Job ID = 14160110 SRX = SRX3180778 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:48 20986887 reads; of these: 20986887 (100.00%) were unpaired; of these: 449130 (2.14%) aligned 0 times 16645899 (79.32%) aligned exactly 1 time 3891858 (18.54%) aligned >1 times 97.86% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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] 3714843 / 20537757 = 0.1809 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:59:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.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 @ Thu, 09 Dec 2021 00:59:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:59:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:59:21: 1000000 INFO @ Thu, 09 Dec 2021 00:59:27: 2000000 INFO @ Thu, 09 Dec 2021 00:59:33: 3000000 INFO @ Thu, 09 Dec 2021 00:59:38: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:59:44: 5000000 INFO @ Thu, 09 Dec 2021 00:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.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 @ Thu, 09 Dec 2021 00:59:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:59:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:59:50: 6000000 INFO @ Thu, 09 Dec 2021 00:59:50: 1000000 INFO @ Thu, 09 Dec 2021 00:59:55: 2000000 INFO @ Thu, 09 Dec 2021 00:59:56: 7000000 INFO @ Thu, 09 Dec 2021 01:00:01: 3000000 INFO @ Thu, 09 Dec 2021 01:00:02: 8000000 INFO @ Thu, 09 Dec 2021 01:00:06: 4000000 INFO @ Thu, 09 Dec 2021 01:00:08: 9000000 INFO @ Thu, 09 Dec 2021 01:00:11: 5000000 BedGraph に変換中... INFO @ Thu, 09 Dec 2021 01:00:13: 10000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 01:00:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.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 @ Thu, 09 Dec 2021 01:00:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:00:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:00:16: 6000000 INFO @ Thu, 09 Dec 2021 01:00:19: 11000000 INFO @ Thu, 09 Dec 2021 01:00:20: 1000000 INFO @ Thu, 09 Dec 2021 01:00:21: 7000000 INFO @ Thu, 09 Dec 2021 01:00:25: 12000000 INFO @ Thu, 09 Dec 2021 01:00:26: 2000000 INFO @ Thu, 09 Dec 2021 01:00:26: 8000000 INFO @ Thu, 09 Dec 2021 01:00:30: 13000000 INFO @ Thu, 09 Dec 2021 01:00:31: 3000000 INFO @ Thu, 09 Dec 2021 01:00:31: 9000000 INFO @ Thu, 09 Dec 2021 01:00:36: 4000000 INFO @ Thu, 09 Dec 2021 01:00:36: 14000000 INFO @ Thu, 09 Dec 2021 01:00:36: 10000000 INFO @ Thu, 09 Dec 2021 01:00:41: 5000000 INFO @ Thu, 09 Dec 2021 01:00:41: 11000000 INFO @ Thu, 09 Dec 2021 01:00:42: 15000000 INFO @ Thu, 09 Dec 2021 01:00:46: 6000000 INFO @ Thu, 09 Dec 2021 01:00:46: 12000000 INFO @ Thu, 09 Dec 2021 01:00:47: 16000000 INFO @ Thu, 09 Dec 2021 01:00:51: 7000000 INFO @ Thu, 09 Dec 2021 01:00:51: 13000000 INFO @ Thu, 09 Dec 2021 01:00:52: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:00:52: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:00:52: #1 total tags in treatment: 16822914 INFO @ Thu, 09 Dec 2021 01:00:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:00:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:00:52: #1 tags after filtering in treatment: 16822914 INFO @ Thu, 09 Dec 2021 01:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:00:52: #1 finished! INFO @ Thu, 09 Dec 2021 01:00:52: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:00:53: #2 number of paired peaks: 365 WARNING @ Thu, 09 Dec 2021 01:00:53: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Thu, 09 Dec 2021 01:00:53: start model_add_line... INFO @ Thu, 09 Dec 2021 01:00:53: start X-correlation... INFO @ Thu, 09 Dec 2021 01:00:53: end of X-cor INFO @ Thu, 09 Dec 2021 01:00:53: #2 finished! INFO @ Thu, 09 Dec 2021 01:00:53: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 01:00:53: #2 alternative fragment length(s) may be 2,48,530,567 bps INFO @ Thu, 09 Dec 2021 01:00:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.05_model.r WARNING @ Thu, 09 Dec 2021 01:00:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:00:53: #2 You may need to consider one of the other alternative d(s): 2,48,530,567 WARNING @ Thu, 09 Dec 2021 01:00:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:00:53: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:00:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:00:56: 8000000 INFO @ Thu, 09 Dec 2021 01:00:56: 14000000 INFO @ Thu, 09 Dec 2021 01:01:01: 9000000 INFO @ Thu, 09 Dec 2021 01:01:01: 15000000 INFO @ Thu, 09 Dec 2021 01:01:06: 10000000 INFO @ Thu, 09 Dec 2021 01:01:06: 16000000 INFO @ Thu, 09 Dec 2021 01:01:10: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:01:10: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:01:10: #1 total tags in treatment: 16822914 INFO @ Thu, 09 Dec 2021 01:01:10: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:01:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:01:11: #1 tags after filtering in treatment: 16822914 INFO @ Thu, 09 Dec 2021 01:01:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:01:11: #1 finished! INFO @ Thu, 09 Dec 2021 01:01:11: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:01:11: 11000000 INFO @ Thu, 09 Dec 2021 01:01:12: #2 number of paired peaks: 365 WARNING @ Thu, 09 Dec 2021 01:01:12: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Thu, 09 Dec 2021 01:01:12: start model_add_line... INFO @ Thu, 09 Dec 2021 01:01:12: start X-correlation... INFO @ Thu, 09 Dec 2021 01:01:12: end of X-cor INFO @ Thu, 09 Dec 2021 01:01:12: #2 finished! INFO @ Thu, 09 Dec 2021 01:01:12: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 01:01:12: #2 alternative fragment length(s) may be 2,48,530,567 bps INFO @ Thu, 09 Dec 2021 01:01:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.10_model.r WARNING @ Thu, 09 Dec 2021 01:01:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:01:12: #2 You may need to consider one of the other alternative d(s): 2,48,530,567 WARNING @ Thu, 09 Dec 2021 01:01:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:01:12: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:01:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:01:16: 12000000 INFO @ Thu, 09 Dec 2021 01:01:20: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:01:20: 13000000 INFO @ Thu, 09 Dec 2021 01:01:25: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:01:30: 15000000 INFO @ Thu, 09 Dec 2021 01:01:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:01:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:01:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.05_summits.bed INFO @ Thu, 09 Dec 2021 01:01:34: Done! INFO @ Thu, 09 Dec 2021 01:01:35: 16000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (770 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:01:39: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:01:39: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:01:39: #1 total tags in treatment: 16822914 INFO @ Thu, 09 Dec 2021 01:01:39: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:01:39: #1 tags after filtering in treatment: 16822914 INFO @ Thu, 09 Dec 2021 01:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:01:39: #1 finished! INFO @ Thu, 09 Dec 2021 01:01:39: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:01:39: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:01:40: #2 number of paired peaks: 365 WARNING @ Thu, 09 Dec 2021 01:01:40: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Thu, 09 Dec 2021 01:01:40: start model_add_line... INFO @ Thu, 09 Dec 2021 01:01:40: start X-correlation... INFO @ Thu, 09 Dec 2021 01:01:40: end of X-cor INFO @ Thu, 09 Dec 2021 01:01:40: #2 finished! INFO @ Thu, 09 Dec 2021 01:01:40: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 01:01:40: #2 alternative fragment length(s) may be 2,48,530,567 bps INFO @ Thu, 09 Dec 2021 01:01:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.20_model.r WARNING @ Thu, 09 Dec 2021 01:01:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:01:40: #2 You may need to consider one of the other alternative d(s): 2,48,530,567 WARNING @ Thu, 09 Dec 2021 01:01:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:01:40: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:01:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.10_summits.bed INFO @ Thu, 09 Dec 2021 01:01:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (519 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:02:09: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:02:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:02:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:02:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180778/SRX3180778.20_summits.bed INFO @ Thu, 09 Dec 2021 01:02:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (210 records, 4 fields): 2 millis CompletedMACS2peakCalling