Job ID = 16436195 SRX = SRX13110378 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: 00:06:15 19626111 reads; of these: 19626111 (100.00%) were unpaired; of these: 721405 (3.68%) aligned 0 times 15935816 (81.20%) aligned exactly 1 time 2968890 (15.13%) aligned >1 times 96.32% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 2041700 / 18904706 = 0.1080 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 11:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.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 11:14:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:14:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:14:23: 1000000 INFO @ Tue, 02 Aug 2022 11:14:29: 2000000 INFO @ Tue, 02 Aug 2022 11:14:35: 3000000 INFO @ Tue, 02 Aug 2022 11:14:41: 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 11:14:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.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 11:14:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:14:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:14:48: 5000000 INFO @ Tue, 02 Aug 2022 11:14:54: 1000000 INFO @ Tue, 02 Aug 2022 11:14:55: 6000000 INFO @ Tue, 02 Aug 2022 11:15:01: 2000000 INFO @ Tue, 02 Aug 2022 11:15:02: 7000000 INFO @ Tue, 02 Aug 2022 11:15:08: 3000000 INFO @ Tue, 02 Aug 2022 11:15:09: 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 11:15:15: 4000000 INFO @ Tue, 02 Aug 2022 11:15:16: 9000000 INFO @ Tue, 02 Aug 2022 11:15:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.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 11:15:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:15:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:15:22: 5000000 INFO @ Tue, 02 Aug 2022 11:15:24: 10000000 INFO @ Tue, 02 Aug 2022 11:15:24: 1000000 INFO @ Tue, 02 Aug 2022 11:15:30: 6000000 INFO @ Tue, 02 Aug 2022 11:15:31: 11000000 INFO @ Tue, 02 Aug 2022 11:15:32: 2000000 INFO @ Tue, 02 Aug 2022 11:15:37: 7000000 INFO @ Tue, 02 Aug 2022 11:15:39: 12000000 INFO @ Tue, 02 Aug 2022 11:15:39: 3000000 INFO @ Tue, 02 Aug 2022 11:15:45: 8000000 INFO @ Tue, 02 Aug 2022 11:15:46: 4000000 INFO @ Tue, 02 Aug 2022 11:15:46: 13000000 INFO @ Tue, 02 Aug 2022 11:15:52: 9000000 INFO @ Tue, 02 Aug 2022 11:15:54: 5000000 INFO @ Tue, 02 Aug 2022 11:15:54: 14000000 INFO @ Tue, 02 Aug 2022 11:15:59: 10000000 INFO @ Tue, 02 Aug 2022 11:16:01: 6000000 INFO @ Tue, 02 Aug 2022 11:16:01: 15000000 INFO @ Tue, 02 Aug 2022 11:16:07: 11000000 INFO @ Tue, 02 Aug 2022 11:16:08: 7000000 INFO @ Tue, 02 Aug 2022 11:16:09: 16000000 INFO @ Tue, 02 Aug 2022 11:16:14: 12000000 INFO @ Tue, 02 Aug 2022 11:16:15: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:16:15: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:16:15: #1 total tags in treatment: 16863006 INFO @ Tue, 02 Aug 2022 11:16:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:16:15: #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 11:16:16: #1 tags after filtering in treatment: 16863006 INFO @ Tue, 02 Aug 2022 11:16:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:16:16: #1 finished! INFO @ Tue, 02 Aug 2022 11:16:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:16:16: 8000000 INFO @ Tue, 02 Aug 2022 11:16:17: #2 number of paired peaks: 202 WARNING @ Tue, 02 Aug 2022 11:16:17: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 02 Aug 2022 11:16:17: start model_add_line... INFO @ Tue, 02 Aug 2022 11:16:17: start X-correlation... INFO @ Tue, 02 Aug 2022 11:16:17: end of X-cor INFO @ Tue, 02 Aug 2022 11:16:17: #2 finished! INFO @ Tue, 02 Aug 2022 11:16:17: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 11:16:17: #2 alternative fragment length(s) may be 2,69 bps INFO @ Tue, 02 Aug 2022 11:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.05_model.r WARNING @ Tue, 02 Aug 2022 11:16:17: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:16:17: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Tue, 02 Aug 2022 11:16:17: #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 11:16:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:16:21: 13000000 INFO @ Tue, 02 Aug 2022 11:16:23: 9000000 INFO @ Tue, 02 Aug 2022 11:16:29: 14000000 INFO @ Tue, 02 Aug 2022 11:16:30: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:16:36: 