Job ID = 10165900 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: 00:08:23 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: 00:08:23 Overall time: 00:08:23 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:22:56: # 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 @ Thu, 08 Oct 2020 20:22:56: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:22:56: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:23:01: 1000000 INFO @ Thu, 08 Oct 2020 20:23:07: 2000000 INFO @ Thu, 08 Oct 2020 20:23:12: 3000000 INFO @ Thu, 08 Oct 2020 20:23:17: 4000000 INFO @ Thu, 08 Oct 2020 20:23:23: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:23:26: # 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 @ Thu, 08 Oct 2020 20:23:26: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:23:26: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:23:28: 6000000 INFO @ Thu, 08 Oct 2020 20:23:32: 1000000 INFO @ Thu, 08 Oct 2020 20:23:34: 7000000 INFO @ Thu, 08 Oct 2020 20:23:38: 2000000 INFO @ Thu, 08 Oct 2020 20:23:40: 8000000 INFO @ Thu, 08 Oct 2020 20:23:44: 3000000 INFO @ Thu, 08 Oct 2020 20:23:47: 9000000 INFO @ Thu, 08 Oct 2020 20:23:50: 4000000 INFO @ Thu, 08 Oct 2020 20:23:53: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:23:56: # 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 @ Thu, 08 Oct 2020 20:23:56: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:23:56: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:23:56: 5000000 INFO @ Thu, 08 Oct 2020 20:23:59: 11000000 INFO @ Thu, 08 Oct 2020 20:24:02: 1000000 INFO @ Thu, 08 Oct 2020 20:24:02: 6000000 INFO @ Thu, 08 Oct 2020 20:24:05: 12000000 INFO @ Thu, 08 Oct 2020 20:24:08: 2000000 INFO @ Thu, 08 Oct 2020 20:24:08: 7000000 INFO @ Thu, 08 Oct 2020 20:24:11: 13000000 INFO @ Thu, 08 Oct 2020 20:24:14: 3000000 INFO @ Thu, 08 Oct 2020 20:24:15: 8000000 INFO @ Thu, 08 Oct 2020 20:24:17: 14000000 INFO @ Thu, 08 Oct 2020 20:24:20: 4000000 INFO @ Thu, 08 Oct 2020 20:24:21: 9000000 INFO @ Thu, 08 Oct 2020 20:24:23: 15000000 INFO @ Thu, 08 Oct 2020 20:24:26: 5000000 INFO @ Thu, 08 Oct 2020 20:24:27: 10000000 INFO @ Thu, 08 Oct 2020 20:24:29: 16000000 INFO @ Thu, 08 Oct 2020 20:24:32: 6000000 INFO @ Thu, 08 Oct 2020 20:24:33: 11000000 INFO @ Thu, 08 Oct 2020 20:24:35: 17000000 INFO @ Thu, 08 Oct 2020 20:24:38: 7000000 INFO @ Thu, 08 Oct 2020 20:24:39: 12000000 INFO @ Thu, 08 Oct 2020 20:24:42: 18000000 INFO @ Thu, 08 Oct 2020 20:24:45: 8000000 INFO @ Thu, 08 Oct 2020 20:24:45: 13000000 INFO @ Thu, 08 Oct 2020 20:24:48: 19000000 INFO @ Thu, 08 Oct 2020 20:24:51: 9000000 INFO @ Thu, 08 Oct 2020 20:24:52: 14000000 INFO @ Thu, 08 Oct 2020 20:24:54: 20000000 INFO @ Thu, 08 Oct 2020 20:24:57: 10000000 INFO @ Thu, 08 Oct 2020 20:24:58: 15000000 INFO @ Thu, 08 Oct 2020 20:25:00: 21000000 INFO @ Thu, 08 Oct 2020 20:25:03: 11000000 INFO @ Thu, 08 Oct 2020 20:25:04: 16000000 INFO @ Thu, 08 Oct 2020 20:25:06: 22000000 INFO @ Thu, 08 Oct 2020 20:25:09: 12000000 INFO @ Thu, 08 Oct 2020 20:25:10: 17000000 INFO @ Thu, 08 Oct 2020 20:25:12: 23000000 INFO @ Thu, 08 Oct 2020 20:25:15: 13000000 INFO @ Thu, 08 Oct 2020 20:25:16: 18000000 INFO @ Thu, 08 Oct 2020 20:25:18: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:25:18: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:25:18: #1 total tags in treatment: 23946994 INFO @ Thu, 08 Oct 2020 20:25:18: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:25:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:25:18: #1 tags after filtering in treatment: 23946994 INFO @ Thu, 08 Oct 2020 20:25:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:25:18: #1 finished! INFO @ Thu, 08 Oct 2020 20:25:18: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:25:20: #2 number of paired peaks: 386 WARNING @ Thu, 08 Oct 2020 20:25:20: 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 @ Thu, 08 Oct 2020 20:25:20: start model_add_line... INFO @ Thu, 08 Oct 2020 20:25:20: start X-correlation... INFO @ Thu, 08 Oct 2020 20:25:20: end of X-cor INFO @ Thu, 08 Oct 2020 20:25:20: #2 finished! INFO @ Thu, 08 Oct 2020 20:25:20: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:25:20: #2 alternative fragment length(s) may be 1 bps INFO @ Thu, 08 Oct 2020 20:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.05_model.r WARNING @ Thu, 08 Oct 2020 20:25:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:25:20: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Thu, 08 Oct 2020 