Job ID = 16435504 SRX = SRX13110320 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:09 16561614 reads; of these: 16561614 (100.00%) were unpaired; of these: 1883723 (11.37%) aligned 0 times 12494885 (75.44%) aligned exactly 1 time 2183006 (13.18%) aligned >1 times 88.63% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 1650100 / 14677891 = 0.1124 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:53:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.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, 02 Aug 2022 10:53:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:53:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:53:31: 1000000 INFO @ Tue, 02 Aug 2022 10:53:37: 2000000 INFO @ Tue, 02 Aug 2022 10:53:44: 3000000 INFO @ Tue, 02 Aug 2022 10:53:50: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:53:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.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, 02 Aug 2022 10:53:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:53:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:53:56: 5000000 INFO @ Tue, 02 Aug 2022 10:54:01: 1000000 INFO @ Tue, 02 Aug 2022 10:54:03: 6000000 INFO @ Tue, 02 Aug 2022 10:54:08: 2000000 INFO @ Tue, 02 Aug 2022 10:54:09: 7000000 INFO @ Tue, 02 Aug 2022 10:54:15: 3000000 INFO @ Tue, 02 Aug 2022 10:54:16: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:54:22: 4000000 INFO @ Tue, 02 Aug 2022 10:54:22: 9000000 INFO @ Tue, 02 Aug 2022 10:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.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, 02 Aug 2022 10:54:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:54:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:54:29: 10000000 INFO @ Tue, 02 Aug 2022 10:54:29: 5000000 INFO @ Tue, 02 Aug 2022 10:54:31: 1000000 INFO @ Tue, 02 Aug 2022 10:54:36: 11000000 INFO @ Tue, 02 Aug 2022 10:54:36: 6000000 INFO @ Tue, 02 Aug 2022 10:54:38: 2000000 INFO @ Tue, 02 Aug 2022 10:54:43: 12000000 INFO @ Tue, 02 Aug 2022 10:54:43: 7000000 INFO @ Tue, 02 Aug 2022 10:54:46: 3000000 INFO @ Tue, 02 Aug 2022 10:54:49: 13000000 INFO @ Tue, 02 Aug 2022 10:54:50: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:54:50: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:54:50: #1 total tags in treatment: 13027791 INFO @ Tue, 02 Aug 2022 10:54:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:54:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:54:50: #1 tags after filtering in treatment: 13027791 INFO @ Tue, 02 Aug 2022 10:54:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:54:50: #1 finished! INFO @ Tue, 02 Aug 2022 10:54:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:54:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:54:50: 8000000 INFO @ Tue, 02 Aug 2022 10:54:51: #2 number of paired peaks: 265 WARNING @ Tue, 02 Aug 2022 10:54:51: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 02 Aug 2022 10:54:51: start model_add_line... INFO @ Tue, 02 Aug 2022 10:54:51: start X-correlation... INFO @ Tue, 02 Aug 2022 10:54:51: end of X-cor INFO @ Tue, 02 Aug 2022 10:54:51: #2 finished! INFO @ Tue, 02 Aug 2022 10:54:51: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 10:54:51: #2 alternative fragment length(s) may be 4,82 bps INFO @ Tue, 02 Aug 2022 10:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.05_model.r WARNING @ Tue, 02 Aug 2022 10:54:51: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:54:51: #2 You may need to consider one of the other alternative d(s): 4,82 WARNING @ Tue, 02 Aug 2022 10:54:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:54:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:54:53: 4000000 INFO @ Tue, 02 Aug 2022 10:54:57: 9000000 INFO @ Tue, 02 Aug 2022 10:55:00: 5000000 INFO @ Tue, 02 Aug 2022 10:55:04: 10000000 INFO @ Tue, 02 Aug 2022 10:55:07: 6000000 INFO @ Tue, 02 Aug 2022 10:55:11: 11000000 INFO @ Tue, 02 Aug 2022 10:55:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:55:14: 7000000 INFO @ Tue, 02 Aug 2022 10:55:18: 12000000 INFO @ Tue, 02 Aug 2022 10:55:21: 8000000 INFO @ Tue, 02 Aug 2022 10:55:25: 13000000 INFO @ Tue, 02 Aug 2022 10:55:25: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:55:25: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:55:25: #1 total tags in treatment: 13027791 INFO @ Tue, 02 Aug 2022 10:55:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:55:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:55:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.05_summits.bed INFO @ Tue, 02 Aug 2022 10:55:25: Done! INFO @ Tue, 02 Aug 2022 10:55:25: #1 tags after filtering in treatment: 13027791 INFO @ Tue, 02 Aug 2022 10:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:55:25: #1 finished! INFO @ Tue, 02 Aug 2022 10:55:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:55:25: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1447 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:55:26: #2 number of paired peaks: 265 WARNING @ Tue, 02 Aug 2022 10:55:26: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 02 Aug 2022 10:55:26: start model_add_line... INFO @ Tue, 02 Aug 2022 10:55:26: start X-correlation... INFO @ Tue, 02 Aug 2022 10:55:26: end of X-cor INFO @ Tue, 02 Aug 2022 10:55:26: #2 finished! INFO @ Tue, 02 Aug 2022 10:55:26: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 10:55:26: #2 alternative fragment length(s) may be 4,82 bps INFO @ Tue, 02 Aug 2022 10:55:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.10_model.r WARNING @ Tue, 02 Aug 2022 10:55:26: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:55:26: #2 You may need to consider one of the other alternative d(s): 4,82 WARNING @ Tue, 02 Aug 2022 10:55:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:55:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:55:28: 9000000 INFO @ Tue, 02 Aug 2022 10:55:35: 10000000 INFO @ Tue, 02 Aug 2022 10:55:42: 11000000 INFO @ Tue, 02 Aug 2022 10:55:48: 12000000 INFO @ Tue, 02 Aug 2022 10:55:49: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:55:55: 13000000 INFO @ Tue, 02 Aug 2022 10:55:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:55:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:55:55: #1 total tags in treatment: 13027791 INFO @ Tue, 02 Aug 2022 10:55:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:55:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:55:56: #1 tags after filtering in treatment: 13027791 INFO @ Tue, 02 Aug 2022 10:55:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:55:56: #1 finished! INFO @ Tue, 02 Aug 2022 10:55:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:55:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:55:56: #2 number of paired peaks: 265 WARNING @ Tue, 02 Aug 2022 10:55:56: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 02 Aug 2022 10:55:56: start model_add_line... INFO @ Tue, 02 Aug 2022 10:55:57: start X-correlation... INFO @ Tue, 02 Aug 2022 10:55:57: end of X-cor INFO @ Tue, 02 Aug 2022 10:55:57: #2 finished! INFO @ Tue, 02 Aug 2022 10:55:57: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 10:55:57: #2 alternative fragment length(s) may be 4,82 bps INFO @ Tue, 02 Aug 2022 10:55:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.20_model.r WARNING @ Tue, 02 Aug 2022 10:55:57: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:55:57: #2 You may need to consider one of the other alternative d(s): 4,82 WARNING @ Tue, 02 Aug 2022 10:55:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:55:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:55:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.10_summits.bed INFO @ Tue, 02 Aug 2022 10:56:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (757 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:56:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:56:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:56:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:56:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110320/SRX13110320.20_summits.bed INFO @ Tue, 02 Aug 2022 10:56:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (315 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。