Job ID = 14158057 SRX = SRX6799191 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: 00:08:35 38761251 reads; of these: 38761251 (100.00%) were unpaired; of these: 742930 (1.92%) aligned 0 times 27373831 (70.62%) aligned exactly 1 time 10644490 (27.46%) aligned >1 times 98.08% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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] 12071568 / 38018321 = 0.3175 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 14:21:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.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 14:21:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:21:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:21:18: 1000000 INFO @ Wed, 08 Dec 2021 14:21:23: 2000000 INFO @ Wed, 08 Dec 2021 14:21:28: 3000000 INFO @ Wed, 08 Dec 2021 14:21:34: 4000000 INFO @ Wed, 08 Dec 2021 14:21:39: 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 14:21:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.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 14:21:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:21:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:21:45: 6000000 INFO @ Wed, 08 Dec 2021 14:21:48: 1000000 INFO @ Wed, 08 Dec 2021 14:21:51: 7000000 INFO @ Wed, 08 Dec 2021 14:21:54: 2000000 INFO @ Wed, 08 Dec 2021 14:21:56: 8000000 INFO @ Wed, 08 Dec 2021 14:22:00: 3000000 INFO @ Wed, 08 Dec 2021 14:22:02: 9000000 INFO @ Wed, 08 Dec 2021 14:22:06: 4000000 INFO @ Wed, 08 Dec 2021 14:22:08: 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 14:22:12: 5000000 INFO @ Wed, 08 Dec 2021 14:22:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.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 14:22:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:22:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:22:14: 11000000 INFO @ Wed, 08 Dec 2021 14:22:19: 6000000 INFO @ Wed, 08 Dec 2021 14:22:20: 1000000 INFO @ Wed, 08 Dec 2021 14:22:21: 12000000 INFO @ Wed, 08 Dec 2021 14:22:25: 7000000 INFO @ Wed, 08 Dec 2021 14:22:27: 2000000 INFO @ Wed, 08 Dec 2021 14:22:27: 13000000 INFO @ Wed, 08 Dec 2021 14:22:32: 8000000 INFO @ Wed, 08 Dec 2021 14:22:34: 14000000 INFO @ Wed, 08 Dec 2021 14:22:35: 3000000 INFO @ Wed, 08 Dec 2021 14:22:38: 9000000 INFO @ Wed, 08 Dec 2021 14:22:41: 15000000 INFO @ Wed, 08 Dec 2021 14:22:42: 4000000 INFO @ Wed, 08 Dec 2021 14:22:45: 10000000 INFO @ Wed, 08 Dec 2021 14:22:47: 16000000 INFO @ Wed, 08 Dec 2021 14:22:49: 5000000 INFO @ Wed, 08 Dec 2021 14:22:52: 11000000 INFO @ Wed, 08 Dec 2021 14:22:54: 17000000 INFO @ Wed, 08 Dec 2021 14:22:57: 6000000 INFO @ Wed, 08 Dec 2021 14:22:58: 12000000 INFO @ Wed, 08 Dec 2021 14:23:00: 18000000 INFO @ Wed, 08 Dec 2021 14:23:04: 7000000 INFO @ Wed, 08 Dec 2021 14:23:05: 13000000 INFO @ Wed, 08 Dec 2021 14:23:07: 19000000 INFO @ Wed, 08 Dec 2021 14:23:11: 8000000 INFO @ Wed, 08 Dec 2021 14:23:11: 14000000 INFO @ Wed, 08 Dec 2021 14:23:13: 20000000 INFO @ Wed, 08 Dec 2021 14:23:18: 15000000 INFO @ Wed, 08 Dec 2021 14:23:19: 9000000 INFO @ Wed, 08 Dec 2021 14:23:20: 21000000 INFO @ Wed, 08 Dec 2021 14:23:25: 16000000 INFO @ Wed, 08 Dec 2021 14:23:26: 10000000 INFO @ Wed, 08 Dec 2021 14:23:26: 22000000 INFO @ Wed, 08 Dec 2021 14:23:31: 17000000 INFO @ Wed, 08 Dec 2021 14:23:33: 23000000 INFO @ Wed, 08 Dec 2021 14:23:34: 11000000 INFO @ Wed, 08 Dec 2021 14:23:38: 18000000 INFO @ Wed, 08 Dec 2021 14:23:39: 24000000 INFO @ Wed, 08 Dec 2021 14:23:41: 12000000 INFO @ Wed, 08 Dec 2021 14:23:44: 19000000 INFO @ Wed, 08 Dec 2021 14:23:46: 25000000 INFO @ Wed, 08 Dec 2021 14:23:48: 13000000 INFO @ Wed, 08 Dec 2021 14:23:51: 20000000 INFO @ Wed, 08 Dec 2021 14:23:52: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:23:52: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:23:52: #1 total tags in treatment: 25946753 INFO @ Wed, 08 Dec 2021 14:23:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:23:52: #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 14:23:52: #1 tags after filtering in treatment: 25946753 INFO @ Wed, 08 Dec 2021 14:23:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:23:52: #1 finished! INFO @ Wed, 08 Dec 2021 14:23:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:23:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:23:54: #2 number of paired peaks: 258 WARNING @ Wed, 08 Dec 2021 14:23:54: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Wed, 08 Dec 2021 14:23:54: start model_add_line... INFO @ Wed, 08 Dec 2021 14:23:54: start X-correlation... INFO @ Wed, 08 Dec 2021 14:23:54: end of X-cor INFO @ Wed, 08 Dec 2021 14:23:54: #2 finished! INFO @ Wed, 08 Dec 2021 14:23:54: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:23:54: #2 alternative fragment length(s) may be 1,531,554,568 bps INFO @ Wed, 08 Dec 2021 14:23:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.05_model.r WARNING @ Wed, 08 Dec 2021 14:23:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:23:54: #2 You may need to consider one of the