Job ID = 14159951 SRX = SRX3180776 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: 00:00:01 Multiseed full-index search: 00:04:34 18134381 reads; of these: 18134381 (100.00%) were unpaired; of these: 704282 (3.88%) aligned 0 times 14515052 (80.04%) aligned exactly 1 time 2915047 (16.07%) aligned >1 times 96.12% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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] 3350512 / 17430099 = 0.1922 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 00:52:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.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 00:52:28: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:52:28: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:52:35: 1000000 INFO @ Thu, 09 Dec 2021 00:52:42: 2000000 INFO @ Thu, 09 Dec 2021 00:52:49: 3000000 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 00:52:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.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 00:52:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:52:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:52:56: 4000000 INFO @ Thu, 09 Dec 2021 00:53:04: 5000000 INFO @ Thu, 09 Dec 2021 00:53:06: 1000000 INFO @ Thu, 09 Dec 2021 00:53:11: 6000000 INFO @ Thu, 09 Dec 2021 00:53:15: 2000000 INFO @ Thu, 09 Dec 2021 00:53:19: 7000000 INFO @ Thu, 09 Dec 2021 00:53:24: 3000000 BedGraph に変換中... 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 00:53:26: 8000000 INFO @ Thu, 09 Dec 2021 00:53:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.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 00:53:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:53:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:53:33: 4000000 INFO @ Thu, 09 Dec 2021 00:53:34: 9000000 INFO @ Thu, 09 Dec 2021 00:53:35: 1000000 INFO @ Thu, 09 Dec 2021 00:53:42: 10000000 INFO @ Thu, 09 Dec 2021 00:53:42: 5000000 INFO @ Thu, 09 Dec 2021 00:53:43: 2000000 INFO @ Thu, 09 Dec 2021 00:53:50: 11000000 INFO @ Thu, 09 Dec 2021 00:53:51: 3000000 INFO @ Thu, 09 Dec 2021 00:53:51: 6000000 INFO @ Thu, 09 Dec 2021 00:53:58: 12000000 INFO @ Thu, 09 Dec 2021 00:53:59: 4000000 INFO @ Thu, 09 Dec 2021 00:54:01: 7000000 INFO @ Thu, 09 Dec 2021 00:54:06: 13000000 INFO @ Thu, 09 Dec 2021 00:54:07: 5000000 INFO @ Thu, 09 Dec 2021 00:54:10: 8000000 INFO @ Thu, 09 Dec 2021 00:54:14: 14000000 INFO @ Thu, 09 Dec 2021 00:54:15: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:54:15: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:54:15: #1 total tags in treatment: 14079587 INFO @ Thu, 09 Dec 2021 00:54:15: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:54:15: #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 00:54:15: #1 tags after filtering in treatment: 14079587 INFO @ Thu, 09 Dec 2021 00:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:54:15: #1 finished! INFO @ Thu, 09 Dec 2021 00:54:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:54:15: 6000000 INFO @ Thu, 09 Dec 2021 00:54:16: #2 number of paired peaks: 315 WARNING @ Thu, 09 Dec 2021 00:54:16: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Thu, 09 Dec 2021 00:54:16: start model_add_line... INFO @ Thu, 09 Dec 2021 00:54:16: start X-correlation... INFO @ Thu, 09 Dec 2021 00:54:16: end of X-cor INFO @ Thu, 09 Dec 2021 00:54:16: #2 finished! INFO @ Thu, 09 Dec 2021 00:54:16: #2 predicted fragment length is 45 bps INFO @ Thu, 09 Dec 2021 00:54:16: #2 alternative fragment length(s) may be 2,45,560 bps INFO @ Thu, 09 Dec 2021 00:54:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.05_model.r WARNING @ Thu, 09 Dec 2021 00:54:16: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:54:16: #2 You may need to consider one of the other alternative d(s): 2,45,560 WARNING @ Thu, 09 Dec 2021 00:54:16: #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 00:54:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:54:19: 9000000 INFO @ Thu, 09 Dec 2021 00:54:22: 7000000 INFO @ Thu, 09 Dec 2021 00:54:28: 10000000 INFO @ Thu, 09 Dec 2021 00:54:30: 8000000 INFO @ Thu, 09 Dec 2021 00:54:37: 9000000 INFO @ Thu, 09 Dec 2021 00:54:38: 11000000 INFO @ Thu, 09 Dec 2021 00:54:44: 10000000 INFO @ Thu, 09 Dec 2021 00:54:47: 12000000 INFO @ Thu, 09 Dec 2021 00:54:51: 11000000 INFO @ Thu, 09 Dec 2021 