Job ID = 16436209 SRX = SRX13110394 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: 00:04:31 20130019 reads; of these: 20130019 (100.00%) were unpaired; of these: 6904423 (34.30%) aligned 0 times 11241065 (55.84%) aligned exactly 1 time 1984531 (9.86%) aligned >1 times 65.70% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 1136680 / 13225596 = 0.0859 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 11:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.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 11:13:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:13:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:13:54: 1000000 INFO @ Tue, 02 Aug 2022 11:13:59: 2000000 INFO @ Tue, 02 Aug 2022 11:14:05: 3000000 INFO @ Tue, 02 Aug 2022 11:14:11: 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 11:14:16: 5000000 INFO @ Tue, 02 Aug 2022 11:14:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.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 11:14:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:14:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:14:22: 6000000 INFO @ Tue, 02 Aug 2022 11:14:22: 1000000 INFO @ Tue, 02 Aug 2022 11:14:27: 7000000 INFO @ Tue, 02 Aug 2022 11:14:27: 2000000 INFO @ Tue, 02 Aug 2022 11:14:33: 3000000 INFO @ Tue, 02 Aug 2022 11:14:33: 8000000 INFO @ Tue, 02 Aug 2022 11:14:38: 4000000 INFO @ Tue, 02 Aug 2022 11:14:38: 9000000 INFO @ Tue, 02 Aug 2022 11:14:43: 5000000 INFO @ Tue, 02 Aug 2022 11:14:44: 10000000 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 11:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.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 11:14:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:14:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:14:48: 6000000 INFO @ Tue, 02 Aug 2022 11:14:49: 11000000 INFO @ Tue, 02 Aug 2022 11:14:52: 1000000 INFO @ Tue, 02 Aug 2022 11:14:54: 7000000 INFO @ Tue, 02 Aug 2022 11:14:54: 12000000 INFO @ Tue, 02 Aug 2022 11:14:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:14:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:14:55: #1 total tags in treatment: 12088916 INFO @ Tue, 02 Aug 2022 11:14:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:14:55: #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 11:14:55: #1 tags after filtering in treatment: 12088916 INFO @ Tue, 02 Aug 2022 11:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:14:55: #1 finished! INFO @ Tue, 02 Aug 2022 11:14:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:14:56: #2 number of paired peaks: 243 WARNING @ Tue, 02 Aug 2022 11:14:56: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Tue, 02 Aug 2022 11:14:56: start model_add_line... INFO @ Tue, 02 Aug 2022 11:14:56: start X-correlation... INFO @ Tue, 02 Aug 2022 11:14:56: end of X-cor INFO @ Tue, 02 Aug 2022 11:14:56: #2 finished! INFO @ Tue, 02 Aug 2022 11:14:56: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:14:56: #2 alternative fragment length(s) may be 4,73,520,542,579 bps INFO @ Tue, 02 Aug 2022 11:14:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.05_model.r WARNING @ Tue, 02 Aug 2022 11:14:56: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:14:56: #2 You may need to consider one of the other alternative d(s): 4,73,520,542,579 WARNING @ Tue, 02 Aug 2022 11:14:56: #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 11:14:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:14:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:14:58: 2000000 INFO @ Tue, 02 Aug 2022 11:14:59: 8000000 INFO @ Tue, 02 Aug 2022 11:15:03: 3000000 INFO @ Tue, 02 Aug 2022 11:15:04: 9000000 INFO @ Tue, 02 Aug 2022 11:15:08: 4000000 INFO @ Tue, 02 Aug 2022 11:15:10: 10000000 INFO @ Tue, 02 Aug 2022 11:15:14: 5000000 INFO @ Tue, 02 Aug 2022 11:15:15: 11000000 INFO @ Tue, 02 Aug 2022 11:15:19: 6000000 INFO @ Tue, 02 Aug 2022 11:15:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:15:21: 12000000 INFO @ Tue, 02 Aug 2022 11:15:21: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:15:21: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:15:21: #1 total tags in treatment: 12088916 INFO @ Tue, 02 Aug 2022 11:15:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:15:21: #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 11:15:22: #1 tags after filtering in treatment: 12088916 INFO @ Tue, 02 Aug 2022 11:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:15:22: #1 finished! INFO @ Tue, 02 Aug 2022 11:15:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:15:22: #2 number of paired peaks: 243 WARNING @ Tue, 02 Aug 2022 11:15:22: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Tue, 02 Aug 2022 11:15:22: start model_add_line... INFO @ Tue, 02 Aug 2022 11:15:23: start X-correlation... INFO @ Tue, 02 Aug 2022 11:15:23: end of X-cor INFO @ Tue, 02 Aug 2022 11:15:23: #2 finished! INFO @ Tue, 02 Aug 2022 11:15:23: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:15:23: #2 alternative fragment length(s) may be 4,73,520,542,579 bps INFO @ Tue, 02 Aug 2022 11:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.10_model.r WARNING @ Tue, 02 Aug 2022 11:15:23: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:15:23: #2 You may need to consider one of the other alternative d(s): 4,73,520,542,579 WARNING @ Tue, 02 Aug 2022 11:15:23: #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 11:15:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:15:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:15:24: 7000000 INFO @ Tue, 02 Aug 2022 11:15:29: 8000000 INFO @ Tue, 02 Aug 2022 11:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.05_summits.bed INFO @ Tue, 02 Aug 2022 11:15:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (538 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:15:34: 9000000 INFO @ Tue, 02 Aug 2022 11:15:39: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:15:44: 11000000 INFO @ Tue, 02 Aug 2022 11:15:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:15:49: 12000000 INFO @ Tue, 02 Aug 2022 11:15:49: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:15:49: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:15:49: #1 total tags in treatment: 12088916 INFO @ Tue, 02 Aug 2022 11:15:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:15:49: #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 11:15:50: #1 tags after filtering in treatment: 12088916 INFO @ Tue, 02 Aug 2022 11:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:15:50: #1 finished! INFO @ Tue, 02 Aug 2022 11:15:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:15:50: #2 number of paired peaks: 243 WARNING @ Tue, 02 Aug 2022 11:15:50: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Tue, 02 Aug 2022 11:15:50: start model_add_line... INFO @ Tue, 02 Aug 2022 11:15:50: start X-correlation... INFO @ Tue, 02 Aug 2022 11:15:50: end of X-cor INFO @ Tue, 02 Aug 2022 11:15:50: #2 finished! INFO @ Tue, 02 Aug 2022 11:15:50: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:15:50: #2 alternative fragment length(s) may be 4,73,520,542,579 bps INFO @ Tue, 02 Aug 2022 11:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.20_model.r WARNING @ Tue, 02 Aug 2022 11:15:50: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:15:50: #2 You may need to consider one of the other alternative d(s): 4,73,520,542,579 WARNING @ Tue, 02 Aug 2022 11:15:50: #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 11:15:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:15:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:15:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:15:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.10_summits.bed INFO @ Tue, 02 Aug 2022 11:15:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (368 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:16:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:16:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:16:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:16:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110394/SRX13110394.20_summits.bed INFO @ Tue, 02 Aug 2022 11:16:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 18 millis CompletedMACS2peakCalling