15000000 INFO @ Tue, 02 Aug 2022 11:16:37: 11000000 INFO @ Tue, 02 Aug 2022 11:16:43: 16000000 INFO @ Tue, 02 Aug 2022 11:16:44: 12000000 INFO @ Tue, 02 Aug 2022 11:16:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:16:49: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:16:49: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:16:49: #1 total tags in treatment: 16863006 INFO @ Tue, 02 Aug 2022 11:16:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:16:49: #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 11:16:50: #1 tags after filtering in treatment: 16863006 INFO @ Tue, 02 Aug 2022 11:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:16:50: #1 finished! INFO @ Tue, 02 Aug 2022 11:16:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:16:51: #2 number of paired peaks: 202 WARNING @ Tue, 02 Aug 2022 11:16:51: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 02 Aug 2022 11:16:51: start model_add_line... INFO @ Tue, 02 Aug 2022 11:16:51: start X-correlation... INFO @ Tue, 02 Aug 2022 11:16:51: end of X-cor INFO @ Tue, 02 Aug 2022 11:16:51: #2 finished! INFO @ Tue, 02 Aug 2022 11:16:51: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 11:16:51: #2 alternative fragment length(s) may be 2,69 bps INFO @ Tue, 02 Aug 2022 11:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.10_model.r WARNING @ Tue, 02 Aug 2022 11:16:51: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:16:51: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Tue, 02 Aug 2022 11:16:51: #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 11:16:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:16:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:16:52: 13000000 INFO @ Tue, 02 Aug 2022 11:16:58: 14000000 INFO @ Tue, 02 Aug 2022 11:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.05_summits.bed INFO @ Tue, 02 Aug 2022 11:17:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (697 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:17:04: 15000000 INFO @ Tue, 02 Aug 2022 11:17:10: 16000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:17:16: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:17:16: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:17:16: #1 total tags in treatment: 16863006 INFO @ Tue, 02 Aug 2022 11:17:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:17:16: #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 11:17:16: #1 tags after filtering in treatment: 16863006 INFO @ Tue, 02 Aug 2022 11:17:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:17:16: #1 finished! INFO @ Tue, 02 Aug 2022 11:17:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:17:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:17:17: #2 number of paired peaks: 202 WARNING @ Tue, 02 Aug 2022 11:17:17: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Tue, 02 Aug 2022 11:17:17: start model_add_line... INFO @ Tue, 02 Aug 2022 11:17:17: start X-correlation... INFO @ Tue, 02 Aug 2022 11:17:17: end of X-cor INFO @ Tue, 02 Aug 2022 11:17:17: #2 finished! INFO @ Tue, 02 Aug 2022 11:17:17: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 11:17:17: #2 alternative fragment length(s) may be 2,69 bps INFO @ Tue, 02 Aug 2022 11:17:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.20_model.r WARNING @ Tue, 02 Aug 2022 11:17:17: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:17:17: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Tue, 02 Aug 2022 11:17:17: #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 11:17:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:17:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:17:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:17:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:17:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.10_summits.bed INFO @ Tue, 02 Aug 2022 11:17:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:17:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:18:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:18:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:18:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110378/SRX13110378.20_summits.bed INFO @ Tue, 02 Aug 2022 11:18:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 19 millis CompletedMACS2peakCalling