Job ID = 6367008 SRX = SRX257706 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:15:17 prefetch.2.10.7: 1) Downloading 'SRR800724'... 2020-06-15T23:15:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:16:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:16:29 prefetch.2.10.7: 'SRR800724' is valid 2020-06-15T23:16:29 prefetch.2.10.7: 1) 'SRR800724' was downloaded successfully Read 6914368 spots for SRR800724/SRR800724.sra Written 6914368 spots for SRR800724/SRR800724.sra 2020-06-15T23:17:01 prefetch.2.10.7: 1) Downloading 'SRR800725'... 2020-06-15T23:17:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:54 prefetch.2.10.7: 'SRR800725' is valid 2020-06-15T23:17:54 prefetch.2.10.7: 1) 'SRR800725' was downloaded successfully Read 8907367 spots for SRR800725/SRR800725.sra Written 8907367 spots for SRR800725/SRR800725.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:45 15821735 reads; of these: 15821735 (100.00%) were unpaired; of these: 241594 (1.53%) aligned 0 times 12969069 (81.97%) aligned exactly 1 time 2611072 (16.50%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 1382479 / 15580141 = 0.0887 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 08:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.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 08:26:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:50: 1000000 INFO @ Tue, 16 Jun 2020 08:26:56: 2000000 INFO @ Tue, 16 Jun 2020 08:27:02: 3000000 INFO @ Tue, 16 Jun 2020 08:27:08: 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 08:27:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.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 08:27:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:14: 5000000 INFO @ Tue, 16 Jun 2020 08:27:21: 1000000 INFO @ Tue, 16 Jun 2020 08:27:21: 6000000 INFO @ Tue, 16 Jun 2020 08:27:27: 2000000 INFO @ Tue, 16 Jun 2020 08:27:27: 7000000 INFO @ Tue, 16 Jun 2020 08:27:34: 3000000 INFO @ Tue, 16 Jun 2020 08:27:34: 8000000 INFO @ Tue, 16 Jun 2020 08:27:40: 4000000 INFO @ Tue, 16 Jun 2020 08:27:41: 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 08:27:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.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 08:27:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:48: 5000000 INFO @ Tue, 16 Jun 2020 08:27:48: 10000000 INFO @ Tue, 16 Jun 2020 08:27:51: 1000000 INFO @ Tue, 16 Jun 2020 08:27:55: 6000000 INFO @ Tue, 16 Jun 2020 08:27:55: 11000000 INFO @ Tue, 16 Jun 2020 08:27:59: 2000000 INFO @ Tue, 16 Jun 2020 08:28:02: 7000000 INFO @ Tue, 16 Jun 2020 08:28:02: 12000000 INFO @ Tue, 16 Jun 2020 08:28:06: 3000000 INFO @ Tue, 16 Jun 2020 08:28:10: 13000000 INFO @ Tue, 16 Jun 2020 08:28:10: 8000000 INFO @ Tue, 16 Jun 2020 08:28:15: 4000000 INFO @ Tue, 16 Jun 2020 08:28:17: 14000000 INFO @ Tue, 16 Jun 2020 08:28:17: 9000000 INFO @ Tue, 16 Jun 2020 08:28:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:18: #1 total tags in treatment: 14197662 INFO @ Tue, 16 Jun 2020 08:28:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:18: #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 08:28:19: #1 tags after filtering in treatment: 14197662 INFO @ Tue, 16 Jun 2020 08:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:20: #2 number of paired peaks: 281 WARNING @ Tue, 16 Jun 2020 08:28:20: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:20: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:28:20: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 08:28:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.05_model.r WARNING @ Tue, 16 Jun 2020 08:28:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:20: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 08:28:20: #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 08:28:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:23: 5000000 INFO @ Tue, 16 Jun 2020 08:28:24: 10000000 INFO @ Tue, 16 Jun 2020 08:28:30: 6000000 INFO @ Tue, 16 Jun 2020 08:28:31: 11000000 INFO @ Tue, 16 Jun 2020 08:28:38: 7000000 INFO @ Tue, 16 Jun 2020 08:28:38: 12000000 INFO @ Tue, 16 Jun 2020 08:28:45: 8000000 INFO @ Tue, 16 Jun 2020 08:28:45: 13000000 INFO @ Tue, 16 Jun 2020 08:28:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:53: 14000000 INFO @ Tue, 16 Jun 2020 08:28:53: 9000000 INFO @ Tue, 16 Jun 2020 08:28:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:54: #1 total tags in treatment: 14197662 INFO @ Tue, 16 Jun 2020 08:28:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:54: #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 08:28:54: #1 tags after filtering in treatment: 14197662 INFO @ Tue, 16 Jun 2020 08:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:55: #2 number of paired peaks: 281 WARNING @ Tue, 16 Jun 2020 08:28:55: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:55: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:28:55: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 08:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.10_model.r WARNING @ Tue, 16 Jun 2020 08:28:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:55: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 08:28:55: #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 08:28:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:00: 10000000 INFO @ Tue, 16 Jun 2020 08:29:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.05_summits.bed INFO @ Tue, 16 Jun 2020 08:29:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:29:06: 11000000 INFO @ Tue, 16 Jun 2020 08:29:13: 12000000 INFO @ Tue, 16 Jun 2020 08:29:20: 13000000 INFO @ Tue, 16 Jun 2020 08:29:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:27: 14000000 INFO @ Tue, 16 Jun 2020 08:29:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:29:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:29:28: #1 total tags in treatment: 14197662 INFO @ Tue, 16 Jun 2020 08:29:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:28: #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 08:29:28: #1 tags after filtering in treatment: 14197662 INFO @ Tue, 16 Jun 2020 08:29:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:29: #2 number of paired peaks: 281 WARNING @ Tue, 16 Jun 2020 08:29:29: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:29: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:29:29: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 08:29:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.20_model.r WARNING @ Tue, 16 Jun 2020 08:29:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:29:29: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 08:29:29: #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 08:29:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.10_summits.bed INFO @ Tue, 16 Jun 2020 08:29:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (464 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:29:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257706/SRX257706.20_summits.bed INFO @ Tue, 16 Jun 2020 08:30:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (184 records, 4 fields): 2 millis CompletedMACS2peakCalling