Job ID = 6368813 SRX = SRX5985667 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:34 prefetch.2.10.7: 1) Downloading 'SRR9214972'... 2020-06-16T00:26:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:26 prefetch.2.10.7: 1) 'SRR9214972' was downloaded successfully Read 19891097 spots for SRR9214972/SRR9214972.sra Written 19891097 spots for SRR9214972/SRR9214972.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: 00:06:46 19891097 reads; of these: 19891097 (100.00%) were unpaired; of these: 1359497 (6.83%) aligned 0 times 15416989 (77.51%) aligned exactly 1 time 3114611 (15.66%) aligned >1 times 93.17% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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 8 files... [bam_rmdupse_core] 1836679 / 18531600 = 0.0991 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 09:47:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.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 09:47:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:44: 1000000 INFO @ Tue, 16 Jun 2020 09:47:50: 2000000 INFO @ Tue, 16 Jun 2020 09:47:55: 3000000 INFO @ Tue, 16 Jun 2020 09:48:01: 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 09:48:07: 5000000 INFO @ Tue, 16 Jun 2020 09:48:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.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 09:48:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:13: 6000000 INFO @ Tue, 16 Jun 2020 09:48:15: 1000000 INFO @ Tue, 16 Jun 2020 09:48:18: 7000000 INFO @ Tue, 16 Jun 2020 09:48:22: 2000000 INFO @ Tue, 16 Jun 2020 09:48:24: 8000000 INFO @ Tue, 16 Jun 2020 09:48:29: 3000000 INFO @ Tue, 16 Jun 2020 09:48:30: 9000000 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 09:48:36: 10000000 INFO @ Tue, 16 Jun 2020 09:48:36: 4000000 INFO @ Tue, 16 Jun 2020 09:48:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.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 09:48:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:42: 11000000 INFO @ Tue, 16 Jun 2020 09:48:44: 5000000 INFO @ Tue, 16 Jun 2020 09:48:46: 1000000 INFO @ Tue, 16 Jun 2020 09:48:48: 12000000 INFO @ Tue, 16 Jun 2020 09:48:52: 6000000 INFO @ Tue, 16 Jun 2020 09:48:53: 13000000 INFO @ Tue, 16 Jun 2020 09:48:54: 2000000 INFO @ Tue, 16 Jun 2020 09:48:59: 14000000 INFO @ Tue, 16 Jun 2020 09:49:00: 7000000 INFO @ Tue, 16 Jun 2020 09:49:01: 3000000 INFO @ Tue, 16 Jun 2020 09:49:05: 15000000 INFO @ Tue, 16 Jun 2020 09:49:08: 8000000 INFO @ Tue, 16 Jun 2020 09:49:09: 4000000 INFO @ Tue, 16 Jun 2020 09:49:11: 16000000 INFO @ Tue, 16 Jun 2020 09:49:15: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:49:15: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:49:15: #1 total tags in treatment: 16694921 INFO @ Tue, 16 Jun 2020 09:49:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:15: #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 09:49:15: #1 tags after filtering in treatment: 16694921 INFO @ Tue, 16 Jun 2020 09:49:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:15: 9000000 INFO @ Tue, 16 Jun 2020 09:49:16: #2 number of paired peaks: 280 WARNING @ Tue, 16 Jun 2020 09:49:16: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:17: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:49:17: #2 alternative fragment length(s) may be 2,69,593 bps INFO @ Tue, 16 Jun 2020 09:49:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.05_model.r WARNING @ Tue, 16 Jun 2020 09:49:17: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:17: #2 You may need to consider one of the other alternative d(s): 2,69,593 WARNING @ Tue, 16 Jun 2020 09:49:17: #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 09:49:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:17: 5000000 INFO @ Tue, 16 Jun 2020 09:49:23: 10000000 INFO @ Tue, 16 Jun 2020 09:49:25: 6000000 INFO @ Tue, 16 Jun 2020 09:49:31: 11000000 INFO @ Tue, 16 Jun 2020 09:49:33: 7000000 INFO @ Tue, 16 Jun 2020 09:49:39: 12000000 INFO @ Tue, 16 Jun 2020 09:49:41: 8000000 INFO @ Tue, 16 Jun 2020 09:49:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:46: 13000000 INFO @ Tue, 16 Jun 2020 09:49:49: 9000000 INFO @ Tue, 16 Jun 2020 09:49:54: 14000000 INFO @ Tue, 16 Jun 2020 09:49:56: 10000000 INFO @ Tue, 16 Jun 2020 09:49:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (625 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:01: 15000000 INFO @ Tue, 16 Jun 2020 09:50:04: 11000000 INFO @ Tue, 16 Jun 2020 09:50:09: 16000000 INFO @ Tue, 16 Jun 2020 09:50:12: 12000000 INFO @ Tue, 16 Jun 2020 09:50:14: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:50:14: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:50:14: #1 total tags in treatment: 16694921 INFO @ Tue, 16 Jun 2020 09:50:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:14: #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 09:50:14: #1 tags after filtering in treatment: 16694921 INFO @ Tue, 16 Jun 2020 09:50:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:15: #2 number of paired peaks: 280 WARNING @ Tue, 16 Jun 2020 09:50:15: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:16: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:50:16: #2 alternative fragment length(s) may be 2,69,593 bps INFO @ Tue, 16 Jun 2020 09:50:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.10_model.r WARNING @ Tue, 16 Jun 2020 09:50:16: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:16: #2 You may need to consider one of the other alternative d(s): 2,69,593 WARNING @ Tue, 16 Jun 2020 09:50:16: #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 09:50:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:16: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:50:19: 13000000 INFO @ Tue, 16 Jun 2020 09:50:25: 14000000 INFO @ Tue, 16 Jun 2020 09:50:32: 15000000 INFO @ Tue, 16 Jun 2020 09:50:39: 16000000 INFO @ Tue, 16 Jun 2020 09:50:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:43: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:50:43: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:50:43: #1 total tags in treatment: 16694921 INFO @ Tue, 16 Jun 2020 09:50:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:43: #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 09:50:44: #1 tags after filtering in treatment: 16694921 INFO @ Tue, 16 Jun 2020 09:50:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:45: #2 number of paired peaks: 280 WARNING @ Tue, 16 Jun 2020 09:50:45: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:45: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:50:45: #2 alternative fragment length(s) may be 2,69,593 bps INFO @ Tue, 16 Jun 2020 09:50:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.20_model.r WARNING @ Tue, 16 Jun 2020 09:50:45: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:45: #2 You may need to consider one of the other alternative d(s): 2,69,593 WARNING @ Tue, 16 Jun 2020 09:50:45: #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 09:50:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.10_summits.bed INFO @ Tue, 16 Jun 2020 09:50:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (480 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:51:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985667/SRX5985667.20_summits.bed INFO @ Tue, 16 Jun 2020 09:51:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (261 records, 4 fields): 1 millis CompletedMACS2peakCalling