00:54:52: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:54:56: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:54:59: 12000000 INFO @ Thu, 09 Dec 2021 00:55:05: 14000000 INFO @ Thu, 09 Dec 2021 00:55:05: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:55:05: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:55:05: #1 total tags in treatment: 14079587 INFO @ Thu, 09 Dec 2021 00:55:05: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:55:05: #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 00:55:06: #1 tags after filtering in treatment: 14079587 INFO @ Thu, 09 Dec 2021 00:55:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:55:06: #1 finished! INFO @ Thu, 09 Dec 2021 00:55:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:55:06: 13000000 INFO @ Thu, 09 Dec 2021 00:55:07: #2 number of paired peaks: 315 WARNING @ Thu, 09 Dec 2021 00:55:07: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Thu, 09 Dec 2021 00:55:07: start model_add_line... INFO @ Thu, 09 Dec 2021 00:55:07: start X-correlation... INFO @ Thu, 09 Dec 2021 00:55:07: end of X-cor INFO @ Thu, 09 Dec 2021 00:55:07: #2 finished! INFO @ Thu, 09 Dec 2021 00:55:07: #2 predicted fragment length is 45 bps INFO @ Thu, 09 Dec 2021 00:55:07: #2 alternative fragment length(s) may be 2,45,560 bps INFO @ Thu, 09 Dec 2021 00:55:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.10_model.r WARNING @ Thu, 09 Dec 2021 00:55:07: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:55:07: #2 You may need to consider one of the other alternative d(s): 2,45,560 WARNING @ Thu, 09 Dec 2021 00:55:07: #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 00:55:07: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:55:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:55:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:55:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:55:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.05_summits.bed INFO @ Thu, 09 Dec 2021 00:55:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:55:13: 14000000 INFO @ Thu, 09 Dec 2021 00:55:14: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:55:14: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:55:14: #1 total tags in treatment: 14079587 INFO @ Thu, 09 Dec 2021 00:55:14: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:55:14: #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 00:55:14: #1 tags after filtering in treatment: 14079587 INFO @ Thu, 09 Dec 2021 00:55:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:55:14: #1 finished! INFO @ Thu, 09 Dec 2021 00:55:14: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:55:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:55:16: #2 number of paired peaks: 315 WARNING @ Thu, 09 Dec 2021 00:55:16: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Thu, 09 Dec 2021 00:55:16: start model_add_line... INFO @ Thu, 09 Dec 2021 00:55:16: start X-correlation... INFO @ Thu, 09 Dec 2021 00:55:16: end of X-cor INFO @ Thu, 09 Dec 2021 00:55:16: #2 finished! INFO @ Thu, 09 Dec 2021 00:55:16: #2 predicted fragment length is 45 bps INFO @ Thu, 09 Dec 2021 00:55:16: #2 alternative fragment length(s) may be 2,45,560 bps INFO @ Thu, 09 Dec 2021 00:55:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.20_model.r WARNING @ Thu, 09 Dec 2021 00:55:16: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:55:16: #2 You may need to consider one of the other alternative d(s): 2,45,560 WARNING @ Thu, 09 Dec 2021 00:55:16: #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 00:55:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:55:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:55:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:55:51: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:55:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:55:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:55:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.10_summits.bed INFO @ Thu, 09 Dec 2021 00:55:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (454 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:56:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:56:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:56:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180776/SRX3180776.20_summits.bed INFO @ Thu, 09 Dec 2021 00:56:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling