Job ID = 14160537 SRX = SRX10399000 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 3543318 spots for SRR14022393/SRR14022393.sra Written 3543318 spots for SRR14022393/SRR14022393.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160654 ("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: 00:00:42 3543318 reads; of these: 3543318 (100.00%) were unpaired; of these: 729672 (20.59%) aligned 0 times 2343645 (66.14%) aligned exactly 1 time 470001 (13.26%) aligned >1 times 79.41% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 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] 837061 / 2813646 = 0.2975 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 03:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.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 03:06:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:06:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:06:32: 1000000 INFO @ Thu, 09 Dec 2021 03:06:37: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:06:37: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:06:37: #1 total tags in treatment: 1976585 INFO @ Thu, 09 Dec 2021 03:06:37: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:06:37: #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 03:06:37: #1 tags after filtering in treatment: 1976585 INFO @ Thu, 09 Dec 2021 03:06:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:06:37: #1 finished! INFO @ Thu, 09 Dec 2021 03:06:37: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:06:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:06:37: #2 number of paired peaks: 689 WARNING @ Thu, 09 Dec 2021 03:06:37: Fewer paired peaks (689) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 689 pairs to build model! INFO @ Thu, 09 Dec 2021 03:06:37: start model_add_line... INFO @ Thu, 09 Dec 2021 03:06:37: start X-correlation... INFO @ Thu, 09 Dec 2021 03:06:37: end of X-cor INFO @ Thu, 09 Dec 2021 03:06:37: #2 finished! INFO @ Thu, 09 Dec 2021 03:06:37: #2 predicted fragment length is 95 bps INFO @ Thu, 09 Dec 2021 03:06:37: #2 alternative fragment length(s) may be 67,95,108,595 bps INFO @ Thu, 09 Dec 2021 03:06:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.05_model.r WARNING @ Thu, 09 Dec 2021 03:06:37: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:06:37: #2 You may need to consider one of the other alternative d(s): 67,95,108,595 WARNING @ Thu, 09 Dec 2021 03:06:37: #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 03:06:37: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:06:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:06:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:06:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:06:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:06:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.05_summits.bed INFO @ Thu, 09 Dec 2021 03:06:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (611 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 03:06:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.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 03:06:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:06:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:02: 1000000 INFO @ Thu, 09 Dec 2021 03:07:08: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:07:08: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:07:08: #1 total tags in treatment: 1976585 INFO @ Thu, 09 Dec 2021 03:07:08: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:07:08: #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 03:07:08: #1 tags after filtering in treatment: 1976585 INFO @ Thu, 09 Dec 2021 03:07:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:07:08: #1 finished! INFO @ Thu, 09 Dec 2021 03:07:08: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:07:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:07:08: #2 number of paired peaks: 689 WARNING @ Thu, 09 Dec 2021 03:07:08: Fewer paired peaks (689) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 689 pairs to build model! INFO @ Thu, 09 Dec 2021 03:07:08: start model_add_line... INFO @ Thu, 09 Dec 2021 03:07:08: start X-correlation... INFO @ Thu, 09 Dec 2021 03:07:08: end of X-cor INFO @ Thu, 09 Dec 2021 03:07:08: #2 finished! INFO @ Thu, 09 Dec 2021 03:07:08: #2 predicted fragment length is 95 bps INFO @ Thu, 09 Dec 2021 03:07:08: #2 alternative fragment length(s) may be 67,95,108,595 bps INFO @ Thu, 09 Dec 2021 03:07:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.10_model.r WARNING @ Thu, 09 Dec 2021 03:07:08: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:07:08: #2 You may need to consider one of the other alternative d(s): 67,95,108,595 WARNING @ Thu, 09 Dec 2021 03:07:08: #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 03:07:08: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:07:12: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.10_summits.bed INFO @ Thu, 09 Dec 2021 03:07:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 03:07:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.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 03:07:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:32: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:07:37: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:07:37: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:07:37: #1 total tags in treatment: 1976585 INFO @ Thu, 09 Dec 2021 03:07:37: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:07:37: #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 03:07:38: #1 tags after filtering in treatment: 1976585 INFO @ Thu, 09 Dec 2021 03:07:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:07:38: #1 finished! INFO @ Thu, 09 Dec 2021 03:07:38: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:07:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:07:38: #2 number of paired peaks: 689 WARNING @ Thu, 09 Dec 2021 03:07:38: Fewer paired peaks (689) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 689 pairs to build model! INFO @ Thu, 09 Dec 2021 03:07:38: start model_add_line... INFO @ Thu, 09 Dec 2021 03:07:38: start X-correlation... INFO @ Thu, 09 Dec 2021 03:07:38: end of X-cor INFO @ Thu, 09 Dec 2021 03:07:38: #2 finished! INFO @ Thu, 09 Dec 2021 03:07:38: #2 predicted fragment length is 95 bps INFO @ Thu, 09 Dec 2021 03:07:38: #2 alternative fragment length(s) may be 67,95,108,595 bps INFO @ Thu, 09 Dec 2021 03:07:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.20_model.r WARNING @ Thu, 09 Dec 2021 03:07:38: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:07:38: #2 You may need to consider one of the other alternative d(s): 67,95,108,595 WARNING @ Thu, 09 Dec 2021 03:07:38: #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 03:07:38: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:07:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:07:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399000/SRX10399000.20_summits.bed INFO @ Thu, 09 Dec 2021 03:07:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 1 millis CompletedMACS2peakCalling