20:25:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:25:20: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:25:21: 14000000 INFO @ Thu, 08 Oct 2020 20:25:22: 19000000 INFO @ Thu, 08 Oct 2020 20:25:27: 15000000 INFO @ Thu, 08 Oct 2020 20:25:28: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:25:33: 16000000 INFO @ Thu, 08 Oct 2020 20:25:34: 21000000 INFO @ Thu, 08 Oct 2020 20:25:39: 17000000 INFO @ Thu, 08 Oct 2020 20:25:40: 22000000 INFO @ Thu, 08 Oct 2020 20:25:45: 18000000 INFO @ Thu, 08 Oct 2020 20:25:47: 23000000 INFO @ Thu, 08 Oct 2020 20:25:51: 19000000 INFO @ Thu, 08 Oct 2020 20:25:52: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:25:52: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:25:52: #1 total tags in treatment: 23946994 INFO @ Thu, 08 Oct 2020 20:25:52: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:25:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:25:53: #1 tags after filtering in treatment: 23946994 INFO @ Thu, 08 Oct 2020 20:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:25:53: #1 finished! INFO @ Thu, 08 Oct 2020 20:25:53: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:25:53: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:25:54: #2 number of paired peaks: 386 WARNING @ Thu, 08 Oct 2020 20:25:54: 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 @ Thu, 08 Oct 2020 20:25:54: start model_add_line... INFO @ Thu, 08 Oct 2020 20:25:54: start X-correlation... INFO @ Thu, 08 Oct 2020 20:25:54: end of X-cor INFO @ Thu, 08 Oct 2020 20:25:54: #2 finished! INFO @ Thu, 08 Oct 2020 20:25:54: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:25:54: #2 alternative fragment length(s) may be 1 bps INFO @ Thu, 08 Oct 2020 20:25:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.10_model.r WARNING @ Thu, 08 Oct 2020 20:25:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:25:54: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Thu, 08 Oct 2020 20:25:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:25:54: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:25:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:25:57: 20000000 INFO @ Thu, 08 Oct 2020 20:26:03: 21000000 INFO @ Thu, 08 Oct 2020 20:26:08: 22000000 INFO @ Thu, 08 Oct 2020 20:26:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.05_summits.bed INFO @ Thu, 08 Oct 2020 20:26:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:26:13: 23000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:26:19: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:26:19: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:26:19: #1 total tags in treatment: 23946994 INFO @ Thu, 08 Oct 2020 20:26:19: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:26:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:26:19: #1 tags after filtering in treatment: 23946994 INFO @ Thu, 08 Oct 2020 20:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:26:19: #1 finished! INFO @ Thu, 08 Oct 2020 20:26:19: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:26:20: #2 number of paired peaks: 386 WARNING @ Thu, 08 Oct 2020 20:26:20: 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 @ Thu, 08 Oct 2020 20:26:20: start model_add_line... INFO @ Thu, 08 Oct 2020 20:26:21: start X-correlation... INFO @ Thu, 08 Oct 2020 20:26:21: end of X-cor INFO @ Thu, 08 Oct 2020 20:26:21: #2 finished! INFO @ Thu, 08 Oct 2020 20:26:21: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:26:21: #2 alternative fragment length(s) may be 1 bps INFO @ Thu, 08 Oct 2020 20:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.20_model.r WARNING @ Thu, 08 Oct 2020 20:26:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:26:21: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Thu, 08 Oct 2020 20:26:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:26:21: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:26:28: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:26:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:26:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:26:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.10_summits.bed INFO @ Thu, 08 Oct 2020 20:26:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:26:54: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:27:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:27:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:27:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799188/SRX6799188.20_summits.bed INFO @ Thu, 08 Oct 2020 20:27:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling