Job ID = 16433719 SRX = SRX15407778 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: 00:06:43 20407605 reads; of these: 20407605 (100.00%) were unpaired; of these: 3168337 (15.53%) aligned 0 times 14780213 (72.43%) aligned exactly 1 time 2459055 (12.05%) aligned >1 times 84.47% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 2939303 / 17239268 = 0.1705 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 09:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.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 09:54:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:54:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:54:50: 1000000 INFO @ Tue, 02 Aug 2022 09:54:56: 2000000 INFO @ Tue, 02 Aug 2022 09:55:01: 3000000 INFO @ Tue, 02 Aug 2022 09:55:07: 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 09:55:12: 5000000 INFO @ Tue, 02 Aug 2022 09:55:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.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 09:55:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:55:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:55:18: 6000000 INFO @ Tue, 02 Aug 2022 09:55:20: 1000000 INFO @ Tue, 02 Aug 2022 09:55:24: 7000000 INFO @ Tue, 02 Aug 2022 09:55:27: 2000000 INFO @ Tue, 02 Aug 2022 09:55:29: 8000000 INFO @ Tue, 02 Aug 2022 09:55:33: 3000000 INFO @ Tue, 02 Aug 2022 09:55:35: 9000000 INFO @ Tue, 02 Aug 2022 09:55:40: 4000000 INFO @ Tue, 02 Aug 2022 09:55:41: 10000000 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 09:55:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.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 09:55:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:55:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:55:46: 11000000 INFO @ Tue, 02 Aug 2022 09:55:47: 5000000 INFO @ Tue, 02 Aug 2022 09:55:50: 1000000 INFO @ Tue, 02 Aug 2022 09:55:52: 12000000 INFO @ Tue, 02 Aug 2022 09:55:53: 6000000 INFO @ Tue, 02 Aug 2022 09:55:56: 2000000 INFO @ Tue, 02 Aug 2022 09:55:58: 13000000 INFO @ Tue, 02 Aug 2022 09:56:00: 7000000 INFO @ Tue, 02 Aug 2022 09:56:02: 3000000 INFO @ Tue, 02 Aug 2022 09:56:03: 14000000 INFO @ Tue, 02 Aug 2022 09:56:05: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:56:05: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:56:05: #1 total tags in treatment: 14299965 INFO @ Tue, 02 Aug 2022 09:56:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:56:05: #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 09:56:05: #1 tags after filtering in treatment: 14299965 INFO @ Tue, 02 Aug 2022 09:56:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:56:05: #1 finished! INFO @ Tue, 02 Aug 2022 09:56:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:56:06: #2 number of paired peaks: 696 WARNING @ Tue, 02 Aug 2022 09:56:06: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Tue, 02 Aug 2022 09:56:06: start model_add_line... INFO @ Tue, 02 Aug 2022 09:56:06: start X-correlation... INFO @ Tue, 02 Aug 2022 09:56:06: end of X-cor INFO @ Tue, 02 Aug 2022 09:56:06: #2 finished! INFO @ Tue, 02 Aug 2022 09:56:06: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 09:56:06: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 02 Aug 2022 09:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.05_model.r INFO @ Tue, 02 Aug 2022 09:56:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:56:07: 8000000 INFO @ Tue, 02 Aug 2022 09:56:07: 4000000 INFO @ Tue, 02 Aug 2022 09:56:13: 9000000 INFO @ Tue, 02 Aug 2022 09:56:13: 5000000 INFO @ Tue, 02 Aug 2022 09:56:19: 6000000 INFO @ Tue, 02 Aug 2022 09:56:20: 10000000 INFO @ Tue, 02 Aug 2022 09:56:25: 7000000 INFO @ Tue, 02 Aug 2022 09:56:26: 11000000 INFO @ Tue, 02 Aug 2022 09:56:30: 8000000 INFO @ Tue, 02 Aug 2022 09:56:33: 12000000 INFO @ Tue, 02 Aug 2022 09:56:36: 9000000 INFO @ Tue, 02 Aug 2022 09:56:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:56:39: 13000000 INFO @ Tue, 02 Aug 2022 09:56:42: 10000000 INFO @ Tue, 02 Aug 2022 09:56:46: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:56:47: 11000000 INFO @ Tue, 02 Aug 2022 09:56:48: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:56:48: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:56:48: #1 total tags in treatment: 14299965 INFO @ Tue, 02 Aug 2022 09:56:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:56:48: #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 09:56:48: #1 tags after filtering in treatment: 14299965 INFO @ Tue, 02 Aug 2022 09:56:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:56:48: #1 finished! INFO @ Tue, 02 Aug 2022 09:56:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:56:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:56:49: #2 number of paired peaks: 696 WARNING @ Tue, 02 Aug 2022 09:56:49: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Tue, 02 Aug 2022 09:56:49: start model_add_line... INFO @ Tue, 02 Aug 2022 09:56:49: start X-correlation... INFO @ Tue, 02 Aug 2022 09:56:49: end of X-cor INFO @ Tue, 02 Aug 2022 09:56:49: #2 finished! INFO @ Tue, 02 Aug 2022 09:56:49: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 09:56:49: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 02 Aug 2022 09:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.10_model.r INFO @ Tue, 02 Aug 2022 09:56:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:56:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:56:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:56:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.05_summits.bed INFO @ Tue, 02 Aug 2022 09:56:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2491 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:56:53: 12000000 INFO @ Tue, 02 Aug 2022 09:56:58: 13000000 INFO @ Tue, 02 Aug 2022 09:57:03: 14000000 INFO @ Tue, 02 Aug 2022 09:57:05: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:57:05: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:57:05: #1 total tags in treatment: 14299965 INFO @ Tue, 02 Aug 2022 09:57:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:57:05: #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 09:57:05: #1 tags after filtering in treatment: 14299965 INFO @ Tue, 02 Aug 2022 09:57:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:57:05: #1 finished! INFO @ Tue, 02 Aug 2022 09:57:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:57:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:57:06: #2 number of paired peaks: 696 WARNING @ Tue, 02 Aug 2022 09:57:06: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Tue, 02 Aug 2022 09:57:06: start model_add_line... INFO @ Tue, 02 Aug 2022 09:57:06: start X-correlation... INFO @ Tue, 02 Aug 2022 09:57:06: end of X-cor INFO @ Tue, 02 Aug 2022 09:57:06: #2 finished! INFO @ Tue, 02 Aug 2022 09:57:06: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 09:57:06: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 02 Aug 2022 09:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.20_model.r INFO @ Tue, 02 Aug 2022 09:57:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:57:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:57:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:57:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:57:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:57:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.10_summits.bed INFO @ Tue, 02 Aug 2022 09:57:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1623 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:57:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:57:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:57:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:57:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407778/SRX15407778.20_summits.bed INFO @ Tue, 02 Aug 2022 09:57:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1033 records, 4 fields): 25 millis CompletedMACS2peakCalling