Job ID = 16435491 SRX = SRX13110319 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: 00:03:24 16705645 reads; of these: 16705645 (100.00%) were unpaired; of these: 7480688 (44.78%) aligned 0 times 7806661 (46.73%) aligned exactly 1 time 1418296 (8.49%) aligned >1 times 55.22% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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_rmdupse_core] 793210 / 9224957 = 0.0860 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 10:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.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 10:49:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:49:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:49:52: 1000000 INFO @ Tue, 02 Aug 2022 10:49:58: 2000000 INFO @ Tue, 02 Aug 2022 10:50:04: 3000000 INFO @ Tue, 02 Aug 2022 10:50:10: 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 10:50:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.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 10:50:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:50:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:50:16: 5000000 INFO @ Tue, 02 Aug 2022 10:50:21: 1000000 INFO @ Tue, 02 Aug 2022 10:50:22: 6000000 INFO @ Tue, 02 Aug 2022 10:50:27: 2000000 INFO @ Tue, 02 Aug 2022 10:50:28: 7000000 INFO @ Tue, 02 Aug 2022 10:50:33: 3000000 INFO @ Tue, 02 Aug 2022 10:50:34: 8000000 INFO @ Tue, 02 Aug 2022 10:50:37: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:50:37: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:50:37: #1 total tags in treatment: 8431747 INFO @ Tue, 02 Aug 2022 10:50:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:50:37: #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 10:50:37: #1 tags after filtering in treatment: 8431747 INFO @ Tue, 02 Aug 2022 10:50:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:50:37: #1 finished! INFO @ Tue, 02 Aug 2022 10:50:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:50:37: #2 number of paired peaks: 317 WARNING @ Tue, 02 Aug 2022 10:50:37: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 02 Aug 2022 10:50:37: start model_add_line... INFO @ Tue, 02 Aug 2022 10:50:37: start X-correlation... INFO @ Tue, 02 Aug 2022 10:50:37: end of X-cor INFO @ Tue, 02 Aug 2022 10:50:37: #2 finished! INFO @ Tue, 02 Aug 2022 10:50:37: #2 predicted fragment length is 87 bps INFO @ Tue, 02 Aug 2022 10:50:37: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 02 Aug 2022 10:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.05_model.r WARNING @ Tue, 02 Aug 2022 10:50:37: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:50:37: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 02 Aug 2022 10:50:37: #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 10:50:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:50:39: 4000000 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 10:50:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.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 10:50:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:50:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:50:45: 5000000 INFO @ Tue, 02 Aug 2022 10:50:51: 6000000 INFO @ Tue, 02 Aug 2022 10:50:51: 1000000 INFO @ Tue, 02 Aug 2022 10:50:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:50:57: 7000000 INFO @ Tue, 02 Aug 2022 10:50:58: 2000000 INFO @ Tue, 02 Aug 2022 10:51:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:51:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:51:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.05_summits.bed INFO @ Tue, 02 Aug 2022 10:51:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1351 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:51:03: 8000000 INFO @ Tue, 02 Aug 2022 10:51:05: 3000000 INFO @ Tue, 02 Aug 2022 10:51:06: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:51:06: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:51:06: #1 total tags in treatment: 8431747 INFO @ Tue, 02 Aug 2022 10:51:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:51:06: #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 10:51:06: #1 tags after filtering in treatment: 8431747 INFO @ Tue, 02 Aug 2022 10:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:51:06: #1 finished! INFO @ Tue, 02 Aug 2022 10:51:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:51:07: #2 number of paired peaks: 317 WARNING @ Tue, 02 Aug 2022 10:51:07: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 02 Aug 2022 10:51:07: start model_add_line... INFO @ Tue, 02 Aug 2022 10:51:07: start X-correlation... INFO @ Tue, 02 Aug 2022 10:51:07: end of X-cor INFO @ Tue, 02 Aug 2022 10:51:07: #2 finished! INFO @ Tue, 02 Aug 2022 10:51:07: #2 predicted fragment length is 87 bps INFO @ Tue, 02 Aug 2022 10:51:07: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 02 Aug 2022 10:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.10_model.r WARNING @ Tue, 02 Aug 2022 10:51:07: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:51:07: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 02 Aug 2022 10:51:07: #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 10:51:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:51:12: 4000000 INFO @ Tue, 02 Aug 2022 10:51:19: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:51:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:51:26: 6000000 INFO @ Tue, 02 Aug 2022 10:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.10_summits.bed INFO @ Tue, 02 Aug 2022 10:51:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (647 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:51:33: 7000000 INFO @ Tue, 02 Aug 2022 10:51:39: 8000000 INFO @ Tue, 02 Aug 2022 10:51:42: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:51:42: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:51:42: #1 total tags in treatment: 8431747 INFO @ Tue, 02 Aug 2022 10:51:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:51:42: #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 10:51:42: #1 tags after filtering in treatment: 8431747 INFO @ Tue, 02 Aug 2022 10:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:51:42: #1 finished! INFO @ Tue, 02 Aug 2022 10:51:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:51:43: #2 number of paired peaks: 317 WARNING @ Tue, 02 Aug 2022 10:51:43: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 02 Aug 2022 10:51:43: start model_add_line... INFO @ Tue, 02 Aug 2022 10:51:43: start X-correlation... INFO @ Tue, 02 Aug 2022 10:51:43: end of X-cor INFO @ Tue, 02 Aug 2022 10:51:43: #2 finished! INFO @ Tue, 02 Aug 2022 10:51:43: #2 predicted fragment length is 87 bps INFO @ Tue, 02 Aug 2022 10:51:43: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 02 Aug 2022 10:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.20_model.r WARNING @ Tue, 02 Aug 2022 10:51:43: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:51:43: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 02 Aug 2022 10:51:43: #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 10:51:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:51:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:52:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110319/SRX13110319.20_summits.bed INFO @ Tue, 02 Aug 2022 10:52:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (270 records, 4 fields): 25 millis CompletedMACS2peakCalling