Job ID = 14157864 SRX = SRX6799182 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 28244193 spots for SRR10065389/SRR10065389.sra Written 28244193 spots for SRR10065389/SRR10065389.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158024 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:02 28244193 reads; of these: 28244193 (100.00%) were unpaired; of these: 1685509 (5.97%) aligned 0 times 20337517 (72.01%) aligned exactly 1 time 6221167 (22.03%) aligned >1 times 94.03% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 7172859 / 26558684 = 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 11:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 11:59:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:59:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:59:10: 1000000 INFO @ Wed, 08 Dec 2021 11:59:15: 2000000 INFO @ Wed, 08 Dec 2021 11:59:20: 3000000 INFO @ Wed, 08 Dec 2021 11:59:25: 4000000 INFO @ Wed, 08 Dec 2021 11:59:30: 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 11:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 11:59:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:59:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:59:35: 6000000 INFO @ Wed, 08 Dec 2021 11:59:41: 7000000 INFO @ Wed, 08 Dec 2021 11:59:42: 1000000 INFO @ Wed, 08 Dec 2021 11:59:47: 8000000 INFO @ Wed, 08 Dec 2021 11:59:48: 2000000 INFO @ Wed, 08 Dec 2021 11:59:53: 9000000 INFO @ Wed, 08 Dec 2021 11:59:55: 3000000 INFO @ Wed, 08 Dec 2021 11:59:59: 10000000 INFO @ Wed, 08 Dec 2021 12:00:01: 4000000 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 12:00:04: 11000000 INFO @ Wed, 08 Dec 2021 12:00:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 12:00:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:00:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:00:08: 5000000 INFO @ Wed, 08 Dec 2021 12:00:10: 12000000 INFO @ Wed, 08 Dec 2021 12:00:12: 1000000 INFO @ Wed, 08 Dec 2021 12:00:14: 6000000 INFO @ Wed, 08 Dec 2021 12:00:16: 13000000 INFO @ Wed, 08 Dec 2021 12:00:19: 2000000 INFO @ Wed, 08 Dec 2021 12:00:21: 7000000 INFO @ Wed, 08 Dec 2021 12:00:22: 14000000 INFO @ Wed, 08 Dec 2021 12:00:25: 3000000 INFO @ Wed, 08 Dec 2021 12:00:27: 8000000 INFO @ Wed, 08 Dec 2021 12:00:28: 15000000 INFO @ Wed, 08 Dec 2021 12:00:32: 4000000 INFO @ Wed, 08 Dec 2021 12:00:34: 9000000 INFO @ Wed, 08 Dec 2021 12:00:34: 16000000 INFO @ Wed, 08 Dec 2021 12:00:39: 5000000 INFO @ Wed, 08 Dec 2021 12:00:40: 17000000 INFO @ Wed, 08 Dec 2021 12:00:40: 10000000 INFO @ Wed, 08 Dec 2021 12:00:45: 6000000 INFO @ Wed, 08 Dec 2021 12:00:46: 18000000 INFO @ Wed, 08 Dec 2021 12:00:46: 11000000 INFO @ Wed, 08 Dec 2021 12:00:51: 19000000 INFO @ Wed, 08 Dec 2021 12:00:52: 7000000 INFO @ Wed, 08 Dec 2021 12:00:53: 12000000 INFO @ Wed, 08 Dec 2021 12:00:54: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:00:54: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:00:54: #1 total tags in treatment: 19385825 INFO @ Wed, 08 Dec 2021 12:00:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:00:54: #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 12:00:54: #1 tags after filtering in treatment: 19385825 INFO @ Wed, 08 Dec 2021 12:00:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:00:54: #1 finished! INFO @ Wed, 08 Dec 2021 12:00:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:00:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:00:55: #2 number of paired peaks: 419 WARNING @ Wed, 08 Dec 2021 12:00:55: 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 12:00:55: start model_add_line... INFO @ Wed, 08 Dec 2021 12:00:55: start X-correlation... INFO @ Wed, 08 Dec 2021 12:00:55: end of X-cor INFO @ Wed, 08 Dec 2021 12:00:55: #2 finished! INFO @ Wed, 08 Dec 2021 12:00:55: #2 predicted fragment length is 236 bps INFO @ Wed, 08 Dec 2021 12:00:55: #2 alternative fragment length(s) may be 4,236 bps INFO @ Wed, 08 Dec 2021 12:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.05_model.r INFO @ Wed, 08 Dec 2021 12:00:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:00:58: 8000000 INFO @ Wed, 08 Dec 2021 12:01:00: 13000000 INFO @ Wed, 08 Dec 2021 12:01:05: 9000000 INFO @ Wed, 08 Dec 2021 12:01:06: 14000000 INFO @ Wed, 08 Dec 2021 12:01:11: 