Job ID = 14159777 SRX = SRX8832069 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14729232 spots for SRR12332011/SRR12332011.sra Written 14729232 spots for SRR12332011/SRR12332011.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160312 ("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: 00:03:16 14729232 reads; of these: 14729232 (100.00%) were unpaired; of these: 689125 (4.68%) aligned 0 times 11959769 (81.20%) aligned exactly 1 time 2080338 (14.12%) aligned >1 times 95.32% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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 8 files... [bam_rmdupse_core] 1740732 / 14040107 = 0.1240 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 @ Thu, 09 Dec 2021 00:39:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.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, 09 Dec 2021 00:39:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:39:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:39:15: 1000000 INFO @ Thu, 09 Dec 2021 00:39:20: 2000000 INFO @ Thu, 09 Dec 2021 00:39:25: 3000000 INFO @ Thu, 09 Dec 2021 00:39:30: 4000000 INFO @ Thu, 09 Dec 2021 00:39:35: 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 @ Thu, 09 Dec 2021 00:39:40: 6000000 INFO @ Thu, 09 Dec 2021 00:39:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.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, 09 Dec 2021 00:39:40: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:39:40: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:39:45: 7000000 INFO @ Thu, 09 Dec 2021 00:39:46: 1000000 INFO @ Thu, 09 Dec 2021 00:39:51: 8000000 INFO @ Thu, 09 Dec 2021 00:39:53: 2000000 INFO @ Thu, 09 Dec 2021 00:39:56: 9000000 INFO @ Thu, 09 Dec 2021 00:39:59: 3000000 INFO @ Thu, 09 Dec 2021 00:40:02: 10000000 INFO @ Thu, 09 Dec 2021 00:40:06: 4000000 INFO @ Thu, 09 Dec 2021 00:40:08: 11000000 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 @ Thu, 09 Dec 2021 00:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.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, 09 Dec 2021 00:40:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:40:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:40:12: 5000000 INFO @ Thu, 09 Dec 2021 00:40:13: 12000000 INFO @ Thu, 09 Dec 2021 00:40:15: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:40:15: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:40:15: #1 total tags in treatment: 12299375 INFO @ Thu, 09 Dec 2021 00:40:15: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:40:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:40:15: #1 tags after filtering in treatment: 12299375 INFO @ Thu, 09 Dec 2021 00:40:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:40:15: #1 finished! INFO @ Thu, 09 Dec 2021 00:40:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:40:16: 1000000 INFO @ Thu, 09 Dec 2021 00:40:16: #2 number of paired peaks: 889 WARNING @ Thu, 09 Dec 2021 00:40:16: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Thu, 09 Dec 2021 00:40:16: start model_add_line... INFO @ Thu, 09 Dec 2021 00:40:16: start X-correlation... INFO @ Thu, 09 Dec 2021 00:40:16: end of X-cor INFO @ Thu, 09 Dec 2021 00:40:16: #2 finished! INFO @ Thu, 09 Dec 2021 00:40:16: #2 predicted fragment length is 163 bps INFO @ Thu, 09 Dec 2021 00:40:16: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 09 Dec 2021 00:40:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05_model.r INFO @ Thu, 09 Dec 2021 00:40:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:40:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:40:19: 6000000 INFO @ Thu, 09 Dec 2021 00:40:21: 2000000 INFO @ Thu, 09 Dec 2021 00:40:25: 7000000 INFO @ Thu, 09 Dec 2021 00:40:27: 3000000 INFO @ Thu, 09 Dec 2021 00:40:31: 8000000 INFO @ Thu, 09 Dec 2021 00:40:32: 4000000 INFO @ Thu, 09 Dec 2021 00:40:38: 9000000 INFO @ Thu, 09 Dec 2021 00:40:38: 5000000 INFO @ Thu, 09 Dec 2021 00:40:43: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:40:43: 6000000 INFO @ Thu, 09 Dec 2021 00:40:44: 10000000 INFO @ Thu, 09 Dec 2021 00:40:49: 7000000 INFO @ Thu, 09 Dec 2021 00:40:50: 11000000 INFO @ Thu, 09 Dec 2021 00:40:55: 8000000 INFO @ Thu, 09 Dec 2021 00:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.05_summits.bed INFO @ Thu, 09 Dec 2021 00:40:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7391 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:40:56: 12000000 INFO @ Thu, 09 Dec 2021 00:40:58: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:40:58: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:40:58: #1 total tags in treatment: 12299375 INFO @ Thu, 09 Dec 2021 00:40:58: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:40:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:40:58: #1 tags after filtering in treatment: 12299375 INFO @ Thu, 09 Dec 2021 00:40:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:40:58: #1 finished! INFO @ Thu, 09 Dec 2021 00:40:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:40:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:40:59: #2 number of paired peaks: 889 WARNING @ Thu, 09 Dec 2021 00:40:59: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Thu, 09 Dec 2021 00:40:59: start model_add_line... INFO @ Thu, 09 Dec 2021 00:40:59: start X-correlation... INFO @ Thu, 09 Dec 2021 00:40:59: end of X-cor INFO @ Thu, 09 Dec 2021 00:40:59: #2 finished! INFO @ Thu, 09 Dec 2021 00:40:59: #2 predicted fragment length is 163 bps INFO @ Thu, 09 Dec 2021 00:40:59: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 09 Dec 2021 00:40:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10_model.r INFO @ Thu, 09 Dec 2021 00:40:59: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:41:00: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:41:05: 10000000 INFO @ Thu, 09 Dec 2021 00:41:10: 11000000 INFO @ Thu, 09 Dec 2021 00:41:15: 12000000 INFO @ Thu, 09 Dec 2021 00:41:17: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:41:17: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:41:17: #1 total tags in treatment: 12299375 INFO @ Thu, 09 Dec 2021 00:41:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:41:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:41:17: #1 tags after filtering in treatment: 12299375 INFO @ Thu, 09 Dec 2021 00:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:41:17: #1 finished! INFO @ Thu, 09 Dec 2021 00:41:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:41:18: #2 number of paired peaks: 889 WARNING @ Thu, 09 Dec 2021 00:41:18: Fewer paired peaks (889) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 889 pairs to build model! INFO @ Thu, 09 Dec 2021 00:41:18: start model_add_line... INFO @ Thu, 09 Dec 2021 00:41:18: start X-correlation... INFO @ Thu, 09 Dec 2021 00:41:18: end of X-cor INFO @ Thu, 09 Dec 2021 00:41:18: #2 finished! INFO @ Thu, 09 Dec 2021 00:41:18: #2 predicted fragment length is 163 bps INFO @ Thu, 09 Dec 2021 00:41:18: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 09 Dec 2021 00:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20_model.r INFO @ Thu, 09 Dec 2021 00:41:18: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:41:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:41:26: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:41:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:41:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:41:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.10_summits.bed INFO @ Thu, 09 Dec 2021 00:41:39: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4922 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:41:44: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:41:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:41:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:41:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832069/SRX8832069.20_summits.bed INFO @ Thu, 09 Dec 2021 00:41:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2380 records, 4 fields): 3 millis CompletedMACS2peakCalling