Job ID = 10165625 SRX = SRX6799183 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 36690704 spots for SRR10065390/SRR10065390.sra Written 36690704 spots for SRR10065390/SRR10065390.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165898 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:09 36690704 reads; of these: 36690704 (100.00%) were unpaired; of these: 1385509 (3.78%) aligned 0 times 28070165 (76.50%) aligned exactly 1 time 7235030 (19.72%) aligned >1 times 96.22% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 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] 10358503 / 35305195 = 0.2934 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 19:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.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 19:47:51: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:51: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:57: 1000000 INFO @ Thu, 08 Oct 2020 19:48:02: 2000000 INFO @ Thu, 08 Oct 2020 19:48:07: 3000000 INFO @ Thu, 08 Oct 2020 19:48:12: 4000000 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 19:48:18: 5000000 INFO @ Thu, 08 Oct 2020 19:48:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.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 19:48:22: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:22: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:23: 6000000 INFO @ Thu, 08 Oct 2020 19:48:27: 1000000 INFO @ Thu, 08 Oct 2020 19:48:29: 7000000 INFO @ Thu, 08 Oct 2020 19:48:33: 2000000 INFO @ Thu, 08 Oct 2020 19:48:35: 8000000 INFO @ Thu, 08 Oct 2020 19:48:39: 3000000 INFO @ Thu, 08 Oct 2020 19:48:40: 9000000 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 19:48:45: 4000000 INFO @ Thu, 08 Oct 2020 19:48:46: 10000000 INFO @ Thu, 08 Oct 2020 19:48:51: 5000000 INFO @ Thu, 08 Oct 2020 19:48:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.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 19:48:51: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:51: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:52: 11000000 INFO @ Thu, 08 Oct 2020 19:48:57: 6000000 INFO @ Thu, 08 Oct 2020 19:48:57: 1000000 INFO @ Thu, 08 Oct 2020 19:48:58: 12000000 INFO @ Thu, 08 Oct 2020 19:49:03: 7000000 INFO @ Thu, 08 Oct 2020 19:49:03: 2000000 INFO @ Thu, 08 Oct 2020 19:49:04: 13000000 INFO @ Thu, 08 Oct 2020 19:49:08: 8000000 INFO @ Thu, 08 Oct 2020 19:49:09: 3000000 INFO @ Thu, 08 Oct 2020 19:49:09: 14000000 INFO @ Thu, 08 Oct 2020 19:49:14: 9000000 INFO @ Thu, 08 Oct 2020 19:49:15: 4000000 INFO @ Thu, 08 Oct 2020 19:49:15: 15000000 INFO @ Thu, 08 Oct 2020 19:49:20: 10000000 INFO @ Thu, 08 Oct 2020 19:49:21: 5000000 INFO @ Thu, 08 Oct 2020 19:49:21: 16000000 INFO @ Thu, 08 Oct 2020 19:49:26: 11000000 INFO @ Thu, 08 Oct 2020 19:49:27: 6000000 INFO @ Thu, 08 Oct 2020 19:49:27: 17000000 INFO @ Thu, 08 Oct 2020 19:49:32: 12000000 INFO @ Thu, 08 Oct 2020 19:49:33: 7000000 INFO @ Thu, 08 Oct 2020 19:49:33: 18000000 INFO @ Thu, 08 Oct 2020 19:49:38: 13000000 INFO @ Thu, 08 Oct 2020 19:49:39: 8000000 INFO @ Thu, 08 Oct 2020 19:49:39: 19000000 INFO @ Thu, 08 Oct 2020 19:49:44: 14000000 INFO @ Thu, 08 Oct 2020 19:49:45: 9000000 INFO @ Thu, 08 Oct 2020 19:49:45: 20000000 INFO @ Thu, 08 Oct 2020 19:49:50: 15000000 INFO @ Thu, 08 Oct 2020 19:49:50: 10000000 INFO @ Thu, 08 Oct 2020 19:49:51: 21000000 INFO @ Thu, 08 Oct 2020 19:49:55: 16000000 INFO @ Thu, 08 Oct 2020 19:49:56: 11000000 INFO @ Thu, 08 Oct 2020 19:49:56: 22000000 INFO @ Thu, 08 Oct 2020 19:50:01: 17000000 INFO @ Thu, 08 Oct 2020 19:50:02: 12000000 INFO @ Thu, 08 Oct 2020 19:50:02: 23000000 INFO @ Thu, 08 Oct 2020 19:50:07: 18000000 INFO @ Thu, 08 Oct 2020 19:50:08: 13000000 INFO @ Thu, 08 Oct 2020 19:50:08: 24000000 INFO @ Thu, 08 Oct 2020 19:50:13: 19000000 INFO @ Thu, 08 Oct 2020 19:50:13: 14000000 INFO @ Thu, 08 Oct 2020 19:50:14: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:14: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:14: #1 total tags in treatment: 24946692 INFO @ Thu, 08 Oct 2020 19:50:14: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:14: #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 19:50:14: #1 tags after filtering in treatment: 24946692 INFO @ Thu, 08 Oct 2020 19:50:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:14: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:14: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:15: #2 number of paired peaks: 142 WARNING @ Thu, 08 Oct 2020 19:50:15: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:15: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:16: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:16: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:16: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:16: #2 predicted fragment length is 188 bps INFO @ Thu, 08 Oct 2020 19:50:16: #2 alternative fragment length(s) may be 3,138,188,205,226 bps INFO @ Thu, 08 Oct 2020 19:50:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.05_model.r INFO @ Thu, 08 Oct 2020 19:50:16: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:19: 20000000 INFO @ Thu, 08 Oct 2020 19:50:19: 15000000 INFO @ Thu, 08 Oct 2020 19:50:24: 21000000 INFO @ Thu, 08 Oct 2020 19:50:25: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:50:30: 22000000 INFO @ Thu, 08 Oct 2020 19:50:31: 17000000 INFO @ Thu, 08 Oct 2020 19:50:36: 23000000 INFO @ Thu, 08 Oct 2020 19:50:36: 18000000 INFO @ Thu, 08 Oct 2020 19:50:42: 24000000 INFO @ Thu, 08 Oct 2020 19:50:42: 19000000 INFO @ Thu, 08 Oct 2020 19:50:47: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:47: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:47: #1 total tags in treatment: 24946692 INFO @ Thu, 08 Oct 2020 19:50:47: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:47: #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 19:50:47: #1 tags after filtering in treatment: 24946692 INFO @ Thu, 08 Oct 2020 19:50:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:47: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:47: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:48: 20000000 INFO @ Thu, 08 Oct 2020 19:50:49: #2 number of paired peaks: 142 WARNING @ Thu, 08 Oct 2020 19:50:49: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:49: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:49: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:49: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:49: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:49: #2 predicted fragment length is 188 bps INFO @ Thu, 08 Oct 2020 19:50:49: #2 alternative fragment length(s) may be 3,138,188,205,226 bps INFO @ Thu, 08 Oct 2020 19:50:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.10_model.r INFO @ Thu, 08 Oct 2020 19:50:49: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:53: 21000000 INFO @ Thu, 08 Oct 2020 19:50:59: 22000000 INFO @ Thu, 08 Oct 2020 19:51:04: 23000000 INFO @ Thu, 08 Oct 2020 19:51:06: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:10: 24000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:51:15: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:51:15: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:51:15: #1 total tags in treatment: 24946692 INFO @ Thu, 08 Oct 2020 19:51:15: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:51:15: #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 19:51:15: #1 tags after filtering in treatment: 24946692 INFO @ Thu, 08 Oct 2020 19:51:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:51:15: #1 finished! INFO @ Thu, 08 Oct 2020 19:51:15: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:51:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:51:17: #2 number of paired peaks: 142 WARNING @ Thu, 08 Oct 2020 19:51:17: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Thu, 08 Oct 2020 19:51:17: start model_add_line... INFO @ Thu, 08 Oct 2020 19:51:17: start X-correlation... INFO @ Thu, 08 Oct 2020 19:51:17: end of X-cor INFO @ Thu, 08 Oct 2020 19:51:17: #2 finished! INFO @ Thu, 08 Oct 2020 19:51:17: #2 predicted fragment length is 188 bps INFO @ Thu, 08 Oct 2020 19:51:17: #2 alternative fragment length(s) may be 3,138,188,205,226 bps INFO @ Thu, 08 Oct 2020 19:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.20_model.r INFO @ Thu, 08 Oct 2020 19:51:17: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:51:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.05_summits.bed INFO @ Thu, 08 Oct 2020 19:51:30: Done! INFO @ Thu, 08 Oct 2020 19:51:40: #3 Call peaks for each chromosome... pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (14108 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.10_summits.bed INFO @ Thu, 08 Oct 2020 19:52:05: Done! INFO @ Thu, 08 Oct 2020 19:52:08: #3 Call peaks for each chromosome... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9178 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799183/SRX6799183.20_summits.bed INFO @ Thu, 08 Oct 2020 19:52:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3928 records, 4 fields): 5 millis CompletedMACS2peakCalling