10000000 INFO @ Wed, 08 Dec 2021 12:01:12: 15000000 INFO @ Wed, 08 Dec 2021 12:01:18: 11000000 INFO @ Wed, 08 Dec 2021 12:01:19: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:01:24: 12000000 INFO @ Wed, 08 Dec 2021 12:01:25: 17000000 INFO @ Wed, 08 Dec 2021 12:01:31: 13000000 INFO @ Wed, 08 Dec 2021 12:01:32: 18000000 INFO @ Wed, 08 Dec 2021 12:01:37: 14000000 INFO @ Wed, 08 Dec 2021 12:01:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:01:38: 19000000 INFO @ Wed, 08 Dec 2021 12:01:40: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:01:40: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:01:40: #1 total tags in treatment: 19385825 INFO @ Wed, 08 Dec 2021 12:01:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:01:40: #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 12:01:41: #1 tags after filtering in treatment: 19385825 INFO @ Wed, 08 Dec 2021 12:01:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:01:41: #1 finished! INFO @ Wed, 08 Dec 2021 12:01:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:01:42: #2 number of paired peaks: 419 WARNING @ Wed, 08 Dec 2021 12:01:42: 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 12:01:42: start model_add_line... INFO @ Wed, 08 Dec 2021 12:01:42: start X-correlation... INFO @ Wed, 08 Dec 2021 12:01:42: end of X-cor INFO @ Wed, 08 Dec 2021 12:01:42: #2 finished! INFO @ Wed, 08 Dec 2021 12:01:42: #2 predicted fragment length is 236 bps INFO @ Wed, 08 Dec 2021 12:01:42: #2 alternative fragment length(s) may be 4,236 bps INFO @ Wed, 08 Dec 2021 12:01:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.10_model.r INFO @ Wed, 08 Dec 2021 12:01:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:01:44: 15000000 INFO @ Wed, 08 Dec 2021 12:01:50: 16000000 INFO @ Wed, 08 Dec 2021 12:01:56: 17000000 INFO @ Wed, 08 Dec 2021 12:01:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:01:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:01:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.05_summits.bed INFO @ Wed, 08 Dec 2021 12:01:57: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (14247 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:02:02: 18000000 INFO @ Wed, 08 Dec 2021 12:02:08: 19000000 INFO @ Wed, 08 Dec 2021 12:02:11: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:02:11: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:02:11: #1 total tags in treatment: 19385825 INFO @ Wed, 08 Dec 2021 12:02:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:02:11: #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 12:02:11: #1 tags after filtering in treatment: 19385825 INFO @ Wed, 08 Dec 2021 12:02:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:02:11: #1 finished! INFO @ Wed, 08 Dec 2021 12:02:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:02:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:02:12: #2 number of paired peaks: 419 WARNING @ Wed, 08 Dec 2021 12:02:12: 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 12:02:12: start model_add_line... INFO @ Wed, 08 Dec 2021 12:02:12: start X-correlation... INFO @ Wed, 08 Dec 2021 12:02:13: end of X-cor INFO @ Wed, 08 Dec 2021 12:02:13: #2 finished! INFO @ Wed, 08 Dec 2021 12:02:13: #2 predicted fragment length is 236 bps INFO @ Wed, 08 Dec 2021 12:02:13: #2 alternative fragment length(s) may be 4,236 bps INFO @ Wed, 08 Dec 2021 12:02:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.20_model.r INFO @ Wed, 08 Dec 2021 12:02:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:02:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:02:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:02:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:02:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.10_summits.bed INFO @ Wed, 08 Dec 2021 12:02:47: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10168 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:02:56: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:03:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:03:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.20_summits.bed INFO @ Wed, 08 Dec 2021 12:03:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5132 records, 4 fields): 6 millis CompletedMACS2peakCalling