Job ID = 6368751 SRX = SRX5402774 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:05 prefetch.2.10.7: 1) Downloading 'SRR8603008'... 2020-06-16T00:28:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:14 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:14 prefetch.2.10.7: 'SRR8603008' is valid 2020-06-16T00:30:14 prefetch.2.10.7: 1) 'SRR8603008' was downloaded successfully 2020-06-16T00:30:15 prefetch.2.10.7: 'SRR8603008' has 0 unresolved dependencies Read 24152034 spots for SRR8603008/SRR8603008.sra Written 24152034 spots for SRR8603008/SRR8603008.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: 00:03:59 24152034 reads; of these: 24152034 (100.00%) were unpaired; of these: 10424850 (43.16%) aligned 0 times 11417202 (47.27%) aligned exactly 1 time 2309982 (9.56%) aligned >1 times 56.84% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 4126007 / 13727184 = 0.3006 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 09:38:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.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 09:38:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:16: 1000000 INFO @ Tue, 16 Jun 2020 09:38:21: 2000000 INFO @ Tue, 16 Jun 2020 09:38:26: 3000000 INFO @ Tue, 16 Jun 2020 09:38:32: 4000000 INFO @ Tue, 16 Jun 2020 09:38:37: 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 09:38:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.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 09:38:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:42: 6000000 INFO @ Tue, 16 Jun 2020 09:38:46: 1000000 INFO @ Tue, 16 Jun 2020 09:38:48: 7000000 INFO @ Tue, 16 Jun 2020 09:38:51: 2000000 INFO @ Tue, 16 Jun 2020 09:38:53: 8000000 INFO @ Tue, 16 Jun 2020 09:38:57: 3000000 INFO @ Tue, 16 Jun 2020 09:38:59: 9000000 INFO @ Tue, 16 Jun 2020 09:39:03: 4000000 INFO @ Tue, 16 Jun 2020 09:39:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:39:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:39:03: #1 total tags in treatment: 9601177 INFO @ Tue, 16 Jun 2020 09:39:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:03: #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 09:39:03: #1 tags after filtering in treatment: 9601177 INFO @ Tue, 16 Jun 2020 09:39:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:03: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 09:39:03: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:03: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:39:03: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:39:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.05_model.r WARNING @ Tue, 16 Jun 2020 09:39:03: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:39:03: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:39:03: #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 09:39:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:08: 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 09:39:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.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 09:39:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:14: 6000000 INFO @ Tue, 16 Jun 2020 09:39:16: 1000000 INFO @ Tue, 16 Jun 2020 09:39:20: 7000000 INFO @ Tue, 16 Jun 2020 09:39:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:22: 2000000 INFO @ Tue, 16 Jun 2020 09:39:26: 8000000 INFO @ Tue, 16 Jun 2020 09:39:28: 3000000 INFO @ Tue, 16 Jun 2020 09:39:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.05_summits.bed INFO @ Tue, 16 Jun 2020 09:39:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (702 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:39:32: 9000000 INFO @ Tue, 16 Jun 2020 09:39:34: 4000000 INFO @ Tue, 16 Jun 2020 09:39:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:39:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:39:35: #1 total tags in treatment: 9601177 INFO @ Tue, 16 Jun 2020 09:39:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:35: #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 09:39:35: #1 tags after filtering in treatment: 9601177 INFO @ Tue, 16 Jun 2020 09:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:36: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 09:39:36: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:36: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:39:36: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:39:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.10_model.r WARNING @ Tue, 16 Jun 2020 09:39:36: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:39:36: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:39:36: #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 09:39:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:40: 5000000 INFO @ Tue, 16 Jun 2020 09:39:45: 6000000 INFO @ Tue, 16 Jun 2020 09:39:51: 7000000 INFO @ Tue, 16 Jun 2020 09:39:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:56: 8000000 INFO @ Tue, 16 Jun 2020 09:40:01: 9000000 INFO @ Tue, 16 Jun 2020 09:40:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:04: #1 total tags in treatment: 9601177 INFO @ Tue, 16 Jun 2020 09:40:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:40:05: #1 tags after filtering in treatment: 9601177 INFO @ Tue, 16 Jun 2020 09:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:05: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 09:40:05: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:05: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:40:05: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:40:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.20_model.r WARNING @ Tue, 16 Jun 2020 09:40:05: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:05: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:40:05: #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 09:40:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:40:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402774/SRX5402774.20_summits.bed INFO @ Tue, 16 Jun 2020 09:40:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (179 records, 4 fields): 1 millis CompletedMACS2peakCalling