Job ID = 14158024 SRX = SRX6799182 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: 00:09:00 28244193 reads; of these: 28244193 (100.00%) were unpaired; of these: 1684882 (5.97%) aligned 0 times 20337970 (72.01%) aligned exactly 1 time 6221341 (22.03%) aligned >1 times 94.03% overall alignment rate Time searching: 00:09:00 Overall time: 00:09:00 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 12 files... [bam_rmdupse_core] 7173181 / 26559311 = 0.2701 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 14:12:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.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 14:12:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:12:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:12:43: 1000000 INFO @ Wed, 08 Dec 2021 14:12:50: 2000000 INFO @ Wed, 08 Dec 2021 14:12:58: 3000000 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 14:13:05: 4000000 INFO @ Wed, 08 Dec 2021 14:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.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 14:13:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:13:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:13:11: 5000000 INFO @ Wed, 08 Dec 2021 14:13:15: 1000000 INFO @ Wed, 08 Dec 2021 14:13:18: 6000000 INFO @ Wed, 08 Dec 2021 14:13:24: 2000000 INFO @ Wed, 08 Dec 2021 14:13:25: 7000000 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 14:13:32: 8000000 INFO @ Wed, 08 Dec 2021 14:13:34: 3000000 INFO @ Wed, 08 Dec 2021 14:13:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.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 14:13:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:13:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:13:40: 9000000 INFO @ Wed, 08 Dec 2021 14:13:43: 4000000 INFO @ Wed, 08 Dec 2021 14:13:45: 1000000 INFO @ Wed, 08 Dec 2021 14:13:47: 10000000 INFO @ Wed, 08 Dec 2021 14:13:52: 5000000 INFO @ Wed, 08 Dec 2021 14:13:54: 2000000 INFO @ Wed, 08 Dec 2021 14:13:54: 11000000 INFO @ Wed, 08 Dec 2021 14:14:01: 6000000 INFO @ Wed, 08 Dec 2021 14:14:01: 12000000 INFO @ Wed, 08 Dec 2021 14:14:03: 3000000 INFO @ Wed, 08 Dec 2021 14:14:08: 13000000 INFO @ Wed, 08 Dec 2021 14:14:09: 7000000 INFO @ Wed, 08 Dec 2021 14:14:12: 4000000 INFO @ Wed, 08 Dec 2021 14:14:15: 14000000 INFO @ Wed, 08 Dec 2021 14:14:18: 8000000 INFO @ Wed, 08 Dec 2021 14:14:21: 5000000 INFO @ Wed, 08 Dec 2021 14:14:22: 15000000 INFO @ Wed, 08 Dec 2021 14:14:28: 9000000 INFO @ Wed, 08 Dec 2021 14:14:29: 16000000 INFO @ Wed, 08 Dec 2021 14:14:30: 6000000 INFO @ Wed, 08 Dec 2021 14:14:36: 17000000 INFO @ Wed, 08 Dec 2021 14:14:37: 10000000 INFO @ Wed, 08 Dec 2021 14:14:39: 7000000 INFO @ Wed, 08 Dec 2021 14:14:43: 18000000 INFO @ Wed, 08 Dec 2021 14:14:46: 11000000 INFO @ Wed, 08 Dec 2021 14:14:48: 8000000 INFO @ Wed, 08 Dec 2021 14:14:51: 19000000 INFO @ Wed, 08 Dec 2021 14:14:54: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:14:54: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:14:54: #1 total tags in treatment: 19386130 INFO @ Wed, 08 Dec 2021 14:14:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:14:54: #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 14:14:54: #1 tags after filtering in treatment: 19386130 INFO @ Wed, 08 Dec 2021 14:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:14:54: #1 finished! INFO @ Wed, 08 Dec 2021 14:14:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:14:55: 12000000 INFO @ Wed, 08 Dec 2021 14:14:56: #2 number of paired peaks: 419 WARNING @ Wed, 08 Dec 2021 14:14:56: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Wed, 08 Dec 2021 14:14:56: start model_add_line... INFO @ Wed, 08 Dec 2021 14:14:56: start X-correlation... INFO @ Wed, 08 Dec 2021 14:14:56: end of X-cor INFO @ Wed, 08 Dec 2021 14:14:56: #2 finished! INFO @ Wed, 08 Dec 2021 14:14:56: #2 predicted fragment length is 236 bps INFO @ Wed, 08 Dec 2021 14:14:56: #2 alternative fragment length(s) may be 4,236 bps INFO @ Wed, 08 Dec 2021 14:14:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.05_model.r INFO @ Wed, 08 Dec 2021 14:14:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:14:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:14:57: 9000000 INFO @ Wed, 08 Dec 2021 14:15:04: 13000000 INFO @ Wed, 08 Dec 2021 14:15:06: 10000000 INFO @ Wed, 08 Dec 2021 14:15:13: 14000000 INFO @ Wed, 08 Dec 2021 