Job ID = 14159483 SRX = SRX3180813 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: 00:03:35 15765933 reads; of these: 15765933 (100.00%) were unpaired; of these: 663667 (4.21%) aligned 0 times 12361844 (78.41%) aligned exactly 1 time 2740422 (17.38%) aligned >1 times 95.79% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 2723329 / 15102266 = 0.1803 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:14:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.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 @ Wed, 08 Dec 2021 22:14:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:14:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:14:34: 1000000 INFO @ Wed, 08 Dec 2021 22:14:40: 2000000 INFO @ Wed, 08 Dec 2021 22:14:46: 3000000 INFO @ Wed, 08 Dec 2021 22:14:52: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:14:58: 5000000 INFO @ Wed, 08 Dec 2021 22:14:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.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 @ Wed, 08 Dec 2021 22:14:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:14:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:15:04: 6000000 INFO @ Wed, 08 Dec 2021 22:15:05: 1000000 INFO @ Wed, 08 Dec 2021 22:15:10: 7000000 INFO @ Wed, 08 Dec 2021 22:15:12: 2000000 INFO @ Wed, 08 Dec 2021 22:15:16: 8000000 INFO @ Wed, 08 Dec 2021 22:15:18: 3000000 INFO @ Wed, 08 Dec 2021 22:15:23: 9000000 INFO @ Wed, 08 Dec 2021 22:15:25: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:15:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.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 @ Wed, 08 Dec 2021 22:15:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:15:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:15:29: 10000000 INFO @ Wed, 08 Dec 2021 22:15:32: 5000000 INFO @ Wed, 08 Dec 2021 22:15:35: 11000000 INFO @ Wed, 08 Dec 2021 22:15:35: 1000000 INFO @ Wed, 08 Dec 2021 22:15:39: 6000000 INFO @ Wed, 08 Dec 2021 22:15:41: 12000000 INFO @ Wed, 08 Dec 2021 22:15:42: 2000000 INFO @ Wed, 08 Dec 2021 22:15:43: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:15:43: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:15:43: #1 total tags in treatment: 12378937 INFO @ Wed, 08 Dec 2021 22:15:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:15:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:15:44: #1 tags after filtering in treatment: 12378937 INFO @ Wed, 08 Dec 2021 22:15:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:15:44: #1 finished! INFO @ Wed, 08 Dec 2021 22:15:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:15:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:15:44: #2 number of paired peaks: 406 WARNING @ Wed, 08 Dec 2021 22:15:44: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Wed, 08 Dec 2021 22:15:44: start model_add_line... INFO @ Wed, 08 Dec 2021 22:15:44: start X-correlation... INFO @ Wed, 08 Dec 2021 22:15:44: end of X-cor INFO @ Wed, 08 Dec 2021 22:15:44: #2 finished! INFO @ Wed, 08 Dec 2021 22:15:44: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:15:44: #2 alternative fragment length(s) may be 2,50,563 bps INFO @ Wed, 08 Dec 2021 22:15:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.05_model.r WARNING @ Wed, 08 Dec 2021 22:15:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:15:44: #2 You may need to consider one of the other alternative d(s): 2,50,563 WARNING @ Wed, 08 Dec 2021 22:15:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:15:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:15:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:15:45: 7000000 INFO @ Wed, 08 Dec 2021 22:15:49: 3000000 INFO @ Wed, 08 Dec 2021 22:15:52: 8000000 INFO @ Wed, 08 Dec 2021 22:15:55: 4000000 INFO @ Wed, 08 Dec 2021 22:15:58: 9000000 INFO @ Wed, 08 Dec 2021 22:16:02: 5000000 INFO @ Wed, 08 Dec 2021 22:16:04: 10000000 INFO @ Wed, 08 Dec 2021 22:16:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:16:08: 6000000 INFO @ Wed, 08 Dec 2021 22:16:11: 11000000 INFO @ Wed, 08 Dec 2021 22:16:14: 7000000 INFO @ Wed, 08 Dec 2021 22:16:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:16:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:16:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.05_summits.bed INFO @ Wed, 08 Dec 2021 22:16:17: Done! INFO @ Wed, 08 Dec 2021 22:16:17: 12000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (681 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:16:19: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:16:19: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:16:19: #1 total tags in treatment: 12378937 INFO @ Wed, 08 Dec 2021 22:16:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:16:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:16:20: #1 tags after filtering in treatment: 12378937 INFO @ Wed, 08 Dec 2021 22:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:16:20: #1 finished! INFO @ Wed, 08 Dec 2021 22:16:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:16:20: #2 number of paired peaks: 406 WARNING @ Wed, 08 Dec 2021 22:16:20: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Wed, 08 Dec 2021 22:16:20: start model_add_line... INFO @ Wed, 08 Dec 2021 22:16:20: start X-correlation... INFO @ Wed, 08 Dec 2021 22:16:20: end of X-cor INFO @ Wed, 08 Dec 2021 22:16:20: #2 finished! INFO @ Wed, 08 Dec 2021 22:16:20: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:16:20: #2 alternative fragment length(s) may be 2,50,563 bps INFO @ Wed, 08 Dec 2021 22:16:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.10_model.r WARNING @ Wed, 08 Dec 2021 22:16:20: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:16:20: #2 You may need to consider one of the other alternative d(s): 2,50,563 WARNING @ Wed, 08 Dec 2021 22:16:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:16:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:16:21: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:16:26: 9000000 INFO @ Wed, 08 Dec 2021 22:16:32: 10000000 INFO @ Wed, 08 Dec 2021 22:16:38: 11000000 INFO @ Wed, 08 Dec 2021 22:16:42: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:16:44: 12000000 INFO @ Wed, 08 Dec 2021 22:16:46: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:16:46: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:16:46: #1 total tags in treatment: 12378937 INFO @ Wed, 08 Dec 2021 22:16:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:16:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:16:46: #1 tags after filtering in treatment: 12378937 INFO @ Wed, 08 Dec 2021 22:16:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:16:46: #1 finished! INFO @ Wed, 08 Dec 2021 22:16:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:16:47: #2 number of paired peaks: 406 WARNING @ Wed, 08 Dec 2021 22:16:47: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Wed, 08 Dec 2021 22:16:47: start model_add_line... INFO @ Wed, 08 Dec 2021 22:16:47: start X-correlation... INFO @ Wed, 08 Dec 2021 22:16:47: end of X-cor INFO @ Wed, 08 Dec 2021 22:16:47: #2 finished! INFO @ Wed, 08 Dec 2021 22:16:47: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:16:47: #2 alternative fragment length(s) may be 2,50,563 bps INFO @ Wed, 08 Dec 2021 22:16:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.20_model.r WARNING @ Wed, 08 Dec 2021 22:16:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:16:47: #2 You may need to consider one of the other alternative d(s): 2,50,563 WARNING @ Wed, 08 Dec 2021 22:16:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:16:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:16:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:16:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:16:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:16:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.10_summits.bed INFO @ Wed, 08 Dec 2021 22:16:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (479 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:17:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:17:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:17:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:17:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180813/SRX3180813.20_summits.bed INFO @ Wed, 08 Dec 2021 22:17:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (205 records, 4 fields): 2 millis CompletedMACS2peakCalling