Job ID = 6366656 SRX = SRX216755 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:59 prefetch.2.10.7: 1) Downloading 'SRR648390'... 2020-06-15T22:54:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:07 prefetch.2.10.7: 1) 'SRR648390' was downloaded successfully Read 21662435 spots for SRR648390/SRR648390.sra Written 21662435 spots for SRR648390/SRR648390.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: 00:04:56 21662435 reads; of these: 21662435 (100.00%) were unpaired; of these: 926265 (4.28%) aligned 0 times 17801852 (82.18%) aligned exactly 1 time 2934318 (13.55%) aligned >1 times 95.72% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 2174592 / 20736170 = 0.1049 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 08:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.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 08:08:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:28: 1000000 INFO @ Tue, 16 Jun 2020 08:08:34: 2000000 INFO @ Tue, 16 Jun 2020 08:08:40: 3000000 INFO @ Tue, 16 Jun 2020 08:08:45: 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 08:08:51: 5000000 INFO @ Tue, 16 Jun 2020 08:08:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.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 08:08:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:57: 6000000 INFO @ Tue, 16 Jun 2020 08:08:58: 1000000 INFO @ Tue, 16 Jun 2020 08:09:02: 7000000 INFO @ Tue, 16 Jun 2020 08:09:04: 2000000 INFO @ Tue, 16 Jun 2020 08:09:08: 8000000 INFO @ Tue, 16 Jun 2020 08:09:09: 3000000 INFO @ Tue, 16 Jun 2020 08:09:14: 9000000 INFO @ Tue, 16 Jun 2020 08:09:15: 4000000 INFO @ Tue, 16 Jun 2020 08:09:20: 10000000 INFO @ Tue, 16 Jun 2020 08:09:20: 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 08:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.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 08:09:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:26: 11000000 INFO @ Tue, 16 Jun 2020 08:09:26: 6000000 INFO @ Tue, 16 Jun 2020 08:09:28: 1000000 INFO @ Tue, 16 Jun 2020 08:09:31: 7000000 INFO @ Tue, 16 Jun 2020 08:09:32: 12000000 INFO @ Tue, 16 Jun 2020 08:09:33: 2000000 INFO @ Tue, 16 Jun 2020 08:09:37: 8000000 INFO @ Tue, 16 Jun 2020 08:09:38: 13000000 INFO @ Tue, 16 Jun 2020 08:09:38: 3000000 INFO @ Tue, 16 Jun 2020 08:09:43: 9000000 INFO @ Tue, 16 Jun 2020 08:09:43: 4000000 INFO @ Tue, 16 Jun 2020 08:09:43: 14000000 INFO @ Tue, 16 Jun 2020 08:09:48: 5000000 INFO @ Tue, 16 Jun 2020 08:09:48: 10000000 INFO @ Tue, 16 Jun 2020 08:09:49: 15000000 INFO @ Tue, 16 Jun 2020 08:09:53: 6000000 INFO @ Tue, 16 Jun 2020 08:09:54: 11000000 INFO @ Tue, 16 Jun 2020 08:09:55: 16000000 INFO @ Tue, 16 Jun 2020 08:09:58: 7000000 INFO @ Tue, 16 Jun 2020 08:10:00: 12000000 INFO @ Tue, 16 Jun 2020 08:10:01: 17000000 INFO @ Tue, 16 Jun 2020 08:10:03: 8000000 INFO @ Tue, 16 Jun 2020 08:10:05: 13000000 INFO @ Tue, 16 Jun 2020 08:10:07: 18000000 INFO @ Tue, 16 Jun 2020 08:10:08: 9000000 INFO @ Tue, 16 Jun 2020 08:10:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:10:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:10:10: #1 total tags in treatment: 18561578 INFO @ Tue, 16 Jun 2020 08:10:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:10: #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 08:10:11: #1 tags after filtering in treatment: 18561578 INFO @ Tue, 16 Jun 2020 08:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:11: 14000000 INFO @ Tue, 16 Jun 2020 08:10:12: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 08:10:12: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:12: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:10:12: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:10:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.05_model.r WARNING @ Tue, 16 Jun 2020 08:10:12: #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 08:10:12: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:10:12: #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 08:10:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:13: 10000000 INFO @ Tue, 16 Jun 2020 08:10:16: 15000000 INFO @ Tue, 16 Jun 2020 08:10:18: 11000000 INFO @ Tue, 16 Jun 2020 08:10:22: 16000000 INFO @ Tue, 16 Jun 2020 08:10:24: 12000000 INFO @ Tue, 16 Jun 2020 08:10:28: 17000000 INFO @ Tue, 16 Jun 2020 08:10:29: 13000000 INFO @ Tue, 16 Jun 2020 08:10:33: 18000000 INFO @ Tue, 16 Jun 2020 08:10:34: 14000000 INFO @ Tue, 16 Jun 2020 08:10:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:10:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:10:37: #1 total tags in treatment: 18561578 INFO @ Tue, 16 Jun 2020 08:10:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:37: #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 08:10:37: #1 tags after filtering in treatment: 18561578 INFO @ Tue, 16 Jun 2020 08:10:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:38: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 08:10:38: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:38: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:10:38: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.10_model.r WARNING @ Tue, 16 Jun 2020 08:10:38: #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 08:10:38: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:10:38: #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 08:10:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:39: 15000000 INFO @ Tue, 16 Jun 2020 08:10:44: 16000000 INFO @ Tue, 16 Jun 2020 08:10:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:49: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:10:54: 18000000 INFO @ Tue, 16 Jun 2020 08:10:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:10:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:10:57: #1 total tags in treatment: 18561578 INFO @ Tue, 16 Jun 2020 08:10:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:57: #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 08:10:58: #1 tags after filtering in treatment: 18561578 INFO @ Tue, 16 Jun 2020 08:10:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:59: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 08:10:59: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:59: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:10:59: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:10:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.20_model.r WARNING @ Tue, 16 Jun 2020 08:10:59: #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 08:10:59: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:10:59: #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 08:10:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (934 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.10_summits.bed INFO @ Tue, 16 Jun 2020 08:11:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (448 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX216755/SRX216755.20_summits.bed INFO @ Tue, 16 Jun 2020 08:11:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling