Job ID = 16433604 SRX = SRX15407779 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: 00:05:56 19314090 reads; of these: 19314090 (100.00%) were unpaired; of these: 2732016 (14.15%) aligned 0 times 14375761 (74.43%) aligned exactly 1 time 2206313 (11.42%) aligned >1 times 85.85% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 3386064 / 16582074 = 0.2042 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 09:53:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.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 09:53:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:53:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:53:53: 1000000 INFO @ Tue, 02 Aug 2022 09:54:01: 2000000 INFO @ Tue, 02 Aug 2022 09:54:09: 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 09:54:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.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 09:54:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:54:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:54:18: 4000000 INFO @ Tue, 02 Aug 2022 09:54:22: 1000000 INFO @ Tue, 02 Aug 2022 09:54:26: 5000000 INFO @ Tue, 02 Aug 2022 09:54:29: 2000000 INFO @ Tue, 02 Aug 2022 09:54:35: 6000000 INFO @ Tue, 02 Aug 2022 09:54:36: 3000000 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 09:54:43: 7000000 INFO @ Tue, 02 Aug 2022 09:54:43: 4000000 INFO @ Tue, 02 Aug 2022 09:54:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.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 09:54:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:54:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:54:50: 5000000 INFO @ Tue, 02 Aug 2022 09:54:51: 8000000 INFO @ Tue, 02 Aug 2022 09:54:53: 1000000 INFO @ Tue, 02 Aug 2022 09:54:57: 6000000 INFO @ Tue, 02 Aug 2022 09:55:00: 9000000 INFO @ Tue, 02 Aug 2022 09:55:02: 2000000 INFO @ Tue, 02 Aug 2022 09:55:04: 7000000 INFO @ Tue, 02 Aug 2022 09:55:08: 10000000 INFO @ Tue, 02 Aug 2022 09:55:11: 3000000 INFO @ Tue, 02 Aug 2022 09:55:11: 8000000 INFO @ Tue, 02 Aug 2022 09:55:17: 11000000 INFO @ Tue, 02 Aug 2022 09:55:18: 9000000 INFO @ Tue, 02 Aug 2022 09:55:19: 4000000 INFO @ Tue, 02 Aug 2022 09:55:25: 10000000 INFO @ Tue, 02 Aug 2022 09:55:25: 12000000 INFO @ Tue, 02 Aug 2022 09:55:27: 5000000 INFO @ Tue, 02 Aug 2022 09:55:32: 11000000 INFO @ Tue, 02 Aug 2022 09:55:33: 13000000 INFO @ Tue, 02 Aug 2022 09:55:35: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:55:35: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:55:35: #1 total tags in treatment: 13196010 INFO @ Tue, 02 Aug 2022 09:55:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:55:35: #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 09:55:35: #1 tags after filtering in treatment: 13196010 INFO @ Tue, 02 Aug 2022 09:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:55:35: #1 finished! INFO @ Tue, 02 Aug 2022 09:55:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:55:36: 6000000 INFO @ Tue, 02 Aug 2022 09:55:36: #2 number of paired peaks: 628 WARNING @ Tue, 02 Aug 2022 09:55:36: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Tue, 02 Aug 2022 09:55:36: start model_add_line... INFO @ Tue, 02 Aug 2022 09:55:36: start X-correlation... INFO @ Tue, 02 Aug 2022 09:55:36: end of X-cor INFO @ Tue, 02 Aug 2022 09:55:36: #2 finished! INFO @ Tue, 02 Aug 2022 09:55:36: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 09:55:36: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 09:55:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.05_model.r INFO @ Tue, 02 Aug 2022 09:55:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:55:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:55:38: 12000000 INFO @ Tue, 02 Aug 2022 09:55:44: 7000000 INFO @ Tue, 02 Aug 2022 09:55:45: 13000000 INFO @ Tue, 02 Aug 2022 09:55:46: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:55:46: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:55:46: #1 total tags in treatment: 13196010 INFO @ Tue, 02 Aug 2022 09:55:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:55:46: #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 09:55:46: #1 tags after filtering in treatment: 13196010 INFO @ Tue, 02 Aug 2022 09:55:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:55:46: #1 finished! INFO @ Tue, 02 Aug 2022 09:55:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:55:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:55:47: #2 number of paired peaks: 628 WARNING @ Tue, 02 Aug 2022 09:55:47: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Tue, 02 Aug 2022 09:55:47: start model_add_line... INFO @ Tue, 02 Aug 2022 09:55:47: start X-correlation... INFO @ Tue, 02 Aug 2022 09:55:47: end of X-cor INFO @ Tue, 02 Aug 2022 09:55:47: #2 finished! INFO @ Tue, 02 Aug 2022 09:55:47: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 09:55:47: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 09:55:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.10_model.r INFO @ Tue, 02 Aug 2022 09:55:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:55:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:55:52: 8000000 INFO @ Tue, 02 Aug 2022 09:56:00: 9000000 INFO @ Tue, 02 Aug 2022 09:56:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:56:08: 10000000 INFO @ Tue, 02 Aug 2022 09:56:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:56:16: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.05_summits.bed INFO @ Tue, 02 Aug 2022 09:56:18: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6638 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:56:24: 12000000 INFO @ Tue, 02 Aug 2022 09:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.10_summits.bed INFO @ Tue, 02 Aug 2022 09:56:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4533 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:56:32: 13000000 INFO @ Tue, 02 Aug 2022 09:56:34: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:56:34: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:56:34: #1 total tags in treatment: 13196010 INFO @ Tue, 02 Aug 2022 09:56:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:56:34: #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 09:56:34: #1 tags after filtering in treatment: 13196010 INFO @ Tue, 02 Aug 2022 09:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:56:34: #1 finished! INFO @ Tue, 02 Aug 2022 09:56:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:56:35: #2 number of paired peaks: 628 WARNING @ Tue, 02 Aug 2022 09:56:35: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Tue, 02 Aug 2022 09:56:35: start model_add_line... INFO @ Tue, 02 Aug 2022 09:56:35: start X-correlation... INFO @ Tue, 02 Aug 2022 09:56:35: end of X-cor INFO @ Tue, 02 Aug 2022 09:56:35: #2 finished! INFO @ Tue, 02 Aug 2022 09:56:35: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 09:56:35: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 09:56:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.20_model.r INFO @ Tue, 02 Aug 2022 09:56:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:56:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:57:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:57:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:57:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:57:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407779/SRX15407779.20_summits.bed INFO @ Tue, 02 Aug 2022 09:57:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2609 records, 4 fields): 21 millis CompletedMACS2peakCalling