other alternative d(s): 1,531,554,568 WARNING @ Wed, 08 Dec 2021 14:23:54: #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 14:23:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:23:54: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:23:56: 14000000 INFO @ Wed, 08 Dec 2021 14:23:57: 21000000 INFO @ Wed, 08 Dec 2021 14:24:03: 15000000 INFO @ Wed, 08 Dec 2021 14:24:03: 22000000 INFO @ Wed, 08 Dec 2021 14:24:10: 23000000 INFO @ Wed, 08 Dec 2021 14:24:10: 16000000 INFO @ Wed, 08 Dec 2021 14:24:16: 24000000 INFO @ Wed, 08 Dec 2021 14:24:18: 17000000 INFO @ Wed, 08 Dec 2021 14:24:22: 25000000 INFO @ Wed, 08 Dec 2021 14:24:25: 18000000 INFO @ Wed, 08 Dec 2021 14:24:29: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:24:29: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:24:29: #1 total tags in treatment: 25946753 INFO @ Wed, 08 Dec 2021 14:24:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:24:29: #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 14:24:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:24:29: #1 tags after filtering in treatment: 25946753 INFO @ Wed, 08 Dec 2021 14:24:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:24:29: #1 finished! INFO @ Wed, 08 Dec 2021 14:24:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:24:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:24:31: #2 number of paired peaks: 258 WARNING @ Wed, 08 Dec 2021 14:24:31: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Wed, 08 Dec 2021 14:24:31: start model_add_line... INFO @ Wed, 08 Dec 2021 14:24:31: start X-correlation... INFO @ Wed, 08 Dec 2021 14:24:31: end of X-cor INFO @ Wed, 08 Dec 2021 14:24:31: #2 finished! INFO @ Wed, 08 Dec 2021 14:24:31: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:24:31: #2 alternative fragment length(s) may be 1,531,554,568 bps INFO @ Wed, 08 Dec 2021 14:24:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.10_model.r WARNING @ Wed, 08 Dec 2021 14:24:31: #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 14:24:31: #2 You may need to consider one of the other alternative d(s): 1,531,554,568 WARNING @ Wed, 08 Dec 2021 14:24:31: #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 14:24:31: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:24:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:24:32: 19000000 INFO @ Wed, 08 Dec 2021 14:24:39: 20000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:24:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:24:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:24:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.05_summits.bed INFO @ Wed, 08 Dec 2021 14:24:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:24:46: 21000000 INFO @ Wed, 08 Dec 2021 14:24:53: 22000000 INFO @ Wed, 08 Dec 2021 14:24:59: 23000000 INFO @ Wed, 08 Dec 2021 14:25:05: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:25:06: 24000000 INFO @ Wed, 08 Dec 2021 14:25:13: 25000000 INFO @ Wed, 08 Dec 2021 14:25:19: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:25:19: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:25:19: #1 total tags in treatment: 25946753 INFO @ Wed, 08 Dec 2021 14:25:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:25:19: #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 14:25:19: #1 tags after filtering in treatment: 25946753 INFO @ Wed, 08 Dec 2021 14:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:25:19: #1 finished! INFO @ Wed, 08 Dec 2021 14:25:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:25:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:25:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:25:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.10_summits.bed INFO @ Wed, 08 Dec 2021 14:25:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:25:21: #2 number of paired peaks: 258 WARNING @ Wed, 08 Dec 2021 14:25:21: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Wed, 08 Dec 2021 14:25:21: start model_add_line... INFO @ Wed, 08 Dec 2021 14:25:21: start X-correlation... INFO @ Wed, 08 Dec 2021 14:25:21: end of X-cor INFO @ Wed, 08 Dec 2021 14:25:21: #2 finished! INFO @ Wed, 08 Dec 2021 14:25:21: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 14:25:21: #2 alternative fragment length(s) may be 1,531,554,568 bps INFO @ Wed, 08 Dec 2021 14:25:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.20_model.r WARNING @ Wed, 08 Dec 2021 14:25:21: #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 14:25:21: #2 You may need to consider one of the other alternative d(s): 1,531,554,568 WARNING @ Wed, 08 Dec 2021 14:25:21: #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 14:25:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:25:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:25:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:26:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799191/SRX6799191.20_summits.bed INFO @ Wed, 08 Dec 2021 14:26:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling