Job ID = 6368673 SRX = SRX5402700 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:49 prefetch.2.10.7: 1) Downloading 'SRR8602934'... 2020-06-16T00:26:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:29:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:29:13 prefetch.2.10.7: 1) 'SRR8602934' was downloaded successfully Read 27481793 spots for SRR8602934/SRR8602934.sra Written 27481793 spots for SRR8602934/SRR8602934.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: 00:05:27 27481793 reads; of these: 27481793 (100.00%) were unpaired; of these: 5497248 (20.00%) aligned 0 times 16134265 (58.71%) aligned exactly 1 time 5850280 (21.29%) aligned >1 times 80.00% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 9162864 / 21984545 = 0.4168 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 09:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.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 09:40:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:26: 1000000 INFO @ Tue, 16 Jun 2020 09:40:32: 2000000 INFO @ Tue, 16 Jun 2020 09:40:38: 3000000 INFO @ Tue, 16 Jun 2020 09:40:44: 4000000 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 09:40:50: 5000000 INFO @ Tue, 16 Jun 2020 09:40:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.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 09:40:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:57: 6000000 INFO @ Tue, 16 Jun 2020 09:40:57: 1000000 INFO @ Tue, 16 Jun 2020 09:41:03: 7000000 INFO @ Tue, 16 Jun 2020 09:41:03: 2000000 INFO @ Tue, 16 Jun 2020 09:41:09: 8000000 INFO @ Tue, 16 Jun 2020 09:41:10: 3000000 INFO @ Tue, 16 Jun 2020 09:41:16: 9000000 INFO @ Tue, 16 Jun 2020 09:41:16: 4000000 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 09:41:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.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 09:41:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:22: 10000000 INFO @ Tue, 16 Jun 2020 09:41:23: 5000000 INFO @ Tue, 16 Jun 2020 09:41:27: 1000000 INFO @ Tue, 16 Jun 2020 09:41:29: 11000000 INFO @ Tue, 16 Jun 2020 09:41:30: 6000000 INFO @ Tue, 16 Jun 2020 09:41:34: 2000000 INFO @ Tue, 16 Jun 2020 09:41:36: 12000000 INFO @ Tue, 16 Jun 2020 09:41:37: 7000000 INFO @ Tue, 16 Jun 2020 09:41:41: 3000000 INFO @ Tue, 16 Jun 2020 09:41:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:42: #1 total tags in treatment: 12821681 INFO @ Tue, 16 Jun 2020 09:41:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:42: #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 09:41:42: #1 tags after filtering in treatment: 12821681 INFO @ Tue, 16 Jun 2020 09:41:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:43: #2 number of paired peaks: 625 WARNING @ Tue, 16 Jun 2020 09:41:43: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:41:43: #2 alternative fragment length(s) may be 1,41,557 bps INFO @ Tue, 16 Jun 2020 09:41:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.05_model.r WARNING @ Tue, 16 Jun 2020 09:41:43: #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 09:41:43: #2 You may need to consider one of the other alternative d(s): 1,41,557 WARNING @ Tue, 16 Jun 2020 09:41:43: #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 09:41:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:43: 8000000 INFO @ Tue, 16 Jun 2020 09:41:47: 4000000 INFO @ Tue, 16 Jun 2020 09:41:50: 9000000 INFO @ Tue, 16 Jun 2020 09:41:54: 5000000 INFO @ Tue, 16 Jun 2020 09:41:57: 10000000 INFO @ Tue, 16 Jun 2020 09:42:01: 6000000 INFO @ Tue, 16 Jun 2020 09:42:04: 11000000 INFO @ Tue, 16 Jun 2020 09:42:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:07: 7000000 INFO @ Tue, 16 Jun 2020 09:42:11: 12000000 INFO @ Tue, 16 Jun 2020 09:42:14: 8000000 INFO @ Tue, 16 Jun 2020 09:42:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.05_summits.bed INFO @ Tue, 16 Jun 2020 09:42:15: 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... INFO @ Tue, 16 Jun 2020 09:42:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:16: #1 total tags in treatment: 12821681 INFO @ Tue, 16 Jun 2020 09:42:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:16: #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 09:42:16: #1 tags after filtering in treatment: 12821681 INFO @ Tue, 16 Jun 2020 09:42:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:17: #2 number of paired peaks: 625 WARNING @ Tue, 16 Jun 2020 09:42:17: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:17: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:42:17: #2 alternative fragment length(s) may be 1,41,557 bps INFO @ Tue, 16 Jun 2020 09:42:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.10_model.r WARNING @ Tue, 16 Jun 2020 09:42:17: #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 09:42:17: #2 You may need to consider one of the other alternative d(s): 1,41,557 WARNING @ Tue, 16 Jun 2020 09:42:17: #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 09:42:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:20: 9000000 INFO @ Tue, 16 Jun 2020 09:42:26: 10000000 INFO @ Tue, 16 Jun 2020 09:42:32: 11000000 INFO @ Tue, 16 Jun 2020 09:42:38: 12000000 INFO @ Tue, 16 Jun 2020 09:42:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:42: #1 total tags in treatment: 12821681 INFO @ Tue, 16 Jun 2020 09:42:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:42: #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 09:42:42: #1 tags after filtering in treatment: 12821681 INFO @ Tue, 16 Jun 2020 09:42:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:42: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:42:43: #2 number of paired peaks: 625 WARNING @ Tue, 16 Jun 2020 09:42:43: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:43: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:42:43: #2 alternative fragment length(s) may be 1,41,557 bps INFO @ Tue, 16 Jun 2020 09:42:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.20_model.r WARNING @ Tue, 16 Jun 2020 09:42:43: #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 09:42:43: #2 You may need to consider one of the other alternative d(s): 1,41,557 WARNING @ Tue, 16 Jun 2020 09:42:43: #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 09:42:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.10_summits.bed INFO @ Tue, 16 Jun 2020 09:42:48: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402700/SRX5402700.20_summits.bed INFO @ Tue, 16 Jun 2020 09:43:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling