Job ID = 16436126 SRX = SRX13110348 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:47 15860083 reads; of these: 15860083 (100.00%) were unpaired; of these: 256535 (1.62%) aligned 0 times 13420704 (84.62%) aligned exactly 1 time 2182844 (13.76%) aligned >1 times 98.38% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 2505021 / 15603548 = 0.1605 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 11:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.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 11:04:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:04:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:04:59: 1000000 INFO @ Tue, 02 Aug 2022 11:05:05: 2000000 INFO @ Tue, 02 Aug 2022 11:05:11: 3000000 INFO @ Tue, 02 Aug 2022 11:05:18: 4000000 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 11:05:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.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 11:05:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:05:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:05:24: 5000000 INFO @ Tue, 02 Aug 2022 11:05:28: 1000000 INFO @ Tue, 02 Aug 2022 11:05:31: 6000000 INFO @ Tue, 02 Aug 2022 11:05:34: 2000000 INFO @ Tue, 02 Aug 2022 11:05:38: 7000000 INFO @ Tue, 02 Aug 2022 11:05:40: 3000000 INFO @ Tue, 02 Aug 2022 11:05:45: 8000000 INFO @ Tue, 02 Aug 2022 11:05:46: 4000000 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 11:05:51: 9000000 INFO @ Tue, 02 Aug 2022 11:05:51: 5000000 INFO @ Tue, 02 Aug 2022 11:05:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.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 11:05:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:05:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:05:57: 6000000 INFO @ Tue, 02 Aug 2022 11:05:58: 10000000 INFO @ Tue, 02 Aug 2022 11:05:59: 1000000 INFO @ Tue, 02 Aug 2022 11:06:03: 7000000 INFO @ Tue, 02 Aug 2022 11:06:04: 11000000 INFO @ Tue, 02 Aug 2022 11:06:06: 2000000 INFO @ Tue, 02 Aug 2022 11:06:09: 8000000 INFO @ Tue, 02 Aug 2022 11:06:11: 12000000 INFO @ Tue, 02 Aug 2022 11:06:13: 3000000 INFO @ Tue, 02 Aug 2022 11:06:15: 9000000 INFO @ Tue, 02 Aug 2022 11:06:18: 13000000 INFO @ Tue, 02 Aug 2022 11:06:19: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:06:19: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:06:19: #1 total tags in treatment: 13098527 INFO @ Tue, 02 Aug 2022 11:06:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:06:19: #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 11:06:19: #1 tags after filtering in treatment: 13098527 INFO @ Tue, 02 Aug 2022 11:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:06:19: #1 finished! INFO @ Tue, 02 Aug 2022 11:06:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:06:19: 4000000 INFO @ Tue, 02 Aug 2022 11:06:20: #2 number of paired peaks: 852 WARNING @ Tue, 02 Aug 2022 11:06:20: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Tue, 02 Aug 2022 11:06:20: start model_add_line... INFO @ Tue, 02 Aug 2022 11:06:20: start X-correlation... INFO @ Tue, 02 Aug 2022 11:06:20: end of X-cor INFO @ Tue, 02 Aug 2022 11:06:20: #2 finished! INFO @ Tue, 02 Aug 2022 11:06:20: #2 predicted fragment length is 196 bps INFO @ Tue, 02 Aug 2022 11:06:20: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 02 Aug 2022 11:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.05_model.r INFO @ Tue, 02 Aug 2022 11:06:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:06:21: 10000000 INFO @ Tue, 02 Aug 2022 11:06:26: 5000000 INFO @ Tue, 02 Aug 2022 11:06:26: 11000000 INFO @ Tue, 02 Aug 2022 11:06:32: 12000000 INFO @ Tue, 02 Aug 2022 11:06:32: 6000000 INFO @ Tue, 02 Aug 2022 11:06:38: 13000000 INFO @ Tue, 02 Aug 2022 11:06:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:06:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:06:39: #1 total tags in treatment: 13098527 INFO @ Tue, 02 Aug 2022 11:06:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:06:39: #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 11:06:39: #1 tags after filtering in treatment: 13098527 INFO @ Tue, 02 Aug 2022 11:06:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:06:39: #1 finished! INFO @ Tue, 02 Aug 2022 11:06:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:06:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:06:39: 7000000 INFO @ Tue, 02 Aug 2022 11:06:40: #2 number of paired peaks: 852 WARNING @ Tue, 02 Aug 2022 11:06:40: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Tue, 02 Aug 2022 11:06:40: start model_add_line... INFO @ Tue, 02 Aug 2022 11:06:40: start X-correlation... INFO @ Tue, 02 Aug 2022 11:06:40: end of X-cor INFO @ Tue, 02 Aug 2022 11:06:40: #2 finished! INFO @ Tue, 02 Aug 2022 11:06:40: #2 predicted fragment length is 196 bps INFO @ Tue, 02 Aug 2022 11:06:40: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 02 Aug 2022 11:06:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.10_model.r INFO @ Tue, 02 Aug 2022 11:06:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:06:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:06:45: 8000000 INFO @ Tue, 02 Aug 2022 11:06:49: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:06:52: 9000000 INFO @ Tue, 02 Aug 2022 11:06:58: 10000000 INFO @ Tue, 02 Aug 2022 11:07:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:07:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:07:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.05_summits.bed INFO @ Tue, 02 Aug 2022 11:07:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9373 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:07:04: 11000000 INFO @ Tue, 02 Aug 2022 11:07:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:07:10: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:07:17: 13000000 INFO @ Tue, 02 Aug 2022 11:07:17: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:07:17: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:07:17: #1 total tags in treatment: 13098527 INFO @ Tue, 02 Aug 2022 11:07:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:07:17: #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 11:07:18: #1 tags after filtering in treatment: 13098527 INFO @ Tue, 02 Aug 2022 11:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:07:18: #1 finished! INFO @ Tue, 02 Aug 2022 11:07:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:07:19: #2 number of paired peaks: 852 WARNING @ Tue, 02 Aug 2022 11:07:19: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Tue, 02 Aug 2022 11:07:19: start model_add_line... INFO @ Tue, 02 Aug 2022 11:07:19: start X-correlation... INFO @ Tue, 02 Aug 2022 11:07:19: end of X-cor INFO @ Tue, 02 Aug 2022 11:07:19: #2 finished! INFO @ Tue, 02 Aug 2022 11:07:19: #2 predicted fragment length is 196 bps INFO @ Tue, 02 Aug 2022 11:07:19: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 02 Aug 2022 11:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.20_model.r INFO @ Tue, 02 Aug 2022 11:07:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:07:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:07:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:07:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.10_summits.bed INFO @ Tue, 02 Aug 2022 11:07:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6594 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:07:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:08:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:08:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:08:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110348/SRX13110348.20_summits.bed INFO @ Tue, 02 Aug 2022 11:08:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3890 records, 4 fields): 21 millis CompletedMACS2peakCalling