Job ID = 14158044 SRX = SRX6799188 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: 00:08:50 36477308 reads; of these: 36477308 (100.00%) were unpaired; of these: 564038 (1.55%) aligned 0 times 25324431 (69.43%) aligned exactly 1 time 10588839 (29.03%) aligned >1 times 98.45% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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 16 files... [bam_rmdupse_core] 11966276 / 35913270 = 0.3332 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 14:16:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.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 14:16:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:16:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:16:27: 1000000 INFO @ Wed, 08 Dec 2021 14:16:32: 2000000 INFO @ Wed, 08 Dec 2021 14:16:38: 3000000 INFO @ Wed, 08 Dec 2021 14:16:43: 4000000 INFO @ Wed, 08 Dec 2021 14:16:48: 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 14:16:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.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 14:16:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:16:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:16:54: 6000000 INFO @ Wed, 08 Dec 2021 14:16:58: 1000000 INFO @ Wed, 08 Dec 2021 14:17:00: 7000000 INFO @ Wed, 08 Dec 2021 14:17:04: 2000000 INFO @ Wed, 08 Dec 2021 14:17:06: 8000000 INFO @ Wed, 08 Dec 2021 14:17:10: 3000000 INFO @ Wed, 08 Dec 2021 14:17:12: 9000000 INFO @ Wed, 08 Dec 2021 14:17:16: 4000000 INFO @ Wed, 08 Dec 2021 14:17:18: 10000000 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 14:17:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.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 14:17:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:17:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:17:22: 5000000 INFO @ Wed, 08 Dec 2021 14:17:24: 11000000 INFO @ Wed, 08 Dec 2021 14:17:28: 1000000 INFO @ Wed, 08 Dec 2021 14:17:28: 6000000 INFO @ Wed, 08 Dec 2021 14:17:30: 12000000 INFO @ Wed, 08 Dec 2021 14:17:34: 2000000 INFO @ Wed, 08 Dec 2021 14:17:34: 7000000 INFO @ Wed, 08 Dec 2021 14:17:36: 13000000 INFO @ Wed, 08 Dec 2021 14:17:40: 3000000 INFO @ Wed, 08 Dec 2021 14:17:41: 8000000 INFO @ Wed, 08 Dec 2021 14:17:42: 14000000 INFO @ Wed, 08 Dec 2021 14:17:46: 4000000 INFO @ Wed, 08 Dec 2021 14:17:47: 9000000 INFO @ Wed, 08 Dec 2021 14:17:48: 15000000 INFO @ Wed, 08 Dec 2021 14:17:52: 5000000 INFO @ Wed, 08 Dec 2021 14:17:53: 10000000 INFO @ Wed, 08 Dec 2021 14:17:55: 16000000 INFO @ Wed, 08 Dec 2021 14:17:58: 6000000 INFO @ Wed, 08 Dec 2021 14:17:59: 11000000 INFO @ Wed, 08 Dec 2021 14:18:01: 17000000 INFO @ Wed, 08 Dec 2021 14:18:04: 7000000 INFO @ Wed, 08 Dec 2021 14:18:05: 12000000 INFO @ Wed, 08 Dec 2021 14:18:07: 18000000 INFO @ Wed, 08 Dec 2021 14:18:11: 8000000 INFO @ Wed, 08 Dec 2021 14:18:12: 13000000 INFO @ Wed, 08 Dec 2021 14:18:13: 19000000 INFO @ Wed, 08 Dec 2021 14:18:17: 9000000 INFO @ Wed, 08 Dec 2021 14:18:18: 14000000 INFO @ Wed, 08 Dec 2021 14:18:19: 20000000 INFO @ Wed, 08 Dec 2021 14:18:23: 10000000 INFO @ Wed, 08 Dec 2021 14:18:24: 15000000 INFO @ Wed, 08 Dec 2021 14:18:25: 21000000 INFO @ Wed, 08 Dec 2021 14:18:29: 11000000 INFO @ Wed, 08 Dec 2021 14:18:30: 16000000 INFO @ Wed, 08 Dec 2021 14:18:31: 22000000 INFO @ Wed, 08 Dec 2021 14:18:35: 12000000 INFO @ Wed, 08 Dec 2021 14:18:36: 17000000 INFO @ Wed, 08 Dec 2021 14:18:37: 23000000 INFO @ Wed, 08 Dec 2021 14:18:41: 13000000 INFO @ Wed, 08 Dec 2021 14:18:42: 18000000 INFO @ Wed, 08 Dec 2021 14:18:43: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:18:43: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:18:43: #1 total tags in treatment: 23946994 INFO @ Wed, 08 Dec 2021 14:18:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:18:43: #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 14:18:43: #1 tags after filtering in treatment: 23946994 INFO @ Wed, 08 Dec 2021 14:18:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:18:43: #1 finished! INFO @ Wed, 08 Dec 2021 14:18:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:18:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:18:45: #2 number of paired peaks: 386 WARNING @ Wed, 08 Dec 2021 14:18:45: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Wed, 08 Dec 2021 14:18:45: start model_add_line... INFO @ Wed, 08 Dec 2021 14:18:45: start X-correlation... INFO @ Wed, 08 Dec 2021 14:18:45: end of X-cor INFO @ Wed, 08 Dec 2021 14:18:45: #2 finished! INFO @ Wed, 08 Dec 2021 14:18:45: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:18:45: #2 alternative fragment length(s) may be 1 bps INFO @ Wed, 08 Dec 2021 14:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.05_model.r WARNING @ Wed, 08 Dec 2021 14:18:45: #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 14:18:45: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Wed, 08 Dec 2021 14:18:45: #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 14:18:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:18:47: 14000000 INFO @ Wed, 08 Dec 2021 14:18:49: 19000000 INFO @ Wed, 08 Dec 2021 14:18:53: 15000000 INFO @ Wed, 08 Dec 2021 14:18:55: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:18:59: 16000000 INFO @ Wed, 08 Dec 2021 14:19:01: 21000000 INFO @ Wed, 08 Dec 2021 14:19:05: 17000000 INFO @ Wed, 08 Dec 2021 14:19:07: 22000000 INFO @ Wed, 08 Dec 2021 14:19:12: 18000000 INFO @ Wed, 08 Dec 2021 14:19:13: 23000000 INFO @ Wed, 08 Dec 2021 14:19:18: 19000000 INFO @ Wed, 08 Dec 2021 14:19:18: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:19:19: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:19:19: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:19:19: #1 total tags in treatment: 23946994 INFO @ Wed, 08 Dec 2021 14:19:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:19:19: #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 14:19:19: #1 tags after filtering in treatment: 23946994 INFO @ Wed, 08 Dec 2021 14:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:19:19: #1 finished! INFO @ Wed, 08 Dec 2021 14:19:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:19:21: #2 number of paired peaks: 386 WARNING @ Wed, 08 Dec 2021 14:19:21: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Wed, 08 Dec 2021 14:19:21: start model_add_line... INFO @ Wed, 08 Dec 2021 14:19:21: start X-correlation... INFO @ Wed, 08 Dec 2021 14:19:21: end of X-cor INFO @ Wed, 08 Dec 2021 14:19:21: #2 finished! INFO @ Wed, 08 Dec 2021 14:19:21: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:19:21: #2 alternative fragment length(s) may be 1 bps INFO @ Wed, 08 Dec 2021 14:19:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.10_model.r WARNING @ Wed, 08 Dec 2021 14:19:21: #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 14:19:21: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Wed, 08 Dec 2021 14:19:21: #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 14:19:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:19:24: 20000000 INFO @ Wed, 08 Dec 2021 14:19:29: 21000000 INFO @ Wed, 08 Dec 2021 14:19:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:19:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:19:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.05_summits.bed INFO @ Wed, 08 Dec 2021 14:19:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:19:34: 22000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:19:39: 23000000 INFO @ Wed, 08 Dec 2021 14:19:45: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:19:45: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:19:45: #1 total tags in treatment: 23946994 INFO @ Wed, 08 Dec 2021 14:19:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:19:45: #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 14:19:45: #1 tags after filtering in treatment: 23946994 INFO @ Wed, 08 Dec 2021 14:19:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:19:45: #1 finished! INFO @ Wed, 08 Dec 2021 14:19:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:19:46: #2 number of paired peaks: 386 WARNING @ Wed, 08 Dec 2021 14:19:46: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Wed, 08 Dec 2021 14:19:46: start model_add_line... INFO @ Wed, 08 Dec 2021 14:19:47: start X-correlation... INFO @ Wed, 08 Dec 2021 14:19:47: end of X-cor INFO @ Wed, 08 Dec 2021 14:19:47: #2 finished! INFO @ Wed, 08 Dec 2021 14:19:47: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:19:47: #2 alternative fragment length(s) may be 1 bps INFO @ Wed, 08 Dec 2021 14:19:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.20_model.r WARNING @ Wed, 08 Dec 2021 14:19:47: #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 14:19:47: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Wed, 08 Dec 2021 14:19:47: #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 14:19:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:19:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:19:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:20:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:20:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.10_summits.bed INFO @ Wed, 08 Dec 2021 14:20:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:20:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:20:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:20:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:20:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.20_summits.bed INFO @ Wed, 08 Dec 2021 14:20:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling