Job ID = 6366868 SRX = SRX2370186 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:38 prefetch.2.10.7: 1) Downloading 'SRR5047587'... 2020-06-15T23:07:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:09:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:09:09 prefetch.2.10.7: 'SRR5047587' is valid 2020-06-15T23:09:09 prefetch.2.10.7: 1) 'SRR5047587' was downloaded successfully Read 20098596 spots for SRR5047587/SRR5047587.sra Written 20098596 spots for SRR5047587/SRR5047587.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: 00:04:36 20098596 reads; of these: 20098596 (100.00%) were unpaired; of these: 1280637 (6.37%) aligned 0 times 15326389 (76.26%) aligned exactly 1 time 3491570 (17.37%) aligned >1 times 93.63% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 9655798 / 18817959 = 0.5131 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 08:19:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.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 08:19:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:08: 1000000 INFO @ Tue, 16 Jun 2020 08:19:13: 2000000 INFO @ Tue, 16 Jun 2020 08:19:18: 3000000 INFO @ Tue, 16 Jun 2020 08:19:22: 4000000 INFO @ Tue, 16 Jun 2020 08:19:27: 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 08:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.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 08:19:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:32: 6000000 INFO @ Tue, 16 Jun 2020 08:19:37: 1000000 INFO @ Tue, 16 Jun 2020 08:19:37: 7000000 INFO @ Tue, 16 Jun 2020 08:19:41: 2000000 INFO @ Tue, 16 Jun 2020 08:19:42: 8000000 INFO @ Tue, 16 Jun 2020 08:19:46: 9000000 INFO @ Tue, 16 Jun 2020 08:19:46: 3000000 INFO @ Tue, 16 Jun 2020 08:19:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:19:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:19:47: #1 total tags in treatment: 9162161 INFO @ Tue, 16 Jun 2020 08:19:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:47: #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 08:19:47: #1 tags after filtering in treatment: 9162161 INFO @ Tue, 16 Jun 2020 08:19:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:48: #2 number of paired peaks: 505 WARNING @ Tue, 16 Jun 2020 08:19:48: Fewer paired peaks (505) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 505 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:48: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:19:48: #2 alternative fragment length(s) may be 2,42,562 bps INFO @ Tue, 16 Jun 2020 08:19:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.05_model.r WARNING @ Tue, 16 Jun 2020 08:19:48: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:48: #2 You may need to consider one of the other alternative d(s): 2,42,562 WARNING @ Tue, 16 Jun 2020 08:19:48: #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 08:19:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:51: 4000000 INFO @ Tue, 16 Jun 2020 08:19:56: 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 08:20:01: 6000000 INFO @ Tue, 16 Jun 2020 08:20:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.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 08:20:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:06: 7000000 INFO @ Tue, 16 Jun 2020 08:20:07: 1000000 INFO @ Tue, 16 Jun 2020 08:20:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:11: 8000000 INFO @ Tue, 16 Jun 2020 08:20:12: 2000000 INFO @ Tue, 16 Jun 2020 08:20:16: 9000000 INFO @ Tue, 16 Jun 2020 08:20:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (710 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:16: 3000000 INFO @ Tue, 16 Jun 2020 08:20:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:20:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:20:17: #1 total tags in treatment: 9162161 INFO @ Tue, 16 Jun 2020 08:20:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:17: #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 08:20:17: #1 tags after filtering in treatment: 9162161 INFO @ Tue, 16 Jun 2020 08:20:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:17: #2 number of paired peaks: 505 WARNING @ Tue, 16 Jun 2020 08:20:17: Fewer paired peaks (505) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 505 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:18: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:20:18: #2 alternative fragment length(s) may be 2,42,562 bps INFO @ Tue, 16 Jun 2020 08:20:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.10_model.r WARNING @ Tue, 16 Jun 2020 08:20:18: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:18: #2 You may need to consider one of the other alternative d(s): 2,42,562 WARNING @ Tue, 16 Jun 2020 08:20:18: #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 08:20:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:21: 4000000 INFO @ Tue, 16 Jun 2020 08:20:26: 5000000 INFO @ Tue, 16 Jun 2020 08:20:31: 6000000 INFO @ Tue, 16 Jun 2020 08:20:35: 7000000 INFO @ Tue, 16 Jun 2020 08:20:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:40: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:45: 9000000 INFO @ Tue, 16 Jun 2020 08:20:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:46: Done! INFO @ Tue, 16 Jun 2020 08:20:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:20:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:20:46: #1 total tags in treatment: 9162161 INFO @ Tue, 16 Jun 2020 08:20:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (484 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:46: #1 tags after filtering in treatment: 9162161 INFO @ Tue, 16 Jun 2020 08:20:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:47: #2 number of paired peaks: 505 WARNING @ Tue, 16 Jun 2020 08:20:47: Fewer paired peaks (505) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 505 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:47: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:20:47: #2 alternative fragment length(s) may be 2,42,562 bps INFO @ Tue, 16 Jun 2020 08:20:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.20_model.r WARNING @ Tue, 16 Jun 2020 08:20:47: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:47: #2 You may need to consider one of the other alternative d(s): 2,42,562 WARNING @ Tue, 16 Jun 2020 08:20:47: #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 08:20:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2370186/SRX2370186.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 1 millis CompletedMACS2peakCalling