Job ID = 14160568 SRX = SRX10399012 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12931999 spots for SRR14022400/SRR14022400.sra Written 12931999 spots for SRR14022400/SRR14022400.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160691 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:33 12931999 reads; of these: 12931999 (100.00%) were unpaired; of these: 3900532 (30.16%) aligned 0 times 7587303 (58.67%) aligned exactly 1 time 1444164 (11.17%) aligned >1 times 69.84% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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_rmdupse_core] 1477326 / 9031467 = 0.1636 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 03:20:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.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 03:20:00: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:20:00: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:20:05: 1000000 INFO @ Thu, 09 Dec 2021 03:20:11: 2000000 INFO @ Thu, 09 Dec 2021 03:20:17: 3000000 INFO @ Thu, 09 Dec 2021 03:20:23: 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 @ Thu, 09 Dec 2021 03:20:29: 5000000 INFO @ Thu, 09 Dec 2021 03:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.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 03:20:30: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:20:30: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:20:36: 6000000 INFO @ Thu, 09 Dec 2021 03:20:38: 1000000 INFO @ Thu, 09 Dec 2021 03:20:42: 7000000 INFO @ Thu, 09 Dec 2021 03:20:45: 2000000 INFO @ Thu, 09 Dec 2021 03:20:46: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:20:46: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:20:46: #1 total tags in treatment: 7554141 INFO @ Thu, 09 Dec 2021 03:20:46: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:20:46: #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 03:20:46: #1 tags after filtering in treatment: 7554141 INFO @ Thu, 09 Dec 2021 03:20:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:20:46: #1 finished! INFO @ Thu, 09 Dec 2021 03:20:46: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:20:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:20:47: #2 number of paired peaks: 606 WARNING @ Thu, 09 Dec 2021 03:20:47: Fewer paired peaks (606) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 606 pairs to build model! INFO @ Thu, 09 Dec 2021 03:20:47: start model_add_line... INFO @ Thu, 09 Dec 2021 03:20:47: start X-correlation... INFO @ Thu, 09 Dec 2021 03:20:47: end of X-cor INFO @ Thu, 09 Dec 2021 03:20:47: #2 finished! INFO @ Thu, 09 Dec 2021 03:20:47: #2 predicted fragment length is 126 bps INFO @ Thu, 09 Dec 2021 03:20:47: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 09 Dec 2021 03:20:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.05_model.r WARNING @ Thu, 09 Dec 2021 03:20:47: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:20:47: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Thu, 09 Dec 2021 03:20:47: #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 03:20:47: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:20:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:20:52: 3000000 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 03:20:59: 4000000 INFO @ Thu, 09 Dec 2021 03:21:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.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 03:21:00: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:21:00: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:21:03: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:21:07: 5000000 INFO @ Thu, 09 Dec 2021 03:21:07: 1000000 INFO @ Thu, 09 Dec 2021 03:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.05_summits.bed INFO @ Thu, 09 Dec 2021 03:21:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1426 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:21:14: 6000000 INFO @ Thu, 09 Dec 2021 03:21:15: 2000000 INFO @ Thu, 09 Dec 2021 03:21:22: 7000000 INFO @ Thu, 09 Dec 2021 03:21:23: 3000000 INFO @ Thu, 09 Dec 2021 03:21:26: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:21:26: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:21:26: #1 total tags in treatment: 7554141 INFO @ Thu, 09 Dec 2021 03:21:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:21:26: #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 03:21:26: #1 tags after filtering in treatment: 7554141 INFO @ Thu, 09 Dec 2021 03:21:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:21:26: #1 finished! INFO @ Thu, 09 Dec 2021 03:21:26: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:21:27: #2 number of paired peaks: 606 WARNING @ Thu, 09 Dec 2021 03:21:27: Fewer paired peaks (606) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 606 pairs to build model! INFO @ Thu, 09 Dec 2021 03:21:27: start model_add_line... INFO @ Thu, 09 Dec 2021 03:21:27: start X-correlation... INFO @ Thu, 09 Dec 2021 03:21:27: end of X-cor INFO @ Thu, 09 Dec 2021 03:21:27: #2 finished! INFO @ Thu, 09 Dec 2021 03:21:27: #2 predicted fragment length is 126 bps INFO @ Thu, 09 Dec 2021 03:21:27: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 09 Dec 2021 03:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.10_model.r WARNING @ Thu, 09 Dec 2021 03:21:27: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:21:27: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Thu, 09 Dec 2021 03:21:27: #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 03:21:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:21:30: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:21:38: 5000000 INFO @ Thu, 09 Dec 2021 03:21:43: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:21:45: 6000000 INFO @ Thu, 09 Dec 2021 03:21:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:21:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:21:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.10_summits.bed INFO @ Thu, 09 Dec 2021 03:21:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (975 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:21:52: 7000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:21:56: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:21:56: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:21:56: #1 total tags in treatment: 7554141 INFO @ Thu, 09 Dec 2021 03:21:56: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:21:56: #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 03:21:56: #1 tags after filtering in treatment: 7554141 INFO @ Thu, 09 Dec 2021 03:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:21:56: #1 finished! INFO @ Thu, 09 Dec 2021 03:21:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:21:57: #2 number of paired peaks: 606 WARNING @ Thu, 09 Dec 2021 03:21:57: Fewer paired peaks (606) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 606 pairs to build model! INFO @ Thu, 09 Dec 2021 03:21:57: start model_add_line... INFO @ Thu, 09 Dec 2021 03:21:57: start X-correlation... INFO @ Thu, 09 Dec 2021 03:21:57: end of X-cor INFO @ Thu, 09 Dec 2021 03:21:57: #2 finished! INFO @ Thu, 09 Dec 2021 03:21:57: #2 predicted fragment length is 126 bps INFO @ Thu, 09 Dec 2021 03:21:57: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 09 Dec 2021 03:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.20_model.r WARNING @ Thu, 09 Dec 2021 03:21:57: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:21:57: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Thu, 09 Dec 2021 03:21:57: #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 03:21:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:22:14: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:22:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:22:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:22:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399012/SRX10399012.20_summits.bed INFO @ Thu, 09 Dec 2021 03:22:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 2 millis CompletedMACS2peakCalling