Job ID = 14158078 SRX = SRX10040016 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: 00:04:30 17069793 reads; of these: 17069793 (100.00%) were unpaired; of these: 191343 (1.12%) aligned 0 times 14338946 (84.00%) aligned exactly 1 time 2539504 (14.88%) aligned >1 times 98.88% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 2329587 / 16878450 = 0.1380 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 @ Wed, 08 Dec 2021 14:22:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.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 @ Wed, 08 Dec 2021 14:22:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:22:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:22:21: 1000000 INFO @ Wed, 08 Dec 2021 14:22:26: 2000000 INFO @ Wed, 08 Dec 2021 14:22:31: 3000000 INFO @ Wed, 08 Dec 2021 14:22:36: 4000000 INFO @ Wed, 08 Dec 2021 14:22:41: 5000000 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 @ Wed, 08 Dec 2021 14:22:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.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 @ Wed, 08 Dec 2021 14:22:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:22:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:22:46: 6000000 INFO @ Wed, 08 Dec 2021 14:22:50: 1000000 INFO @ Wed, 08 Dec 2021 14:22:52: 7000000 INFO @ Wed, 08 Dec 2021 14:22:56: 2000000 INFO @ Wed, 08 Dec 2021 14:22:57: 8000000 INFO @ Wed, 08 Dec 2021 14:23:01: 3000000 INFO @ Wed, 08 Dec 2021 14:23:02: 9000000 INFO @ Wed, 08 Dec 2021 14:23:06: 4000000 INFO @ Wed, 08 Dec 2021 14:23:08: 10000000 INFO @ Wed, 08 Dec 2021 14:23:12: 5000000 INFO @ Wed, 08 Dec 2021 14:23:13: 11000000 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 @ Wed, 08 Dec 2021 14:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.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 @ Wed, 08 Dec 2021 14:23:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:23:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:23:17: 6000000 INFO @ Wed, 08 Dec 2021 14:23:18: 12000000 INFO @ Wed, 08 Dec 2021 14:23:21: 1000000 INFO @ Wed, 08 Dec 2021 14:23:23: 7000000 INFO @ Wed, 08 Dec 2021 14:23:24: 13000000 INFO @ Wed, 08 Dec 2021 14:23:26: 2000000 INFO @ Wed, 08 Dec 2021 14:23:28: 8000000 INFO @ Wed, 08 Dec 2021 14:23:29: 14000000 INFO @ Wed, 08 Dec 2021 14:23:31: 3000000 INFO @ Wed, 08 Dec 2021 14:23:32: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:23:32: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:23:32: #1 total tags in treatment: 14548863 INFO @ Wed, 08 Dec 2021 14:23:32: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:23:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:23:32: #1 tags after filtering in treatment: 14548863 INFO @ Wed, 08 Dec 2021 14:23:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:23:32: #1 finished! INFO @ Wed, 08 Dec 2021 14:23:32: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:23:33: #2 number of paired peaks: 111 WARNING @ Wed, 08 Dec 2021 14:23:33: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 08 Dec 2021 14:23:33: start model_add_line... INFO @ Wed, 08 Dec 2021 14:23:33: start X-correlation... INFO @ Wed, 08 Dec 2021 14:23:33: end of X-cor INFO @ Wed, 08 Dec 2021 14:23:33: #2 finished! INFO @ Wed, 08 Dec 2021 14:23:33: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:23:33: #2 alternative fragment length(s) may be 1,36,53,384,402,406,484,524,571 bps INFO @ Wed, 08 Dec 2021 14:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.05_model.r WARNING @ Wed, 08 Dec 2021 14:23:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:23:33: #2 You may need to consider one of the other alternative d(s): 1,36,53,384,402,406,484,524,571 WARNING @ Wed, 08 Dec 2021 14:23:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:23:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:23:34: 9000000 INFO @ Wed, 08 Dec 2021 14:23:37: 4000000 INFO @ Wed, 08 Dec 2021 14:23:39: 10000000 INFO @ Wed, 08 Dec 2021 14:23:42: 5000000 INFO @ Wed, 08 Dec 2021 14:23:44: 11000000 INFO @ Wed, 08 Dec 2021 14:23:48: 6000000 INFO @ Wed, 08 Dec 2021 14:23:50: 12000000 INFO @ Wed, 08 Dec 2021 14:23:53: 7000000 INFO @ Wed, 08 Dec 2021 14:23:55: 13000000 INFO @ Wed, 08 Dec 2021 