Job ID = 16434849 SRX = SRX11633388 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15812263 spots for SRR15329096/SRR15329096.sra Written 15812263 spots for SRR15329096/SRR15329096.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434896 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:29 15812263 reads; of these: 15812263 (100.00%) were unpaired; of these: 1373084 (8.68%) aligned 0 times 12464447 (78.83%) aligned exactly 1 time 1974732 (12.49%) aligned >1 times 91.32% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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] 912869 / 14439179 = 0.0632 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 10:14:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.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 10:14:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:14:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:14:50: 1000000 INFO @ Tue, 02 Aug 2022 10:14:55: 2000000 INFO @ Tue, 02 Aug 2022 10:15:00: 3000000 INFO @ Tue, 02 Aug 2022 10:15:06: 4000000 INFO @ Tue, 02 Aug 2022 10:15:11: 5000000 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 10:15:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.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 10:15:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:16: 6000000 INFO @ Tue, 02 Aug 2022 10:15:20: 1000000 INFO @ Tue, 02 Aug 2022 10:15:22: 7000000 INFO @ Tue, 02 Aug 2022 10:15:27: 2000000 INFO @ Tue, 02 Aug 2022 10:15:28: 8000000 INFO @ Tue, 02 Aug 2022 10:15:33: 9000000 INFO @ Tue, 02 Aug 2022 10:15:33: 3000000 INFO @ Tue, 02 Aug 2022 10:15:38: 10000000 INFO @ Tue, 02 Aug 2022 10:15:40: 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 10:15:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.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 10:15:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:44: 11000000 INFO @ Tue, 02 Aug 2022 10:15:46: 5000000 INFO @ Tue, 02 Aug 2022 10:15:49: 1000000 INFO @ Tue, 02 Aug 2022 10:15:49: 12000000 INFO @ Tue, 02 Aug 2022 10:15:52: 6000000 INFO @ Tue, 02 Aug 2022 10:15:55: 13000000 INFO @ Tue, 02 Aug 2022 10:15:55: 2000000 INFO @ Tue, 02 Aug 2022 10:15:58: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:15:58: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:15:58: #1 total tags in treatment: 13526310 INFO @ Tue, 02 Aug 2022 10:15:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:58: #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 10:15:58: #1 tags after filtering in treatment: 13526310 INFO @ Tue, 02 Aug 2022 10:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:15:58: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:58: 7000000 INFO @ Tue, 02 Aug 2022 10:15:59: #2 number of paired peaks: 175 WARNING @ Tue, 02 Aug 2022 10:15:59: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:59: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:59: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:59: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:59: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:59: #2 predicted fragment length is 55 bps INFO @ Tue, 02 Aug 2022 10:15:59: #2 alternative fragment length(s) may be 3,55 bps INFO @ Tue, 02 Aug 2022 10:15:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.05_model.r WARNING @ Tue, 02 Aug 2022 10:15:59: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:15:59: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Tue, 02 Aug 2022 10:15:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:15:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:16:00: 3000000 INFO @ Tue, 02 Aug 2022 10:16:05: 8000000 INFO @ Tue, 02 Aug 2022 10:16:06: 4000000 INFO @ Tue, 02 Aug 2022 10:16:11: 9000000 INFO @ Tue, 02 Aug 2022 10:16:12: 5000000 INFO @ Tue, 02 Aug 2022 10:16:17: 6000000 INFO @ Tue, 02 Aug 2022 10:16:17: 10000000 INFO @ Tue, 02 Aug 2022 10:16:23: 7000000 INFO @ Tue, 02 Aug 2022 10:16:24: 11000000 INFO @ Tue, 02 Aug 2022 10:16:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:16:28: 8000000 INFO @ Tue, 02 Aug 2022 10:16:30: 12000000 INFO @ Tue, 02 Aug 2022 10:16:34: 9000000 INFO @ Tue, 02 Aug 2022 10:16:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:16:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:16:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.05_summits.bed INFO @ Tue, 02 Aug 2022 10:16:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (483 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:16:37: 13000000 INFO @ Tue, 02 Aug 2022 10:16:39: 10000000 INFO @ Tue, 02 Aug 2022 10:16:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:16:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:16:40: #1 total tags in treatment: 13526310 INFO @ Tue, 02 Aug 2022 10:16:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:16:40: #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 10:16:40: #1 tags after filtering in treatment: 13526310 INFO @ Tue, 02 Aug 2022 10:16:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:16:40: #1 finished! INFO @ Tue, 02 Aug 2022 10:16:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:16:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:16:41: #2 number of paired peaks: 175 WARNING @ Tue, 02 Aug 2022 10:16:41: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 02 Aug 2022 10:16:41: start model_add_line... INFO @ Tue, 02 Aug 2022 10:16:41: start X-correlation... INFO @ Tue, 02 Aug 2022 10:16:41: end of X-cor INFO @ Tue, 02 Aug 2022 10:16:41: #2 finished! INFO @ Tue, 02 Aug 2022 10:16:41: #2 predicted fragment length is 55 bps INFO @ Tue, 02 Aug 2022 10:16:41: #2 alternative fragment length(s) may be 3,55 bps INFO @ Tue, 02 Aug 2022 10:16:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.10_model.r WARNING @ Tue, 02 Aug 2022 10:16:41: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:16:41: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Tue, 02 Aug 2022 10:16:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:16:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:16:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:16:45: 11000000 INFO @ Tue, 02 Aug 2022 10:16:50: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:16:55: 13000000 INFO @ Tue, 02 Aug 2022 10:16:58: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:16:58: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:16:58: #1 total tags in treatment: 13526310 INFO @ Tue, 02 Aug 2022 10:16:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:16:58: #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 10:16:58: #1 tags after filtering in treatment: 13526310 INFO @ Tue, 02 Aug 2022 10:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:16:58: #1 finished! INFO @ Tue, 02 Aug 2022 10:16:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:16:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:16:59: #2 number of paired peaks: 175 WARNING @ Tue, 02 Aug 2022 10:16:59: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 02 Aug 2022 10:16:59: start model_add_line... INFO @ Tue, 02 Aug 2022 10:16:59: start X-correlation... INFO @ Tue, 02 Aug 2022 10:16:59: end of X-cor INFO @ Tue, 02 Aug 2022 10:16:59: #2 finished! INFO @ Tue, 02 Aug 2022 10:16:59: #2 predicted fragment length is 55 bps INFO @ Tue, 02 Aug 2022 10:16:59: #2 alternative fragment length(s) may be 3,55 bps INFO @ Tue, 02 Aug 2022 10:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.20_model.r WARNING @ Tue, 02 Aug 2022 10:16:59: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:16:59: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Tue, 02 Aug 2022 10:16:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:16:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:16:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:17:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:17:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:17:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:17:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.10_summits.bed INFO @ Tue, 02 Aug 2022 10:17:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (302 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:17:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:17:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:17:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:17:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633388/SRX11633388.20_summits.bed INFO @ Tue, 02 Aug 2022 10:17:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 13 millis CompletedMACS2peakCalling