Job ID = 10165624 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 10165843 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:47 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: 00:05:48 Overall time: 00:05:48 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:43:26: # 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 @ Thu, 08 Oct 2020 19:43:26: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:43:26: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:43:31: 1000000 INFO @ Thu, 08 Oct 2020 19:43:36: 2000000 INFO @ Thu, 08 Oct 2020 19:43:41: 3000000 INFO @ Thu, 08 Oct 2020 19:43:46: 4000000 INFO @ Thu, 08 Oct 2020 19:43:51: 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 19:43:56: # 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 @ Thu, 08 Oct 2020 19:43:56: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:43:56: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:43:56: 6000000 INFO @ Thu, 08 Oct 2020 19:44:01: 1000000 INFO @ Thu, 08 Oct 2020 19:44:02: 7000000 INFO @ Thu, 08 Oct 2020 19:44:06: 2000000 INFO @ Thu, 08 Oct 2020 19:44:07: 8000000 INFO @ Thu, 08 Oct 2020 19:44:12: 3000000 INFO @ Thu, 08 Oct 2020 19:44:13: 9000000 INFO @ Thu, 08 Oct 2020 19:44:17: 4000000 INFO @ Thu, 08 Oct 2020 19:44:18: 10000000 INFO @ Thu, 08 Oct 2020 19:44:23: 5000000 INFO @ Thu, 08 Oct 2020 19:44:23: 11000000 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 19:44:26: # 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 @ Thu, 08 Oct 2020 19:44:26: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:44:26: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:44:28: 6000000 INFO @ Thu, 08 Oct 2020 19:44:29: 12000000 INFO @ Thu, 08 Oct 2020 19:44:32: 1000000 INFO @ Thu, 08 Oct 2020 19:44:34: 7000000 INFO @ Thu, 08 Oct 2020 19:44:35: 13000000 INFO @ Thu, 08 Oct 2020 19:44:39: 2000000 INFO @ Thu, 08 Oct 2020 19:44:40: 8000000 INFO @ Thu, 08 Oct 2020 19:44:41: 14000000 INFO @ Thu, 08 Oct 2020 19:44:45: 3000000 INFO @ Thu, 08 Oct 2020 19:44:46: 9000000 INFO @ Thu, 08 Oct 2020 19:44:47: 15000000 INFO @ Thu, 08 Oct 2020 19:44:52: 4000000 INFO @ Thu, 08 Oct 2020 19:44:52: 10000000 INFO @ Thu, 08 Oct 2020 19:44:53: 16000000 INFO @ Thu, 08 Oct 2020 19:44:58: 11000000 INFO @ Thu, 08 Oct 2020 19:44:58: 5000000 INFO @ Thu, 08 Oct 2020 19:44:59: 17000000 INFO @ Thu, 08 Oct 2020 19:45:04: 12000000 INFO @ Thu, 08 Oct 2020 19:45:04: 18000000 INFO @ Thu, 08 Oct 2020 19:45:05: 6000000 INFO @ Thu, 08 Oct 2020 19:45:10: 13000000 INFO @ Thu, 08 Oct 2020 19:45:10: 19000000 INFO @ Thu, 08 Oct 2020 19:45:11: 7000000 INFO @ Thu, 08 Oct 2020 19:45:13: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:45:13: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:45:13: #1 total tags in treatment: 19385825 INFO @ Thu, 08 Oct 2020 19:45:13: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:45:13: #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 19:45:13: #1 tags after filtering in treatment: 19385825 INFO @ Thu, 08 Oct 2020 19:45:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:45:13: #1 finished! INFO @ Thu, 08 Oct 2020 19:45:13: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:45:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:45:14: #2 number of paired peaks: 419 WARNING @ Thu, 08 Oct 2020 19:45:14: 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 @ Thu, 08 Oct 2020 19:45:14: start model_add_line... INFO @ Thu, 08 Oct 2020 19:45:14: start X-correlation... INFO @ Thu, 08 Oct 2020 19:45:14: end of X-cor INFO @ Thu, 08 Oct 2020 19:45:14: #2 finished! INFO @ Thu, 08 Oct 2020 19:45:14: #2 predicted fragment length is 236 bps INFO @ Thu, 08 Oct 2020 19:45:14: #2 alternative fragment length(s) may be 4,236 bps INFO @ Thu, 08 Oct 2020 19:45:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.05_model.r INFO @ Thu, 08 Oct 2020 19:45:14: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:45:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:45:15: 14000000 INFO @ Thu, 08 Oct 2020 19:45:18: 8000000 INFO @ Thu, 08 Oct 2020 19:45:21: 15000000 INFO @ Thu, 08 Oct 2020 19:45:24: 9000000 INFO @ Thu, 08 Oct 2020 19:45:27: 16000000 INFO @ Thu, 08 Oct 2020 19:45:30: 10000000 INFO @ Thu, 08 Oct 2020 19:45:33: 17000000 INFO @ Thu, 08 Oct 2020 19:45:37: 11000000 INFO @ Thu, 08 Oct 2020 19:45:39: 18000000 INFO @ Thu, 08 Oct 2020 19:45:43: 12000000 INFO @ Thu, 08 Oct 2020 19:45:44: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:45:47: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:45:47: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:45:47: #1 total tags in treatment: 19385825 INFO @ Thu, 08 Oct 2020 19:45:47: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:45:47: #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 19:45:47: #1 tags after filtering in treatment: 19385825 INFO @ Thu, 08 Oct 2020 19:45:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:45:47: #1 finished! INFO @ Thu, 08 Oct 2020 19:45:47: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:45:48: #2 number of paired peaks: 419 WARNING @ Thu, 08 Oct 2020 19:45:48: 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 @ Thu, 08 Oct 2020 19:45:48: start model_add_line... INFO @ Thu, 08 Oct 2020 19:45:48: start X-correlation... INFO @ Thu, 08 Oct 2020 19:45:48: end of X-cor INFO @ Thu, 08 Oct 2020 19:45:48: #2 finished! INFO @ Thu, 08 Oct 2020 19:45:48: #2 predicted fragment length is 236 bps INFO @ Thu, 08 Oct 2020 19:45:48: #2 alternative fragment length(s) may be 4,236 bps INFO @ Thu, 08 Oct 2020 19:45:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.10_model.r INFO @ Thu, 08 Oct 2020 19:45:48: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:45:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:45:50: 13000000 INFO @ Thu, 08 Oct 2020 19:45:56: 14000000 INFO @ Thu, 08 Oct 2020 19:45:59: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:46:02: 15000000 INFO @ Thu, 08 Oct 2020 19:46:08: 16000000 INFO @ Thu, 08 Oct 2020 19:46:14: 17000000 INFO @ Thu, 08 Oct 2020 19:46:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:46:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:46:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.05_summits.bed INFO @ Thu, 08 Oct 2020 19:46:19: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (14247 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:46:20: 18000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:46:26: 19000000 INFO @ Thu, 08 Oct 2020 19:46:29: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:46:29: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:46:29: #1 total tags in treatment: 19385825 INFO @ Thu, 08 Oct 2020 19:46:29: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:46:29: #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 19:46:29: #1 tags after filtering in treatment: 19385825 INFO @ Thu, 08 Oct 2020 19:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:46:29: #1 finished! INFO @ Thu, 08 Oct 2020 19:46:29: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:46:30: #2 number of paired peaks: 419 WARNING @ Thu, 08 Oct 2020 19:46:30: 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 @ Thu, 08 Oct 2020 19:46:30: start model_add_line... INFO @ Thu, 08 Oct 2020 19:46:31: start X-correlation... INFO @ Thu, 08 Oct 2020 19:46:31: end of X-cor INFO @ Thu, 08 Oct 2020 19:46:31: #2 finished! INFO @ Thu, 08 Oct 2020 19:46:31: #2 predicted fragment length is 236 bps INFO @ Thu, 08 Oct 2020 19:46:31: #2 alternative fragment length(s) may be 4,236 bps INFO @ Thu, 08 Oct 2020 19:46:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.20_model.r INFO @ Thu, 08 Oct 2020 19:46:31: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:46:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:46:33: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.10_summits.bed INFO @ Thu, 08 Oct 2020 19:46:53: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10168 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:47:18: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799182/SRX6799182.20_summits.bed INFO @ Thu, 08 Oct 2020 19:47:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5132 records, 4 fields): 6 millis CompletedMACS2peakCalling