14:23:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:23:58: 8000000 INFO @ Wed, 08 Dec 2021 14:24:00: 14000000 INFO @ Wed, 08 Dec 2021 14:24:03: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:24:03: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:24:03: #1 total tags in treatment: 14548863 INFO @ Wed, 08 Dec 2021 14:24:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:24:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:24:04: #1 tags after filtering in treatment: 14548863 INFO @ Wed, 08 Dec 2021 14:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:24:04: #1 finished! INFO @ Wed, 08 Dec 2021 14:24:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:24:04: 9000000 INFO @ Wed, 08 Dec 2021 14:24:05: #2 number of paired peaks: 111 WARNING @ Wed, 08 Dec 2021 14:24:05: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 08 Dec 2021 14:24:05: start model_add_line... INFO @ Wed, 08 Dec 2021 14:24:05: start X-correlation... INFO @ Wed, 08 Dec 2021 14:24:05: end of X-cor INFO @ Wed, 08 Dec 2021 14:24:05: #2 finished! INFO @ Wed, 08 Dec 2021 14:24:05: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:24:05: #2 alternative fragment length(s) may be 1,36,53,384,402,406,484,524,571 bps INFO @ Wed, 08 Dec 2021 14:24:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.10_model.r WARNING @ Wed, 08 Dec 2021 14:24:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:24:05: #2 You may need to consider one of the other alternative d(s): 1,36,53,384,402,406,484,524,571 WARNING @ Wed, 08 Dec 2021 14:24:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:24:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:24:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:24:09: 10000000 INFO @ Wed, 08 Dec 2021 14:24:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:24:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:24:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.05_summits.bed INFO @ Wed, 08 Dec 2021 14:24:10: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:24:14: 11000000 INFO @ Wed, 08 Dec 2021 14:24:20: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:24:25: 13000000 INFO @ Wed, 08 Dec 2021 14:24:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:24:30: 14000000 INFO @ Wed, 08 Dec 2021 14:24:33: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:24:33: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:24:33: #1 total tags in treatment: 14548863 INFO @ Wed, 08 Dec 2021 14:24:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:24:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:24:33: #1 tags after filtering in treatment: 14548863 INFO @ Wed, 08 Dec 2021 14:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:24:33: #1 finished! INFO @ Wed, 08 Dec 2021 14:24:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:24:34: #2 number of paired peaks: 111 WARNING @ Wed, 08 Dec 2021 14:24:34: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 08 Dec 2021 14:24:34: start model_add_line... INFO @ Wed, 08 Dec 2021 14:24:34: start X-correlation... INFO @ Wed, 08 Dec 2021 14:24:34: end of X-cor INFO @ Wed, 08 Dec 2021 14:24:34: #2 finished! INFO @ Wed, 08 Dec 2021 14:24:34: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:24:34: #2 alternative fragment length(s) may be 1,36,53,384,402,406,484,524,571 bps INFO @ Wed, 08 Dec 2021 14:24:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.20_model.r WARNING @ Wed, 08 Dec 2021 14:24:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:24:34: #2 You may need to consider one of the other alternative d(s): 1,36,53,384,402,406,484,524,571 WARNING @ Wed, 08 Dec 2021 14:24:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:24:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:24:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.10_summits.bed INFO @ Wed, 08 Dec 2021 14:24:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:24:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:25:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:25:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:25:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040016/SRX10040016.20_summits.bed INFO @ Wed, 08 Dec 2021 14:25:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling