Job ID = 6368271 SRX = SRX494955 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:17:51 prefetch.2.10.7: 1) Downloading 'SRR1198487'... 2020-06-16T00:17:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:19:07 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:19:08 prefetch.2.10.7: 'SRR1198487' is valid 2020-06-16T00:19:08 prefetch.2.10.7: 1) 'SRR1198487' was downloaded successfully Read 15863850 spots for SRR1198487/SRR1198487.sra Written 15863850 spots for SRR1198487/SRR1198487.sra 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: 00:02:43 15863850 reads; of these: 15863850 (100.00%) were unpaired; of these: 231749 (1.46%) aligned 0 times 12990241 (81.89%) aligned exactly 1 time 2641860 (16.65%) aligned >1 times 98.54% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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_rmdupse_core] 1436425 / 15632101 = 0.0919 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:27:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.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 @ Tue, 16 Jun 2020 09:27:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:22: 1000000 INFO @ Tue, 16 Jun 2020 09:27:31: 2000000 INFO @ Tue, 16 Jun 2020 09:27:39: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:27:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.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 @ Tue, 16 Jun 2020 09:27:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:48: 4000000 INFO @ Tue, 16 Jun 2020 09:27:53: 1000000 INFO @ Tue, 16 Jun 2020 09:27:56: 5000000 INFO @ Tue, 16 Jun 2020 09:28:01: 2000000 INFO @ Tue, 16 Jun 2020 09:28:05: 6000000 INFO @ Tue, 16 Jun 2020 09:28:11: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:28:13: 7000000 INFO @ Tue, 16 Jun 2020 09:28:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.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 @ Tue, 16 Jun 2020 09:28:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:19: 4000000 INFO @ Tue, 16 Jun 2020 09:28:22: 8000000 INFO @ Tue, 16 Jun 2020 09:28:23: 1000000 INFO @ Tue, 16 Jun 2020 09:28:29: 5000000 INFO @ Tue, 16 Jun 2020 09:28:31: 9000000 INFO @ Tue, 16 Jun 2020 09:28:31: 2000000 INFO @ Tue, 16 Jun 2020 09:28:38: 6000000 INFO @ Tue, 16 Jun 2020 09:28:40: 10000000 INFO @ Tue, 16 Jun 2020 09:28:40: 3000000 INFO @ Tue, 16 Jun 2020 09:28:47: 7000000 INFO @ Tue, 16 Jun 2020 09:28:49: 11000000 INFO @ Tue, 16 Jun 2020 09:28:49: 4000000 INFO @ Tue, 16 Jun 2020 09:28:56: 8000000 INFO @ Tue, 16 Jun 2020 09:28:57: 12000000 INFO @ Tue, 16 Jun 2020 09:28:59: 5000000 INFO @ Tue, 16 Jun 2020 09:29:05: 9000000 INFO @ Tue, 16 Jun 2020 09:29:06: 13000000 INFO @ Tue, 16 Jun 2020 09:29:07: 6000000 INFO @ Tue, 16 Jun 2020 09:29:14: 10000000 INFO @ Tue, 16 Jun 2020 09:29:15: 14000000 INFO @ Tue, 16 Jun 2020 09:29:16: 7000000 INFO @ Tue, 16 Jun 2020 09:29:17: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:29:17: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:29:17: #1 total tags in treatment: 14195676 INFO @ Tue, 16 Jun 2020 09:29:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:29:17: #1 tags after filtering in treatment: 14195676 INFO @ Tue, 16 Jun 2020 09:29:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:18: #2 number of paired peaks: 236 WARNING @ Tue, 16 Jun 2020 09:29:18: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:18: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:29:18: #2 alternative fragment length(s) may be 1,31,550,573 bps INFO @ Tue, 16 Jun 2020 09:29:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.05_model.r WARNING @ Tue, 16 Jun 2020 09:29:18: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:18: #2 You may need to consider one of the other alternative d(s): 1,31,550,573 WARNING @ Tue, 16 Jun 2020 09:29:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:29:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:23: 11000000 INFO @ Tue, 16 Jun 2020 09:29:25: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:32: 12000000 INFO @ Tue, 16 Jun 2020 09:29:34: 9000000 INFO @ Tue, 16 Jun 2020 09:29:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:41: 13000000 INFO @ Tue, 16 Jun 2020 09:29:42: 10000000 INFO @ Tue, 16 Jun 2020 09:29:50: 14000000 INFO @ Tue, 16 Jun 2020 09:29:51: 11000000 INFO @ Tue, 16 Jun 2020 09:29:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:52: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:29:52: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:29:52: #1 total tags in treatment: 14195676 INFO @ Tue, 16 Jun 2020 09:29:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:29:52: #1 tags after filtering in treatment: 14195676 INFO @ Tue, 16 Jun 2020 09:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:53: #2 number of paired peaks: 236 WARNING @ Tue, 16 Jun 2020 09:29:53: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:53: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:29:53: #2 alternative fragment length(s) may be 1,31,550,573 bps INFO @ Tue, 16 Jun 2020 09:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.10_model.r WARNING @ Tue, 16 Jun 2020 09:29:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:53: #2 You may need to consider one of the other alternative d(s): 1,31,550,573 WARNING @ Tue, 16 Jun 2020 09:29:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:29:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:59: 12000000 INFO @ Tue, 16 Jun 2020 09:30:08: 13000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:17: 14000000 INFO @ Tue, 16 Jun 2020 09:30:18: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:30:18: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:30:18: #1 total tags in treatment: 14195676 INFO @ Tue, 16 Jun 2020 09:30:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:30:18: #1 tags after filtering in treatment: 14195676 INFO @ Tue, 16 Jun 2020 09:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:19: #2 number of paired peaks: 236 WARNING @ Tue, 16 Jun 2020 09:30:19: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:20: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:30:20: #2 alternative fragment length(s) may be 1,31,550,573 bps INFO @ Tue, 16 Jun 2020 09:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.20_model.r WARNING @ Tue, 16 Jun 2020 09:30:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:20: #2 You may need to consider one of the other alternative d(s): 1,31,550,573 WARNING @ Tue, 16 Jun 2020 09:30:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:30:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494955/SRX494955.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling