Job ID = 14159932 SRX = SRX3180771 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: 00:04:48 23002793 reads; of these: 23002793 (100.00%) were unpaired; of these: 2405523 (10.46%) aligned 0 times 17137616 (74.50%) aligned exactly 1 time 3459654 (15.04%) aligned >1 times 89.54% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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 12 files... [bam_rmdupse_core] 3856765 / 20597270 = 0.1872 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 @ Thu, 09 Dec 2021 00:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.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 @ Thu, 09 Dec 2021 00:46:11: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:46:11: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:46:16: 1000000 INFO @ Thu, 09 Dec 2021 00:46:21: 2000000 INFO @ Thu, 09 Dec 2021 00:46:25: 3000000 INFO @ Thu, 09 Dec 2021 00:46:30: 4000000 INFO @ Thu, 09 Dec 2021 00:46:35: 5000000 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 @ Thu, 09 Dec 2021 00:46:40: 6000000 INFO @ Thu, 09 Dec 2021 00:46:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.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 @ Thu, 09 Dec 2021 00:46:40: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:46:40: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:46:44: 7000000 INFO @ Thu, 09 Dec 2021 00:46:45: 1000000 INFO @ Thu, 09 Dec 2021 00:46:49: 8000000 INFO @ Thu, 09 Dec 2021 00:46:50: 2000000 INFO @ Thu, 09 Dec 2021 00:46:54: 9000000 INFO @ Thu, 09 Dec 2021 00:46:55: 3000000 INFO @ Thu, 09 Dec 2021 00:46:59: 10000000 INFO @ Thu, 09 Dec 2021 00:47:00: 4000000 INFO @ Thu, 09 Dec 2021 00:47:03: 11000000 INFO @ Thu, 09 Dec 2021 00:47:04: 5000000 INFO @ Thu, 09 Dec 2021 00:47:08: 12000000 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 @ Thu, 09 Dec 2021 00:47:09: 6000000 INFO @ Thu, 09 Dec 2021 00:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.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 @ Thu, 09 Dec 2021 00:47:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:47:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:47:13: 13000000 INFO @ Thu, 09 Dec 2021 00:47:14: 7000000 INFO @ Thu, 09 Dec 2021 00:47:16: 1000000 INFO @ Thu, 09 Dec 2021 00:47:18: 14000000 INFO @ Thu, 09 Dec 2021 00:47:19: 8000000 INFO @ Thu, 09 Dec 2021 00:47:22: 2000000 INFO @ Thu, 09 Dec 2021 00:47:23: 15000000 INFO @ Thu, 09 Dec 2021 00:47:24: 9000000 INFO @ Thu, 09 Dec 2021 00:47:28: 3000000 INFO @ Thu, 09 Dec 2021 00:47:28: 16000000 INFO @ Thu, 09 Dec 2021 00:47:29: 10000000 INFO @ Thu, 09 Dec 2021 00:47:31: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:47:31: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:47:31: #1 total tags in treatment: 16740505 INFO @ Thu, 09 Dec 2021 00:47:31: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:47:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:47:32: #1 tags after filtering in treatment: 16740505 INFO @ Thu, 09 Dec 2021 00:47:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:47:32: #1 finished! INFO @ Thu, 09 Dec 2021 00:47:32: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:47:33: #2 number of paired peaks: 309 WARNING @ Thu, 09 Dec 2021 00:47:33: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Thu, 09 Dec 2021 00:47:33: start model_add_line... INFO @ Thu, 09 Dec 2021 00:47:33: start X-correlation... INFO @ Thu, 09 Dec 2021 00:47:33: end of X-cor INFO @ Thu, 09 Dec 2021 00:47:33: #2 finished! INFO @ Thu, 09 Dec 2021 00:47:33: #2 predicted fragment length is 45 bps INFO @ Thu, 09 Dec 2021 00:47:33: #2 alternative fragment length(s) may be 1,45,573 bps INFO @ Thu, 09 Dec 2021 00:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.05_model.r WARNING @ Thu, 09 Dec 2021 00:47:33: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:47:33: #2 You may need to consider one of the other alternative d(s): 1,45,573 WARNING @ Thu, 09 Dec 2021 00:47:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:47:33: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:47:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:47:34: 4000000 INFO @ Thu, 09 Dec 2021 00:47:34: 11000000 INFO @ Thu, 09 Dec 2021 00:47:38: 12000000 INFO @ Thu, 09 Dec 2021 00:47:39: 5000000 INFO @ Thu, 09 Dec 2021 00:47:43: 13000000 INFO @ Thu, 09 Dec 2021 00:47:45: 6000000 INFO @ Thu, 09 Dec 2021 00:47:48: 14000000 INFO @ Thu, 09 Dec 2021 00:47:51: 7000000 INFO @ Thu, 09 Dec 2021 00:47:53: 15000000 INFO @ Thu, 09 Dec 2021 00:47:57: 8000000 INFO @ Thu, 09 Dec 2021 00:47:58: 16000000 INFO @ Thu, 09 Dec 2021 00:48:00: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:48:01: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:48:01: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:48:01: #1 total tags in treatment: 16740505 INFO @ Thu, 09 Dec 2021 00:48:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:48:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:48:02: #1 tags after filtering in treatment: 16740505 INFO @ Thu, 09 Dec 2021 00:48:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:48:02: #1 finished! INFO @ Thu, 09 Dec 2021 00:48:02: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:48:02: 9000000 INFO @ Thu, 09 Dec 2021 00:48:03: #2 number of paired peaks: 309 WARNING @ Thu, 09 Dec 2021 00:48:03: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Thu, 09 Dec 2021 00:48:03: start model_add_line... INFO @ Thu, 09 Dec 2021 00:48:03: start X-correlation... INFO @ Thu, 09 Dec 2021 00:48:03: end of X-cor INFO @ Thu, 09 Dec 2021 00:48:03: #2 finished! INFO @ Thu, 09 Dec 2021 00:48:03: #2 predicted fragment length is 45 bps INFO @ Thu, 09 Dec 2021 00:48:03: #2 alternative fragment length(s) may be 1,45,573 bps INFO @ Thu, 09 Dec 2021 00:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.10_model.r WARNING @ Thu, 09 Dec 2021 00:48:03: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:48:03: #2 You may need to consider one of the other alternative d(s): 1,45,573 WARNING @ Thu, 09 Dec 2021 00:48:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:48:03: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:48:08: 10000000 INFO @ Thu, 09 Dec 2021 00:48:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:48:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:48:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.05_summits.bed INFO @ Thu, 09 Dec 2021 00:48:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (742 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:48:14: 11000000 INFO @ Thu, 09 Dec 2021 00:48:19: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:48:25: 13000000 INFO @ Thu, 09 Dec 2021 00:48:30: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:48:31: 14000000 INFO @ Thu, 09 Dec 2021 00:48:36: 15000000 INFO @ Thu, 09 Dec 2021 00:48:42: 16000000 INFO @ Thu, 09 Dec 2021 00:48:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:48:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:48:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.10_summits.bed INFO @ Thu, 09 Dec 2021 00:48:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (490 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:48:46: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:48:46: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:48:46: #1 total tags in treatment: 16740505 INFO @ Thu, 09 Dec 2021 00:48:46: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:48:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:48:46: #1 tags after filtering in treatment: 16740505 INFO @ Thu, 09 Dec 2021 00:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:48:46: #1 finished! INFO @ Thu, 09 Dec 2021 00:48:46: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:48:47: #2 number of paired peaks: 309 WARNING @ Thu, 09 Dec 2021 00:48:47: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Thu, 09 Dec 2021 00:48:47: start model_add_line... INFO @ Thu, 09 Dec 2021 00:48:47: start X-correlation... INFO @ Thu, 09 Dec 2021 00:48:47: end of X-cor INFO @ Thu, 09 Dec 2021 00:48:47: #2 finished! INFO @ Thu, 09 Dec 2021 00:48:47: #2 predicted fragment length is 45 bps INFO @ Thu, 09 Dec 2021 00:48:47: #2 alternative fragment length(s) may be 1,45,573 bps INFO @ Thu, 09 Dec 2021 00:48:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.20_model.r WARNING @ Thu, 09 Dec 2021 00:48:47: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:48:47: #2 You may need to consider one of the other alternative d(s): 1,45,573 WARNING @ Thu, 09 Dec 2021 00:48:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:48:47: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:48:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:49:15: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180771/SRX3180771.20_summits.bed INFO @ Thu, 09 Dec 2021 00:49:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 millis CompletedMACS2peakCalling