Job ID = 6367003 SRX = SRX257702 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:46 prefetch.2.10.7: 1) Downloading 'SRR800719'... 2020-06-15T23:09:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:13 prefetch.2.10.7: 1) 'SRR800719' was downloaded successfully Read 16440500 spots for SRR800719/SRR800719.sra Written 16440500 spots for SRR800719/SRR800719.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: 00:04:00 16440500 reads; of these: 16440500 (100.00%) were unpaired; of these: 137982 (0.84%) aligned 0 times 13513288 (82.20%) aligned exactly 1 time 2789230 (16.97%) aligned >1 times 99.16% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 1797790 / 16302518 = 0.1103 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 08:22:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.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 08:22:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:06: 1000000 INFO @ Tue, 16 Jun 2020 08:22:13: 2000000 INFO @ Tue, 16 Jun 2020 08:22:19: 3000000 INFO @ Tue, 16 Jun 2020 08:22:26: 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 08:22:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.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 08:22:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:32: 5000000 INFO @ Tue, 16 Jun 2020 08:22:36: 1000000 INFO @ Tue, 16 Jun 2020 08:22:39: 6000000 INFO @ Tue, 16 Jun 2020 08:22:41: 2000000 INFO @ Tue, 16 Jun 2020 08:22:46: 7000000 INFO @ Tue, 16 Jun 2020 08:22:47: 3000000 INFO @ Tue, 16 Jun 2020 08:22:52: 8000000 INFO @ Tue, 16 Jun 2020 08:22:53: 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 08:22:59: 9000000 INFO @ Tue, 16 Jun 2020 08:22:59: 5000000 INFO @ Tue, 16 Jun 2020 08:23:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.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 08:23:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:05: 6000000 INFO @ Tue, 16 Jun 2020 08:23:06: 10000000 INFO @ Tue, 16 Jun 2020 08:23:07: 1000000 INFO @ Tue, 16 Jun 2020 08:23:11: 7000000 INFO @ Tue, 16 Jun 2020 08:23:12: 11000000 INFO @ Tue, 16 Jun 2020 08:23:13: 2000000 INFO @ Tue, 16 Jun 2020 08:23:17: 8000000 INFO @ Tue, 16 Jun 2020 08:23:19: 12000000 INFO @ Tue, 16 Jun 2020 08:23:20: 3000000 INFO @ Tue, 16 Jun 2020 08:23:23: 9000000 INFO @ Tue, 16 Jun 2020 08:23:26: 13000000 INFO @ Tue, 16 Jun 2020 08:23:27: 4000000 INFO @ Tue, 16 Jun 2020 08:23:29: 10000000 INFO @ Tue, 16 Jun 2020 08:23:33: 14000000 INFO @ Tue, 16 Jun 2020 08:23:34: 5000000 INFO @ Tue, 16 Jun 2020 08:23:36: 11000000 INFO @ Tue, 16 Jun 2020 08:23:36: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:36: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:36: #1 total tags in treatment: 14504728 INFO @ Tue, 16 Jun 2020 08:23:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:36: #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 08:23:36: #1 tags after filtering in treatment: 14504728 INFO @ Tue, 16 Jun 2020 08:23:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:38: #2 number of paired peaks: 332 WARNING @ Tue, 16 Jun 2020 08:23:38: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:38: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:23:38: #2 alternative fragment length(s) may be 2,47,537 bps INFO @ Tue, 16 Jun 2020 08:23:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.05_model.r WARNING @ Tue, 16 Jun 2020 08:23:38: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:23:38: #2 You may need to consider one of the other alternative d(s): 2,47,537 WARNING @ Tue, 16 Jun 2020 08:23:38: #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 08:23:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:41: 6000000 INFO @ Tue, 16 Jun 2020 08:23:42: 12000000 INFO @ Tue, 16 Jun 2020 08:23:48: 13000000 INFO @ Tue, 16 Jun 2020 08:23:48: 7000000 INFO @ Tue, 16 Jun 2020 08:23:54: 14000000 INFO @ Tue, 16 Jun 2020 08:23:55: 8000000 INFO @ Tue, 16 Jun 2020 08:23:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:57: #1 total tags in treatment: 14504728 INFO @ Tue, 16 Jun 2020 08:23:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:57: #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 08:23:57: #1 tags after filtering in treatment: 14504728 INFO @ Tue, 16 Jun 2020 08:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:58: #2 number of paired peaks: 332 WARNING @ Tue, 16 Jun 2020 08:23:58: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:58: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:23:58: #2 alternative fragment length(s) may be 2,47,537 bps INFO @ Tue, 16 Jun 2020 08:23:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.10_model.r WARNING @ Tue, 16 Jun 2020 08:23:58: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:23:58: #2 You may need to consider one of the other alternative d(s): 2,47,537 WARNING @ Tue, 16 Jun 2020 08:23:58: #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 08:23:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:02: 9000000 INFO @ Tue, 16 Jun 2020 08:24:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:08: 10000000 INFO @ Tue, 16 Jun 2020 08:24:15: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:24:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (712 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:22: 12000000 INFO @ Tue, 16 Jun 2020 08:24:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:28: 13000000 INFO @ Tue, 16 Jun 2020 08:24:35: 14000000 INFO @ Tue, 16 Jun 2020 08:24:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:24:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:24:39: #1 total tags in treatment: 14504728 INFO @ Tue, 16 Jun 2020 08:24:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:39: #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 08:24:39: #1 tags after filtering in treatment: 14504728 INFO @ Tue, 16 Jun 2020 08:24:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.10_summits.bed INFO @ Tue, 16 Jun 2020 08:24:40: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (502 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:40: #2 number of paired peaks: 332 WARNING @ Tue, 16 Jun 2020 08:24:40: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:40: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:24:40: #2 alternative fragment length(s) may be 2,47,537 bps INFO @ Tue, 16 Jun 2020 08:24:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.20_model.r WARNING @ Tue, 16 Jun 2020 08:24:40: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:40: #2 You may need to consider one of the other alternative d(s): 2,47,537 WARNING @ Tue, 16 Jun 2020 08:24:40: #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 08:24:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257702/SRX257702.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 1 millis CompletedMACS2peakCalling