Job ID = 6368737 SRX = SRX5402761 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:16 prefetch.2.10.7: 1) Downloading 'SRR8602995'... 2020-06-16T00:30:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:34:06 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:34:06 prefetch.2.10.7: 1) 'SRR8602995' was downloaded successfully Read 29798811 spots for SRR8602995/SRR8602995.sra Written 29798811 spots for SRR8602995/SRR8602995.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:14 29798811 reads; of these: 29798811 (100.00%) were unpaired; of these: 5695303 (19.11%) aligned 0 times 19767936 (66.34%) aligned exactly 1 time 4335572 (14.55%) aligned >1 times 80.89% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 5257302 / 24103508 = 0.2181 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 09:47:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.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 09:47:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:09: 1000000 INFO @ Tue, 16 Jun 2020 09:47:14: 2000000 INFO @ Tue, 16 Jun 2020 09:47:19: 3000000 INFO @ Tue, 16 Jun 2020 09:47:25: 4000000 INFO @ Tue, 16 Jun 2020 09:47:30: 5000000 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 09:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.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 09:47:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:35: 6000000 INFO @ Tue, 16 Jun 2020 09:47:39: 1000000 INFO @ Tue, 16 Jun 2020 09:47:41: 7000000 INFO @ Tue, 16 Jun 2020 09:47:44: 2000000 INFO @ Tue, 16 Jun 2020 09:47:46: 8000000 INFO @ Tue, 16 Jun 2020 09:47:50: 3000000 INFO @ Tue, 16 Jun 2020 09:47:51: 9000000 INFO @ Tue, 16 Jun 2020 09:47:55: 4000000 INFO @ Tue, 16 Jun 2020 09:47:57: 10000000 INFO @ Tue, 16 Jun 2020 09:48:01: 5000000 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 09:48:02: 11000000 INFO @ Tue, 16 Jun 2020 09:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.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 09:48:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:06: 6000000 INFO @ Tue, 16 Jun 2020 09:48:08: 12000000 INFO @ Tue, 16 Jun 2020 09:48:09: 1000000 INFO @ Tue, 16 Jun 2020 09:48:12: 7000000 INFO @ Tue, 16 Jun 2020 09:48:13: 13000000 INFO @ Tue, 16 Jun 2020 09:48:15: 2000000 INFO @ Tue, 16 Jun 2020 09:48:18: 8000000 INFO @ Tue, 16 Jun 2020 09:48:19: 14000000 INFO @ Tue, 16 Jun 2020 09:48:20: 3000000 INFO @ Tue, 16 Jun 2020 09:48:23: 9000000 INFO @ Tue, 16 Jun 2020 09:48:25: 15000000 INFO @ Tue, 16 Jun 2020 09:48:26: 4000000 INFO @ Tue, 16 Jun 2020 09:48:29: 10000000 INFO @ Tue, 16 Jun 2020 09:48:30: 16000000 INFO @ Tue, 16 Jun 2020 09:48:32: 5000000 INFO @ Tue, 16 Jun 2020 09:48:34: 11000000 INFO @ Tue, 16 Jun 2020 09:48:36: 17000000 INFO @ Tue, 16 Jun 2020 09:48:38: 6000000 INFO @ Tue, 16 Jun 2020 09:48:40: 12000000 INFO @ Tue, 16 Jun 2020 09:48:41: 18000000 INFO @ Tue, 16 Jun 2020 09:48:43: 7000000 INFO @ Tue, 16 Jun 2020 09:48:45: 13000000 INFO @ Tue, 16 Jun 2020 09:48:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:48:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:48:46: #1 total tags in treatment: 18846206 INFO @ Tue, 16 Jun 2020 09:48:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:46: #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 09:48:46: #1 tags after filtering in treatment: 18846206 INFO @ Tue, 16 Jun 2020 09:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:48: #2 number of paired peaks: 260 WARNING @ Tue, 16 Jun 2020 09:48:48: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:48: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:48:48: #2 alternative fragment length(s) may be 1,39,45,47 bps INFO @ Tue, 16 Jun 2020 09:48:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.05_model.r WARNING @ Tue, 16 Jun 2020 09:48:48: #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 09:48:48: #2 You may need to consider one of the other alternative d(s): 1,39,45,47 WARNING @ Tue, 16 Jun 2020 09:48:48: #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 09:48:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:49: 8000000 INFO @ Tue, 16 Jun 2020 09:48:51: 14000000 INFO @ Tue, 16 Jun 2020 09:48:54: 9000000 INFO @ Tue, 16 Jun 2020 09:48:57: 15000000 INFO @ Tue, 16 Jun 2020 09:49:00: 10000000 INFO @ Tue, 16 Jun 2020 09:49:03: 16000000 INFO @ Tue, 16 Jun 2020 09:49:05: 11000000 INFO @ Tue, 16 Jun 2020 09:49:09: 17000000 INFO @ Tue, 16 Jun 2020 09:49:11: 12000000 INFO @ Tue, 16 Jun 2020 09:49:14: 18000000 INFO @ Tue, 16 Jun 2020 09:49:17: 13000000 INFO @ Tue, 16 Jun 2020 09:49:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:19: #1 total tags in treatment: 18846206 INFO @ Tue, 16 Jun 2020 09:49:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:19: #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 09:49:19: #1 tags after filtering in treatment: 18846206 INFO @ Tue, 16 Jun 2020 09:49:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:21: #2 number of paired peaks: 260 WARNING @ Tue, 16 Jun 2020 09:49:21: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:21: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:49:21: #2 alternative fragment length(s) may be 1,39,45,47 bps INFO @ Tue, 16 Jun 2020 09:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.10_model.r WARNING @ Tue, 16 Jun 2020 09:49:21: #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 09:49:21: #2 You may need to consider one of the other alternative d(s): 1,39,45,47 WARNING @ Tue, 16 Jun 2020 09:49:21: #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 09:49:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:22: 14000000 INFO @ Tue, 16 Jun 2020 09:49:28: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:49:33: 16000000 INFO @ Tue, 16 Jun 2020 09:49:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:38: 17000000 INFO @ Tue, 16 Jun 2020 09:49:44: 18000000 INFO @ Tue, 16 Jun 2020 09:49:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:48: #1 total tags in treatment: 18846206 INFO @ Tue, 16 Jun 2020 09:49:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:48: #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 09:49:48: #1 tags after filtering in treatment: 18846206 INFO @ Tue, 16 Jun 2020 09:49:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:50: #2 number of paired peaks: 260 WARNING @ Tue, 16 Jun 2020 09:49:50: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:50: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:49:50: #2 alternative fragment length(s) may be 1,39,45,47 bps INFO @ Tue, 16 Jun 2020 09:49:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.20_model.r WARNING @ Tue, 16 Jun 2020 09:49:50: #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 09:49:50: #2 You may need to consider one of the other alternative d(s): 1,39,45,47 WARNING @ Tue, 16 Jun 2020 09:49:50: #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 09:49:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.10_summits.bed INFO @ Tue, 16 Jun 2020 09:50:08: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402761/SRX5402761.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling