Job ID = 6368796 SRX = SRX5709762 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:32:30 prefetch.2.10.7: 1) Downloading 'SRR8928712'... 2020-06-16T00:32:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:34:54 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:34:54 prefetch.2.10.7: 1) 'SRR8928712' was downloaded successfully 2020-06-16T00:34:54 prefetch.2.10.7: 'SRR8928712' has 0 unresolved dependencies Read 27392700 spots for SRR8928712/SRR8928712.sra Written 27392700 spots for SRR8928712/SRR8928712.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: 00:05:04 27392700 reads; of these: 27392700 (100.00%) were unpaired; of these: 7611235 (27.79%) aligned 0 times 16407581 (59.90%) aligned exactly 1 time 3373884 (12.32%) aligned >1 times 72.21% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 9366178 / 19781465 = 0.4735 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 09:45:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.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 09:45:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:38: 1000000 INFO @ Tue, 16 Jun 2020 09:45:44: 2000000 INFO @ Tue, 16 Jun 2020 09:45:49: 3000000 INFO @ Tue, 16 Jun 2020 09:45:55: 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 09:46:01: 5000000 INFO @ Tue, 16 Jun 2020 09:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.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 09:46:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:08: 6000000 INFO @ Tue, 16 Jun 2020 09:46:09: 1000000 INFO @ Tue, 16 Jun 2020 09:46:15: 7000000 INFO @ Tue, 16 Jun 2020 09:46:16: 2000000 INFO @ Tue, 16 Jun 2020 09:46:22: 8000000 INFO @ Tue, 16 Jun 2020 09:46:23: 3000000 INFO @ Tue, 16 Jun 2020 09:46:29: 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 09:46:30: 4000000 INFO @ Tue, 16 Jun 2020 09:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.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 09:46:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:36: 10000000 INFO @ Tue, 16 Jun 2020 09:46:38: 5000000 INFO @ Tue, 16 Jun 2020 09:46:39: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:46:39: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:46:39: #1 total tags in treatment: 10415287 INFO @ Tue, 16 Jun 2020 09:46:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:39: #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 09:46:39: #1 tags after filtering in treatment: 10415287 INFO @ Tue, 16 Jun 2020 09:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:40: 1000000 INFO @ Tue, 16 Jun 2020 09:46:40: #2 number of paired peaks: 489 WARNING @ Tue, 16 Jun 2020 09:46:40: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:40: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:46:40: #2 alternative fragment length(s) may be 1,43,527,550 bps INFO @ Tue, 16 Jun 2020 09:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.05_model.r WARNING @ Tue, 16 Jun 2020 09:46:40: #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 09:46:40: #2 You may need to consider one of the other alternative d(s): 1,43,527,550 WARNING @ Tue, 16 Jun 2020 09:46:40: #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 09:46:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:45: 6000000 INFO @ Tue, 16 Jun 2020 09:46:48: 2000000 INFO @ Tue, 16 Jun 2020 09:46:53: 7000000 INFO @ Tue, 16 Jun 2020 09:46:57: 3000000 INFO @ Tue, 16 Jun 2020 09:47:00: 8000000 INFO @ Tue, 16 Jun 2020 09:47:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:05: 4000000 INFO @ Tue, 16 Jun 2020 09:47:08: 9000000 INFO @ Tue, 16 Jun 2020 09:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.05_summits.bed INFO @ Tue, 16 Jun 2020 09:47:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (825 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:13: 5000000 INFO @ Tue, 16 Jun 2020 09:47:16: 10000000 INFO @ Tue, 16 Jun 2020 09:47:19: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:47:19: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:47:19: #1 total tags in treatment: 10415287 INFO @ Tue, 16 Jun 2020 09:47:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:19: #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 09:47:19: #1 tags after filtering in treatment: 10415287 INFO @ Tue, 16 Jun 2020 09:47:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:19: #2 number of paired peaks: 489 WARNING @ Tue, 16 Jun 2020 09:47:19: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:20: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:47:20: #2 alternative fragment length(s) may be 1,43,527,550 bps INFO @ Tue, 16 Jun 2020 09:47:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.10_model.r WARNING @ Tue, 16 Jun 2020 09:47:20: #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 09:47:20: #2 You may need to consider one of the other alternative d(s): 1,43,527,550 WARNING @ Tue, 16 Jun 2020 09:47:20: #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 09:47:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:21: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:47:28: 7000000 INFO @ Tue, 16 Jun 2020 09:47:36: 8000000 INFO @ Tue, 16 Jun 2020 09:47:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:43: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:47:50: 10000000 INFO @ Tue, 16 Jun 2020 09:47:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.10_summits.bed INFO @ Tue, 16 Jun 2020 09:47:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (551 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:53: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:47:53: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:47:53: #1 total tags in treatment: 10415287 INFO @ Tue, 16 Jun 2020 09:47:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:53: #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 09:47:53: #1 tags after filtering in treatment: 10415287 INFO @ Tue, 16 Jun 2020 09:47:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:54: #2 number of paired peaks: 489 WARNING @ Tue, 16 Jun 2020 09:47:54: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:54: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:47:54: #2 alternative fragment length(s) may be 1,43,527,550 bps INFO @ Tue, 16 Jun 2020 09:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.20_model.r WARNING @ Tue, 16 Jun 2020 09:47:54: #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 09:47:54: #2 You may need to consider one of the other alternative d(s): 1,43,527,550 WARNING @ Tue, 16 Jun 2020 09:47:54: #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 09:47:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709762/SRX5709762.20_summits.bed INFO @ Tue, 16 Jun 2020 09:48:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 1 millis CompletedMACS2peakCalling