Job ID = 16433753 SRX = SRX15407777 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: 00:06:00 20540584 reads; of these: 20540584 (100.00%) were unpaired; of these: 2495498 (12.15%) aligned 0 times 15460967 (75.27%) aligned exactly 1 time 2584119 (12.58%) aligned >1 times 87.85% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 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] 3330665 / 18045086 = 0.1846 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 09:54:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.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 09:54:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:54:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:54:57: 1000000 INFO @ Tue, 02 Aug 2022 09:55:03: 2000000 INFO @ Tue, 02 Aug 2022 09:55:10: 3000000 INFO @ Tue, 02 Aug 2022 09:55:16: 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 09:55:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.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 09:55:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:55:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:55:22: 5000000 INFO @ Tue, 02 Aug 2022 09:55:27: 1000000 INFO @ Tue, 02 Aug 2022 09:55:29: 6000000 INFO @ Tue, 02 Aug 2022 09:55:33: 2000000 INFO @ Tue, 02 Aug 2022 09:55:36: 7000000 INFO @ Tue, 02 Aug 2022 09:55:39: 3000000 INFO @ Tue, 02 Aug 2022 09:55:42: 8000000 INFO @ Tue, 02 Aug 2022 09:55:45: 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 09:55:49: 9000000 INFO @ Tue, 02 Aug 2022 09:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.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 09:55:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:55:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:55:51: 5000000 INFO @ Tue, 02 Aug 2022 09:55:56: 10000000 INFO @ Tue, 02 Aug 2022 09:55:57: 1000000 INFO @ Tue, 02 Aug 2022 09:55:57: 6000000 INFO @ Tue, 02 Aug 2022 09:56:03: 11000000 INFO @ Tue, 02 Aug 2022 09:56:03: 2000000 INFO @ Tue, 02 Aug 2022 09:56:03: 7000000 INFO @ Tue, 02 Aug 2022 09:56:09: 3000000 INFO @ Tue, 02 Aug 2022 09:56:09: 12000000 INFO @ Tue, 02 Aug 2022 09:56:10: 8000000 INFO @ Tue, 02 Aug 2022 09:56:15: 4000000 INFO @ Tue, 02 Aug 2022 09:56:16: 9000000 INFO @ Tue, 02 Aug 2022 09:56:16: 13000000 INFO @ Tue, 02 Aug 2022 09:56:22: 5000000 INFO @ Tue, 02 Aug 2022 09:56:22: 10000000 INFO @ Tue, 02 Aug 2022 09:56:23: 14000000 INFO @ Tue, 02 Aug 2022 09:56:28: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:56:28: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:56:28: #1 total tags in treatment: 14714421 INFO @ Tue, 02 Aug 2022 09:56:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:56:28: #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 09:56:28: 6000000 INFO @ Tue, 02 Aug 2022 09:56:28: 11000000 INFO @ Tue, 02 Aug 2022 09:56:28: #1 tags after filtering in treatment: 14714421 INFO @ Tue, 02 Aug 2022 09:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:56:28: #1 finished! INFO @ Tue, 02 Aug 2022 09:56:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:56:29: #2 number of paired peaks: 576 WARNING @ Tue, 02 Aug 2022 09:56:29: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Tue, 02 Aug 2022 09:56:29: start model_add_line... INFO @ Tue, 02 Aug 2022 09:56:29: start X-correlation... INFO @ Tue, 02 Aug 2022 09:56:29: end of X-cor INFO @ Tue, 02 Aug 2022 09:56:29: #2 finished! INFO @ Tue, 02 Aug 2022 09:56:29: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 09:56:29: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 02 Aug 2022 09:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.05_model.r INFO @ Tue, 02 Aug 2022 09:56:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:56:34: 12000000 INFO @ Tue, 02 Aug 2022 09:56:34: 7000000 INFO @ Tue, 02 Aug 2022 09:56:40: 13000000 INFO @ Tue, 02 Aug 2022 09:56:40: 8000000 INFO @ Tue, 02 Aug 2022 09:56:46: 14000000 INFO @ Tue, 02 Aug 2022 09:56:46: 9000000 INFO @ Tue, 02 Aug 2022 09:56:51: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:56:51: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:56:51: #1 total tags in treatment: 14714421 INFO @ Tue, 02 Aug 2022 09:56:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:56:51: #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 09:56:51: #1 tags after filtering in treatment: 14714421 INFO @ Tue, 02 Aug 2022 09:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:56:51: #1 finished! INFO @ Tue, 02 Aug 2022 09:56:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:56:52: #2 number of paired peaks: 576 WARNING @ Tue, 02 Aug 2022 09:56:52: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Tue, 02 Aug 2022 09:56:52: start model_add_line... INFO @ Tue, 02 Aug 2022 09:56:52: start X-correlation... INFO @ Tue, 02 Aug 2022 09:56:52: end of X-cor INFO @ Tue, 02 Aug 2022 09:56:52: #2 finished! INFO @ Tue, 02 Aug 2022 09:56:52: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 09:56:52: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 02 Aug 2022 09:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.10_model.r INFO @ Tue, 02 Aug 2022 09:56:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:56:53: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:56:58: 11000000 INFO @ Tue, 02 Aug 2022 09:57:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:57:04: 12000000 INFO @ Tue, 02 Aug 2022 09:57:09: 13000000 INFO @ Tue, 02 Aug 2022 09:57:15: 14000000 INFO @ Tue, 02 Aug 2022 09:57:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:57:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:57:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.05_summits.bed INFO @ Tue, 02 Aug 2022 09:57:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1979 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:57:19: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:57:19: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:57:19: #1 total tags in treatment: 14714421 INFO @ Tue, 02 Aug 2022 09:57:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:57:19: #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 09:57:19: #1 tags after filtering in treatment: 14714421 INFO @ Tue, 02 Aug 2022 09:57:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:57:19: #1 finished! INFO @ Tue, 02 Aug 2022 09:57:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:57:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:57:20: #2 number of paired peaks: 576 WARNING @ Tue, 02 Aug 2022 09:57:20: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Tue, 02 Aug 2022 09:57:20: start model_add_line... INFO @ Tue, 02 Aug 2022 09:57:20: start X-correlation... INFO @ Tue, 02 Aug 2022 09:57:20: end of X-cor INFO @ Tue, 02 Aug 2022 09:57:20: #2 finished! INFO @ Tue, 02 Aug 2022 09:57:20: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 09:57:20: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 02 Aug 2022 09:57:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.20_model.r INFO @ Tue, 02 Aug 2022 09:57:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:57:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:57:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:57:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:57:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.10_summits.bed INFO @ Tue, 02 Aug 2022 09:57:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1337 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:57:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:58:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:58:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:58:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407777/SRX15407777.20_summits.bed INFO @ Tue, 02 Aug 2022 09:58:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (880 records, 4 fields): 35 millis CompletedMACS2peakCalling