Job ID = 6368650 SRX = SRX529210 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:49 prefetch.2.10.7: 1) Downloading 'SRR1265814'... 2020-06-16T00:22:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:52 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:53 prefetch.2.10.7: 'SRR1265814' is valid 2020-06-16T00:24:53 prefetch.2.10.7: 1) 'SRR1265814' was downloaded successfully Read 19555555 spots for SRR1265814/SRR1265814.sra Written 19555555 spots for SRR1265814/SRR1265814.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: 00:02:32 19555555 reads; of these: 19555555 (100.00%) were unpaired; of these: 8711949 (44.55%) aligned 0 times 9074685 (46.40%) aligned exactly 1 time 1768921 (9.05%) aligned >1 times 55.45% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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_rmdupse_core] 648389 / 10843606 = 0.0598 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 09:30:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.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 09:30:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:04: 1000000 INFO @ Tue, 16 Jun 2020 09:31:09: 2000000 INFO @ Tue, 16 Jun 2020 09:31:14: 3000000 INFO @ Tue, 16 Jun 2020 09:31:20: 4000000 INFO @ Tue, 16 Jun 2020 09:31:25: 5000000 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 09:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.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 09:31:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:30: 6000000 INFO @ Tue, 16 Jun 2020 09:31:35: 1000000 INFO @ Tue, 16 Jun 2020 09:31:36: 7000000 INFO @ Tue, 16 Jun 2020 09:31:40: 2000000 INFO @ Tue, 16 Jun 2020 09:31:41: 8000000 INFO @ Tue, 16 Jun 2020 09:31:46: 3000000 INFO @ Tue, 16 Jun 2020 09:31:47: 9000000 INFO @ Tue, 16 Jun 2020 09:31:52: 4000000 INFO @ Tue, 16 Jun 2020 09:31:53: 10000000 INFO @ Tue, 16 Jun 2020 09:31:54: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:31:54: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:31:54: #1 total tags in treatment: 10195217 INFO @ Tue, 16 Jun 2020 09:31:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:54: #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 09:31:54: #1 tags after filtering in treatment: 10195217 INFO @ Tue, 16 Jun 2020 09:31:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:55: #2 number of paired peaks: 240 WARNING @ Tue, 16 Jun 2020 09:31:55: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:55: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 09:31:55: #2 alternative fragment length(s) may be 3,31,570,590 bps INFO @ Tue, 16 Jun 2020 09:31:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.05_model.r WARNING @ Tue, 16 Jun 2020 09:31:55: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:55: #2 You may need to consider one of the other alternative d(s): 3,31,570,590 WARNING @ Tue, 16 Jun 2020 09:31:55: #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 09:31:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:57: 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 09:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.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 09:31:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:02: 6000000 INFO @ Tue, 16 Jun 2020 09:32:05: 1000000 INFO @ Tue, 16 Jun 2020 09:32:08: 7000000 INFO @ Tue, 16 Jun 2020 09:32:10: 2000000 INFO @ Tue, 16 Jun 2020 09:32:13: 8000000 INFO @ Tue, 16 Jun 2020 09:32:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:15: 3000000 INFO @ Tue, 16 Jun 2020 09:32:19: 9000000 INFO @ Tue, 16 Jun 2020 09:32:21: 4000000 INFO @ Tue, 16 Jun 2020 09:32:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:24: Done! INFO @ Tue, 16 Jun 2020 09:32:24: 10000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (561 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:25: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:32:25: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:32:25: #1 total tags in treatment: 10195217 INFO @ Tue, 16 Jun 2020 09:32:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:25: #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 09:32:25: #1 tags after filtering in treatment: 10195217 INFO @ Tue, 16 Jun 2020 09:32:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:26: #2 number of paired peaks: 240 WARNING @ Tue, 16 Jun 2020 09:32:26: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:26: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 09:32:26: #2 alternative fragment length(s) may be 3,31,570,590 bps INFO @ Tue, 16 Jun 2020 09:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.10_model.r WARNING @ Tue, 16 Jun 2020 09:32:26: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:26: #2 You may need to consider one of the other alternative d(s): 3,31,570,590 WARNING @ Tue, 16 Jun 2020 09:32:26: #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 09:32:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:26: 5000000 INFO @ Tue, 16 Jun 2020 09:32:31: 6000000 INFO @ Tue, 16 Jun 2020 09:32:37: 7000000 INFO @ Tue, 16 Jun 2020 09:32:42: 8000000 INFO @ Tue, 16 Jun 2020 09:32:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:47: 9000000 INFO @ Tue, 16 Jun 2020 09:32:52: 10000000 INFO @ Tue, 16 Jun 2020 09:32:53: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:32:53: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:32:53: #1 total tags in treatment: 10195217 INFO @ Tue, 16 Jun 2020 09:32:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:53: #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 09:32:54: #1 tags after filtering in treatment: 10195217 INFO @ Tue, 16 Jun 2020 09:32:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:54: #2 number of paired peaks: 240 WARNING @ Tue, 16 Jun 2020 09:32:54: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:54: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 09:32:54: #2 alternative fragment length(s) may be 3,31,570,590 bps INFO @ Tue, 16 Jun 2020 09:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.20_model.r WARNING @ Tue, 16 Jun 2020 09:32:54: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:54: #2 You may need to consider one of the other alternative d(s): 3,31,570,590 WARNING @ Tue, 16 Jun 2020 09:32:54: #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 09:32:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (253 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529210/SRX529210.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 1 millis CompletedMACS2peakCalling