Thu, 12 Dec 2019 00:52:15: 8000000 INFO @ Thu, 12 Dec 2019 00:52:20: 17000000 INFO @ Thu, 12 Dec 2019 00:52:22: 15000000 INFO @ Thu, 12 Dec 2019 00:52:25: 9000000 INFO @ Thu, 12 Dec 2019 00:52:28: 18000000 INFO @ Thu, 12 Dec 2019 00:52:29: 16000000 INFO @ Thu, 12 Dec 2019 00:52:30: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:52:30: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:52:30: #1 total tags in treatment: 18155190 INFO @ Thu, 12 Dec 2019 00:52:30: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:52:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:52:30: #1 tags after filtering in treatment: 18155190 INFO @ Thu, 12 Dec 2019 00:52:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:52:30: #1 finished! INFO @ Thu, 12 Dec 2019 00:52:30: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:52:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:52:32: #2 number of paired peaks: 255 WARNING @ Thu, 12 Dec 2019 00:52:32: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Thu, 12 Dec 2019 00:52:32: start model_add_line... INFO @ Thu, 12 Dec 2019 00:52:32: start X-correlation... INFO @ Thu, 12 Dec 2019 00:52:32: end of X-cor INFO @ Thu, 12 Dec 2019 00:52:32: #2 finished! INFO @ Thu, 12 Dec 2019 00:52:32: #2 predicted fragment length is 1 bps INFO @ Thu, 12 Dec 2019 00:52:32: #2 alternative fragment length(s) may be 1,34,46,535,589 bps INFO @ Thu, 12 Dec 2019 00:52:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.05_model.r WARNING @ Thu, 12 Dec 2019 00:52:32: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:52:32: #2 You may need to consider one of the other alternative d(s): 1,34,46,535,589 WARNING @ Thu, 12 Dec 2019 00:52:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:52:32: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:52:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:52:33: 10000000 INFO @ Thu, 12 Dec 2019 00:52:36: 17000000 INFO @ Thu, 12 Dec 2019 00:52:42: 11000000 INFO @ Thu, 12 Dec 2019 00:52:43: 18000000 INFO @ Thu, 12 Dec 2019 00:52:45: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:52:45: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:52:45: #1 total tags in treatment: 18155190 INFO @ Thu, 12 Dec 2019 00:52:45: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:52:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:52:45: #1 tags after filtering in treatment: 18155190 INFO @ Thu, 12 Dec 2019 00:52:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:52:45: #1 finished! INFO @ Thu, 12 Dec 2019 00:52:45: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:52:47: #2 number of paired peaks: 255 WARNING @ Thu, 12 Dec 2019 00:52:47: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Thu, 12 Dec 2019 00:52:47: start model_add_line... INFO @ Thu, 12 Dec 2019 00:52:47: start X-correlation... INFO @ Thu, 12 Dec 2019 00:52:47: end of X-cor INFO @ Thu, 12 Dec 2019 00:52:47: #2 finished! INFO @ Thu, 12 Dec 2019 00:52:47: #2 predicted fragment length is 1 bps INFO @ Thu, 12 Dec 2019 00:52:47: #2 alternative fragment length(s) may be 1,34,46,535,589 bps INFO @ Thu, 12 Dec 2019 00:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.10_model.r WARNING @ Thu, 12 Dec 2019 00:52:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:52:47: #2 You may need to consider one of the other alternative d(s): 1,34,46,535,589 WARNING @ Thu, 12 Dec 2019 00:52:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:52:47: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:52:50: 12000000 INFO @ Thu, 12 Dec 2019 00:52:59: 13000000 INFO @ Thu, 12 Dec 2019 00:53:07: 14000000 INFO @ Thu, 12 Dec 2019 00:53:13: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:53:16: 15000000 INFO @ Thu, 12 Dec 2019 00:53:25: 16000000 INFO @ Thu, 12 Dec 2019 00:53:28: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:53:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:53:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:53:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.05_summits.bed INFO @ Thu, 12 Dec 2019 00:53:31: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:53:33: 17000000 INFO @ Thu, 12 Dec 2019 00:53:42: 18000000 INFO @ Thu, 12 Dec 2019 00:53:43: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:53:43: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:53:43: #1 total tags in treatment: 18155190 INFO @ Thu, 12 Dec 2019 00:53:43: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:53:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:53:44: #1 tags after filtering in treatment: 18155190 INFO @ Thu, 12 Dec 2019 00:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:53:44: #1 finished! INFO @ Thu, 12 Dec 2019 00:53:44: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:53:45: #2 number of paired peaks: 255 WARNING @ Thu, 12 Dec 2019 00:53:45: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Thu, 12 Dec 2019 00:53:45: start model_add_line... INFO @ Thu, 12 Dec 2019 00:53:45: start X-correlation... INFO @ Thu, 12 Dec 2019 00:53:45: end of X-cor INFO @ Thu, 12 Dec 2019 00:53:45: #2 finished! INFO @ Thu, 12 Dec 2019 00:53:45: #2 predicted fragment length is 1 bps INFO @ Thu, 12 Dec 2019 00:53:45: #2 alternative fragment length(s) may be 1,34,46,535,589 bps INFO @ Thu, 12 Dec 2019 00:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.20_model.r WARNING @ Thu, 12 Dec 2019 00:53:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:53:45: #2 You may need to consider one of the other alternative d(s): 1,34,46,535,589 WARNING @ Thu, 12 Dec 2019 00:53:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:53:45: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:53:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:53:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:53:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.10_summits.bed INFO @ Thu, 12 Dec 2019 00:53:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:54:26: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:54:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:54:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:54:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494914/SRX494914.20_summits.bed INFO @ Thu, 12 Dec 2019 00:54:45: 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。