Job ID = 14159441 SRX = SRX3180801 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: 00:03:23 16071294 reads; of these: 16071294 (100.00%) were unpaired; of these: 2126944 (13.23%) aligned 0 times 11122945 (69.21%) aligned exactly 1 time 2821405 (17.56%) aligned >1 times 86.77% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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] 4343607 / 13944350 = 0.3115 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 21:59:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.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 21:59:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:59:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:59:53: 1000000 INFO @ Wed, 08 Dec 2021 21:59:59: 2000000 INFO @ Wed, 08 Dec 2021 22:00:05: 3000000 INFO @ Wed, 08 Dec 2021 22:00:10: 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 22:00:16: 5000000 INFO @ Wed, 08 Dec 2021 22:00:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.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 22:00:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:00:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:00:21: 6000000 INFO @ Wed, 08 Dec 2021 22:00:23: 1000000 INFO @ Wed, 08 Dec 2021 22:00:27: 7000000 INFO @ Wed, 08 Dec 2021 22:00:29: 2000000 INFO @ Wed, 08 Dec 2021 22:00:33: 8000000 INFO @ Wed, 08 Dec 2021 22:00:35: 3000000 INFO @ Wed, 08 Dec 2021 22:00:39: 9000000 INFO @ Wed, 08 Dec 2021 22:00:41: 4000000 INFO @ Wed, 08 Dec 2021 22:00:42: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:00:42: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:00:42: #1 total tags in treatment: 9600743 INFO @ Wed, 08 Dec 2021 22:00:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:00:42: #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 22:00:43: #1 tags after filtering in treatment: 9600743 INFO @ Wed, 08 Dec 2021 22:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:00:43: #1 finished! INFO @ Wed, 08 Dec 2021 22:00:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:00:43: #2 number of paired peaks: 509 WARNING @ Wed, 08 Dec 2021 22:00:43: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Wed, 08 Dec 2021 22:00:43: start model_add_line... INFO @ Wed, 08 Dec 2021 22:00:43: start X-correlation... INFO @ Wed, 08 Dec 2021 22:00:43: end of X-cor INFO @ Wed, 08 Dec 2021 22:00:43: #2 finished! INFO @ Wed, 08 Dec 2021 22:00:43: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:00:43: #2 alternative fragment length(s) may be 2,50,553 bps INFO @ Wed, 08 Dec 2021 22:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.05_model.r WARNING @ Wed, 08 Dec 2021 22:00:43: #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 22:00:43: #2 You may need to consider one of the other alternative d(s): 2,50,553 WARNING @ Wed, 08 Dec 2021 22:00:43: #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 22:00:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:00:43: #3 Pre-compute pvalue-qvalue table... 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 22:00:46: 5000000 INFO @ Wed, 08 Dec 2021 22:00:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.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 22:00:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:00:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:00:52: 6000000 INFO @ Wed, 08 Dec 2021 22:00:54: 1000000 INFO @ Wed, 08 Dec 2021 22:00:58: 7000000 INFO @ Wed, 08 Dec 2021 22:01:00: 2000000 INFO @ Wed, 08 Dec 2021 22:01:01: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:01:04: 8000000 INFO @ Wed, 08 Dec 2021 22:01:07: 3000000 INFO @ Wed, 08 Dec 2021 22:01:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:01:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:01:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.05_summits.bed INFO @ Wed, 08 Dec 2021 22:01:10: Done! INFO @ Wed, 08 Dec 2021 22:01:10: 9000000 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (631 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:01:14: 4000000 INFO @ Wed, 08 Dec 2021 22:01:14: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:01:14: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:01:14: #1 total tags in treatment: 9600743 INFO @ Wed, 08 Dec 2021 22:01:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:01:14: #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 22:01:14: #1 tags after filtering in treatment: 9600743 INFO @ Wed, 08 Dec 2021 22:01:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:01:14: #1 finished! INFO @ Wed, 08 Dec 2021 22:01:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:01:15: #2 number of paired peaks: 509 WARNING @ Wed, 08 Dec 2021 22:01:15: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Wed, 08 Dec 2021 22:01:15: start model_add_line... INFO @ Wed, 08 Dec 2021 22:01:15: start X-correlation... INFO @ Wed, 08 Dec 2021 22:01:15: end of X-cor INFO @ Wed, 08 Dec 2021 22:01:15: #2 finished! INFO @ Wed, 08 Dec 2021 22:01:15: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:01:15: #2 alternative fragment length(s) may be 2,50,553 bps INFO @ Wed, 08 Dec 2021 22:01:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.10_model.r WARNING @ Wed, 08 Dec 2021 22:01:15: #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 22:01:15: #2 You may need to consider one of the other alternative d(s): 2,50,553 WARNING @ Wed, 08 Dec 2021 22:01:15: #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 22:01:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:01:20: 5000000 INFO @ Wed, 08 Dec 2021 22:01:26: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:01:32: 7000000 INFO @ Wed, 08 Dec 2021 22:01:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:01:39: 8000000 INFO @ Wed, 08 Dec 2021 22:01:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:01:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:01:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.10_summits.bed INFO @ Wed, 08 Dec 2021 22:01:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:01:45: 9000000 INFO @ Wed, 08 Dec 2021 22:01:48: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:01:48: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:01:48: #1 total tags in treatment: 9600743 INFO @ Wed, 08 Dec 2021 22:01:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:01:48: #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 22:01:49: #1 tags after filtering in treatment: 9600743 INFO @ Wed, 08 Dec 2021 22:01:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:01:49: #1 finished! INFO @ Wed, 08 Dec 2021 22:01:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:01:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:01:49: #2 number of paired peaks: 509 WARNING @ Wed, 08 Dec 2021 22:01:49: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Wed, 08 Dec 2021 22:01:49: start model_add_line... INFO @ Wed, 08 Dec 2021 22:01:49: start X-correlation... INFO @ Wed, 08 Dec 2021 22:01:49: end of X-cor INFO @ Wed, 08 Dec 2021 22:01:49: #2 finished! INFO @ Wed, 08 Dec 2021 22:01:49: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:01:49: #2 alternative fragment length(s) may be 2,50,553 bps INFO @ Wed, 08 Dec 2021 22:01:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.20_model.r WARNING @ Wed, 08 Dec 2021 22:01:49: #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 22:01:49: #2 You may need to consider one of the other alternative d(s): 2,50,553 WARNING @ Wed, 08 Dec 2021 22:01:49: #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 22:01:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:01:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:02:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:02:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:02:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:02:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180801/SRX3180801.20_summits.bed INFO @ Wed, 08 Dec 2021 22:02:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 1 millis CompletedMACS2peakCalling