Job ID = 6366562 SRX = SRX1936240 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:47:37 prefetch.2.10.7: 1) Downloading 'SRR3879847'... 2020-06-15T22:47:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:24 prefetch.2.10.7: 1) 'SRR3879847' was downloaded successfully Read 23692485 spots for SRR3879847/SRR3879847.sra Written 23692485 spots for SRR3879847/SRR3879847.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: 00:05:23 23692485 reads; of these: 23692485 (100.00%) were unpaired; of these: 1184177 (5.00%) aligned 0 times 19157215 (80.86%) aligned exactly 1 time 3351093 (14.14%) aligned >1 times 95.00% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 3228273 / 22508308 = 0.1434 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 08:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.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 08:01:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:41: 1000000 INFO @ Tue, 16 Jun 2020 08:01:47: 2000000 INFO @ Tue, 16 Jun 2020 08:01:53: 3000000 INFO @ Tue, 16 Jun 2020 08:01:59: 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 08:02:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.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 08:02:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:05: 5000000 INFO @ Tue, 16 Jun 2020 08:02:11: 1000000 INFO @ Tue, 16 Jun 2020 08:02:12: 6000000 INFO @ Tue, 16 Jun 2020 08:02:18: 2000000 INFO @ Tue, 16 Jun 2020 08:02:19: 7000000 INFO @ Tue, 16 Jun 2020 08:02:25: 3000000 INFO @ Tue, 16 Jun 2020 08:02:26: 8000000 INFO @ Tue, 16 Jun 2020 08:02:32: 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 08:02:33: 9000000 INFO @ Tue, 16 Jun 2020 08:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.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 08:02:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:39: 5000000 INFO @ Tue, 16 Jun 2020 08:02:40: 10000000 INFO @ Tue, 16 Jun 2020 08:02:41: 1000000 INFO @ Tue, 16 Jun 2020 08:02:46: 6000000 INFO @ Tue, 16 Jun 2020 08:02:47: 11000000 INFO @ Tue, 16 Jun 2020 08:02:48: 2000000 INFO @ Tue, 16 Jun 2020 08:02:53: 7000000 INFO @ Tue, 16 Jun 2020 08:02:54: 12000000 INFO @ Tue, 16 Jun 2020 08:02:55: 3000000 INFO @ Tue, 16 Jun 2020 08:03:00: 8000000 INFO @ Tue, 16 Jun 2020 08:03:01: 13000000 INFO @ Tue, 16 Jun 2020 08:03:02: 4000000 INFO @ Tue, 16 Jun 2020 08:03:07: 9000000 INFO @ Tue, 16 Jun 2020 08:03:08: 14000000 INFO @ Tue, 16 Jun 2020 08:03:09: 5000000 INFO @ Tue, 16 Jun 2020 08:03:14: 10000000 INFO @ Tue, 16 Jun 2020 08:03:14: 15000000 INFO @ Tue, 16 Jun 2020 08:03:16: 6000000 INFO @ Tue, 16 Jun 2020 08:03:21: 11000000 INFO @ Tue, 16 Jun 2020 08:03:21: 16000000 INFO @ Tue, 16 Jun 2020 08:03:23: 7000000 INFO @ Tue, 16 Jun 2020 08:03:28: 12000000 INFO @ Tue, 16 Jun 2020 08:03:29: 17000000 INFO @ Tue, 16 Jun 2020 08:03:30: 8000000 INFO @ Tue, 16 Jun 2020 08:03:35: 13000000 INFO @ Tue, 16 Jun 2020 08:03:35: 18000000 INFO @ Tue, 16 Jun 2020 08:03:37: 9000000 INFO @ Tue, 16 Jun 2020 08:03:42: 14000000 INFO @ Tue, 16 Jun 2020 08:03:42: 19000000 INFO @ Tue, 16 Jun 2020 08:03:44: 10000000 INFO @ Tue, 16 Jun 2020 08:03:44: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:03:44: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:03:44: #1 total tags in treatment: 19280035 INFO @ Tue, 16 Jun 2020 08:03:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:44: #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 08:03:45: #1 tags after filtering in treatment: 19280035 INFO @ Tue, 16 Jun 2020 08:03:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:46: #2 number of paired peaks: 138 WARNING @ Tue, 16 Jun 2020 08:03:46: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:46: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:03:46: #2 alternative fragment length(s) may be 1,43,491,523,564,587,595 bps INFO @ Tue, 16 Jun 2020 08:03:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.05_model.r WARNING @ Tue, 16 Jun 2020 08:03:46: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:46: #2 You may need to consider one of the other alternative d(s): 1,43,491,523,564,587,595 WARNING @ Tue, 16 Jun 2020 08:03:46: #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 08:03:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:48: 15000000 INFO @ Tue, 16 Jun 2020 08:03:51: 11000000 INFO @ Tue, 16 Jun 2020 08:03:55: 16000000 INFO @ Tue, 16 Jun 2020 08:03:58: 12000000 INFO @ Tue, 16 Jun 2020 08:04:02: 17000000 INFO @ Tue, 16 Jun 2020 08:04:05: 13000000 INFO @ Tue, 16 Jun 2020 08:04:09: 18000000 INFO @ Tue, 16 Jun 2020 08:04:12: 14000000 INFO @ Tue, 16 Jun 2020 08:04:16: 19000000 INFO @ Tue, 16 Jun 2020 08:04:18: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:04:18: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:04:18: #1 total tags in treatment: 19280035 INFO @ Tue, 16 Jun 2020 08:04:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:18: #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 08:04:18: #1 tags after filtering in treatment: 19280035 INFO @ Tue, 16 Jun 2020 08:04:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:18: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:04:19: 15000000 INFO @ Tue, 16 Jun 2020 08:04:20: #2 number of paired peaks: 138 WARNING @ Tue, 16 Jun 2020 08:04:20: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:20: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:04:20: #2 alternative fragment length(s) may be 1,43,491,523,564,587,595 bps INFO @ Tue, 16 Jun 2020 08:04:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.10_model.r WARNING @ Tue, 16 Jun 2020 08:04:20: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:20: #2 You may need to consider one of the other alternative d(s): 1,43,491,523,564,587,595 WARNING @ Tue, 16 Jun 2020 08:04:20: #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 08:04:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:25: 16000000 INFO @ Tue, 16 Jun 2020 08:04:31: 17000000 INFO @ Tue, 16 Jun 2020 08:04:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (634 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:37: 18000000 INFO @ Tue, 16 Jun 2020 08:04:43: 19000000 INFO @ Tue, 16 Jun 2020 08:04:45: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:04:45: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:04:45: #1 total tags in treatment: 19280035 INFO @ Tue, 16 Jun 2020 08:04:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:45: #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 08:04:45: #1 tags after filtering in treatment: 19280035 INFO @ Tue, 16 Jun 2020 08:04:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:46: #2 number of paired peaks: 138 WARNING @ Tue, 16 Jun 2020 08:04:46: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:46: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:04:46: #2 alternative fragment length(s) may be 1,43,491,523,564,587,595 bps INFO @ Tue, 16 Jun 2020 08:04:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.20_model.r WARNING @ Tue, 16 Jun 2020 08:04:46: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:46: #2 You may need to consider one of the other alternative d(s): 1,43,491,523,564,587,595 WARNING @ Tue, 16 Jun 2020 08:04:46: #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 08:04:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.10_summits.bed INFO @ Tue, 16 Jun 2020 08:05:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936240/SRX1936240.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 0 millis CompletedMACS2peakCalling