Job ID = 6368373 SRX = SRX495053 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:12:20 prefetch.2.10.7: 1) Downloading 'SRR1198585'... 2020-06-16T00:12:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:14:27 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:14:28 prefetch.2.10.7: 'SRR1198585' is valid 2020-06-16T00:14:28 prefetch.2.10.7: 1) 'SRR1198585' was downloaded successfully Read 18854814 spots for SRR1198585/SRR1198585.sra Written 18854814 spots for SRR1198585/SRR1198585.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: 00:03:52 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 288235 (1.53%) aligned 0 times 14954456 (79.31%) aligned exactly 1 time 3612123 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 3522767 / 18566579 = 0.1897 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 09:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.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 09:23:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:33: 1000000 INFO @ Tue, 16 Jun 2020 09:23:38: 2000000 INFO @ Tue, 16 Jun 2020 09:23:42: 3000000 INFO @ Tue, 16 Jun 2020 09:23:47: 4000000 INFO @ Tue, 16 Jun 2020 09:23:52: 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 09:23:57: 6000000 INFO @ Tue, 16 Jun 2020 09:23:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.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 09:23:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:02: 7000000 INFO @ Tue, 16 Jun 2020 09:24:03: 1000000 INFO @ Tue, 16 Jun 2020 09:24:07: 8000000 INFO @ Tue, 16 Jun 2020 09:24:08: 2000000 INFO @ Tue, 16 Jun 2020 09:24:12: 9000000 INFO @ Tue, 16 Jun 2020 09:24:13: 3000000 INFO @ Tue, 16 Jun 2020 09:24:17: 10000000 INFO @ Tue, 16 Jun 2020 09:24:18: 4000000 INFO @ Tue, 16 Jun 2020 09:24:22: 11000000 INFO @ Tue, 16 Jun 2020 09:24:23: 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 09:24:27: 12000000 INFO @ Tue, 16 Jun 2020 09:24:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.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 09:24:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:28: 6000000 INFO @ Tue, 16 Jun 2020 09:24:32: 13000000 INFO @ Tue, 16 Jun 2020 09:24:33: 7000000 INFO @ Tue, 16 Jun 2020 09:24:33: 1000000 INFO @ Tue, 16 Jun 2020 09:24:37: 14000000 INFO @ Tue, 16 Jun 2020 09:24:38: 8000000 INFO @ Tue, 16 Jun 2020 09:24:38: 2000000 INFO @ Tue, 16 Jun 2020 09:24:42: 15000000 INFO @ Tue, 16 Jun 2020 09:24:43: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:24:43: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:24:43: #1 total tags in treatment: 15043812 INFO @ Tue, 16 Jun 2020 09:24:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:43: #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 09:24:43: 9000000 INFO @ Tue, 16 Jun 2020 09:24:43: #1 tags after filtering in treatment: 15043812 INFO @ Tue, 16 Jun 2020 09:24:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:44: 3000000 INFO @ Tue, 16 Jun 2020 09:24:44: #2 number of paired peaks: 428 WARNING @ Tue, 16 Jun 2020 09:24:44: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:44: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:24:44: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:24:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.05_model.r WARNING @ Tue, 16 Jun 2020 09:24:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:24:44: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:24:44: #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 09:24:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:48: 10000000 INFO @ Tue, 16 Jun 2020 09:24:49: 4000000 INFO @ Tue, 16 Jun 2020 09:24:53: 11000000 INFO @ Tue, 16 Jun 2020 09:24:54: 5000000 INFO @ Tue, 16 Jun 2020 09:24:58: 12000000 INFO @ Tue, 16 Jun 2020 09:24:59: 6000000 INFO @ Tue, 16 Jun 2020 09:25:03: 13000000 INFO @ Tue, 16 Jun 2020 09:25:05: 7000000 INFO @ Tue, 16 Jun 2020 09:25:08: 14000000 INFO @ Tue, 16 Jun 2020 09:25:10: 8000000 INFO @ Tue, 16 Jun 2020 09:25:13: 15000000 INFO @ Tue, 16 Jun 2020 09:25:13: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:25:13: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:25:13: #1 total tags in treatment: 15043812 INFO @ Tue, 16 Jun 2020 09:25:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:13: #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 09:25:14: #1 tags after filtering in treatment: 15043812 INFO @ Tue, 16 Jun 2020 09:25:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:15: #2 number of paired peaks: 428 WARNING @ Tue, 16 Jun 2020 09:25:15: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:15: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:25:15: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:25:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.10_model.r WARNING @ Tue, 16 Jun 2020 09:25:15: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:15: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:25:15: #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 09:25:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:15: 9000000 INFO @ Tue, 16 Jun 2020 09:25:21: 10000000 INFO @ Tue, 16 Jun 2020 09:25:26: 11000000 INFO @ Tue, 16 Jun 2020 09:25:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.05_summits.bed INFO @ Tue, 16 Jun 2020 09:25:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4701 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:25:31: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:25:36: 13000000 INFO @ Tue, 16 Jun 2020 09:25:41: 14000000 INFO @ Tue, 16 Jun 2020 09:25:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:46: 15000000 INFO @ Tue, 16 Jun 2020 09:25:46: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:25:46: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:25:46: #1 total tags in treatment: 15043812 INFO @ Tue, 16 Jun 2020 09:25:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:46: #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 09:25:47: #1 tags after filtering in treatment: 15043812 INFO @ Tue, 16 Jun 2020 09:25:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:48: #2 number of paired peaks: 428 WARNING @ Tue, 16 Jun 2020 09:25:48: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:48: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:25:48: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:25:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.20_model.r WARNING @ Tue, 16 Jun 2020 09:25:48: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:48: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:25:48: #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 09:25:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.10_summits.bed INFO @ Tue, 16 Jun 2020 09:25:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1090 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:26:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495053/SRX495053.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (314 records, 4 fields): 1 millis CompletedMACS2peakCalling