Job ID = 16434856 SRX = SRX10435524 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17673881 spots for SRR14060924/SRR14060924.sra Written 17673881 spots for SRR14060924/SRR14060924.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434904 ("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: 00:05:26 17673881 reads; of these: 17673881 (100.00%) were unpaired; of these: 2015603 (11.40%) aligned 0 times 13516616 (76.48%) aligned exactly 1 time 2141662 (12.12%) aligned >1 times 88.60% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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] 2511121 / 15658278 = 0.1604 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:13:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.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 @ Tue, 02 Aug 2022 10:13:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:13:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:13:29: 1000000 INFO @ Tue, 02 Aug 2022 10:13:36: 2000000 INFO @ Tue, 02 Aug 2022 10:13:44: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.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 @ Tue, 02 Aug 2022 10:13:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:13:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:13:52: 4000000 INFO @ Tue, 02 Aug 2022 10:13:58: 1000000 INFO @ Tue, 02 Aug 2022 10:14:00: 5000000 INFO @ Tue, 02 Aug 2022 10:14:06: 2000000 INFO @ Tue, 02 Aug 2022 10:14:08: 6000000 INFO @ Tue, 02 Aug 2022 10:14:14: 3000000 INFO @ Tue, 02 Aug 2022 10:14:16: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.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 @ Tue, 02 Aug 2022 10:14:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:14:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:14:21: 4000000 INFO @ Tue, 02 Aug 2022 10:14:24: 8000000 INFO @ Tue, 02 Aug 2022 10:14:28: 1000000 INFO @ Tue, 02 Aug 2022 10:14:29: 5000000 INFO @ Tue, 02 Aug 2022 10:14:32: 9000000 INFO @ Tue, 02 Aug 2022 10:14:37: 2000000 INFO @ Tue, 02 Aug 2022 10:14:37: 6000000 INFO @ Tue, 02 Aug 2022 10:14:40: 10000000 INFO @ Tue, 02 Aug 2022 10:14:45: 3000000 INFO @ Tue, 02 Aug 2022 10:14:45: 7000000 INFO @ Tue, 02 Aug 2022 10:14:48: 11000000 INFO @ Tue, 02 Aug 2022 10:14:53: 4000000 INFO @ Tue, 02 Aug 2022 10:14:53: 8000000 INFO @ Tue, 02 Aug 2022 10:14:57: 12000000 INFO @ Tue, 02 Aug 2022 10:15:01: 5000000 INFO @ Tue, 02 Aug 2022 10:15:01: 9000000 INFO @ Tue, 02 Aug 2022 10:15:05: 13000000 INFO @ Tue, 02 Aug 2022 10:15:06: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:15:06: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:15:06: #1 total tags in treatment: 13147157 INFO @ Tue, 02 Aug 2022 10:15:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:15:06: #1 tags after filtering in treatment: 13147157 INFO @ Tue, 02 Aug 2022 10:15:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:15:06: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:07: #2 number of paired peaks: 867 WARNING @ Tue, 02 Aug 2022 10:15:07: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:07: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:07: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:07: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:07: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:07: #2 predicted fragment length is 158 bps INFO @ Tue, 02 Aug 2022 10:15:07: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 02 Aug 2022 10:15:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.05_model.r INFO @ Tue, 02 Aug 2022 10:15:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:15:09: 10000000 INFO @ Tue, 02 Aug 2022 10:15:09: 6000000 INFO @ Tue, 02 Aug 2022 10:15:17: 11000000 INFO @ Tue, 02 Aug 2022 10:15:17: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:15:25: 12000000 INFO @ Tue, 02 Aug 2022 10:15:25: 8000000 INFO @ Tue, 02 Aug 2022 10:15:33: 13000000 INFO @ Tue, 02 Aug 2022 10:15:33: 9000000 INFO @ Tue, 02 Aug 2022 10:15:34: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:15:34: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:15:34: #1 total tags in treatment: 13147157 INFO @ Tue, 02 Aug 2022 10:15:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:15:34: #1 tags after filtering in treatment: 13147157 INFO @ Tue, 02 Aug 2022 10:15:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:15:34: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:35: #2 number of paired peaks: 867 WARNING @ Tue, 02 Aug 2022 10:15:35: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:35: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:35: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:35: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:35: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:35: #2 predicted fragment length is 158 bps INFO @ Tue, 02 Aug 2022 10:15:35: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 02 Aug 2022 10:15:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.10_model.r INFO @ Tue, 02 Aug 2022 10:15:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:15:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:15:41: 10000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:15:48: 11000000 INFO @ Tue, 02 Aug 2022 10:15:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:15:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:15:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.05_summits.bed INFO @ Tue, 02 Aug 2022 10:15:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2815 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:15:54: 12000000 INFO @ Tue, 02 Aug 2022 10:16:01: 13000000 INFO @ Tue, 02 Aug 2022 10:16:02: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:16:02: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:16:02: #1 total tags in treatment: 13147157 INFO @ Tue, 02 Aug 2022 10:16:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:16:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:16:02: #1 tags after filtering in treatment: 13147157 INFO @ Tue, 02 Aug 2022 10:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:16:02: #1 finished! INFO @ Tue, 02 Aug 2022 10:16:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:16:03: #2 number of paired peaks: 867 WARNING @ Tue, 02 Aug 2022 10:16:03: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Tue, 02 Aug 2022 10:16:03: start model_add_line... INFO @ Tue, 02 Aug 2022 10:16:03: start X-correlation... INFO @ Tue, 02 Aug 2022 10:16:03: end of X-cor INFO @ Tue, 02 Aug 2022 10:16:03: #2 finished! INFO @ Tue, 02 Aug 2022 10:16:03: #2 predicted fragment length is 158 bps INFO @ Tue, 02 Aug 2022 10:16:03: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 02 Aug 2022 10:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.20_model.r INFO @ Tue, 02 Aug 2022 10:16:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:16:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.10_summits.bed INFO @ Tue, 02 Aug 2022 10:16:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1798 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:16:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:16:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:16:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:16:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435524/SRX10435524.20_summits.bed INFO @ Tue, 02 Aug 2022 10:16:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1138 records, 4 fields): 15 millis CompletedMACS2peakCalling