14:15:14: 11000000 INFO @ Wed, 08 Dec 2021 14:15:22: 15000000 INFO @ Wed, 08 Dec 2021 14:15:23: 12000000 INFO @ Wed, 08 Dec 2021 14:15:30: 16000000 INFO @ Wed, 08 Dec 2021 14:15:32: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:15:39: 17000000 INFO @ Wed, 08 Dec 2021 14:15:40: 14000000 INFO @ Wed, 08 Dec 2021 14:15:48: 18000000 INFO @ Wed, 08 Dec 2021 14:15:49: 15000000 INFO @ Wed, 08 Dec 2021 14:15:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:15:56: 19000000 INFO @ Wed, 08 Dec 2021 14:15:58: 16000000 INFO @ Wed, 08 Dec 2021 14:16:00: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:16:00: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:16:00: #1 total tags in treatment: 19386130 INFO @ Wed, 08 Dec 2021 14:16:00: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:16:00: #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 14:16:00: #1 tags after filtering in treatment: 19386130 INFO @ Wed, 08 Dec 2021 14:16:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:16:00: #1 finished! INFO @ Wed, 08 Dec 2021 14:16:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:16:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:16:02: #2 number of paired peaks: 419 WARNING @ Wed, 08 Dec 2021 14:16:02: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Wed, 08 Dec 2021 14:16:02: start model_add_line... INFO @ Wed, 08 Dec 2021 14:16:02: start X-correlation... INFO @ Wed, 08 Dec 2021 14:16:02: end of X-cor INFO @ Wed, 08 Dec 2021 14:16:02: #2 finished! INFO @ Wed, 08 Dec 2021 14:16:02: #2 predicted fragment length is 236 bps INFO @ Wed, 08 Dec 2021 14:16:02: #2 alternative fragment length(s) may be 4,236 bps INFO @ Wed, 08 Dec 2021 14:16:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.10_model.r INFO @ Wed, 08 Dec 2021 14:16:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:16:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:16:06: 17000000 INFO @ Wed, 08 Dec 2021 14:16:15: 18000000 INFO @ Wed, 08 Dec 2021 14:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.05_summits.bed INFO @ Wed, 08 Dec 2021 14:16:19: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (14244 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:16:24: 19000000 INFO @ Wed, 08 Dec 2021 14:16:27: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:16:27: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:16:27: #1 total tags in treatment: 19386130 INFO @ Wed, 08 Dec 2021 14:16:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:16:27: #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 14:16:27: #1 tags after filtering in treatment: 19386130 INFO @ Wed, 08 Dec 2021 14:16:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:16:27: #1 finished! INFO @ Wed, 08 Dec 2021 14:16:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:16:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:16:29: #2 number of paired peaks: 419 WARNING @ Wed, 08 Dec 2021 14:16:29: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Wed, 08 Dec 2021 14:16:29: start model_add_line... INFO @ Wed, 08 Dec 2021 14:16:29: start X-correlation... INFO @ Wed, 08 Dec 2021 14:16:29: end of X-cor INFO @ Wed, 08 Dec 2021 14:16:29: #2 finished! INFO @ Wed, 08 Dec 2021 14:16:29: #2 predicted fragment length is 236 bps INFO @ Wed, 08 Dec 2021 14:16:29: #2 alternative fragment length(s) may be 4,236 bps INFO @ Wed, 08 Dec 2021 14:16:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.20_model.r INFO @ Wed, 08 Dec 2021 14:16:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:16:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:17:02: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:17:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:17:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:17:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.10_summits.bed INFO @ Wed, 08 Dec 2021 14:17:27: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (10172 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:17:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:17:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:17:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:17:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799182/SRX6799182.20_summits.bed INFO @ Wed, 08 Dec 2021 14:17:52: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (5135 records, 4 fields): 12 millis CompletedMACS2peakCalling