Job ID = 14160563 SRX = SRX10399010 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7765878 spots for SRR14022398/SRR14022398.sra Written 7765878 spots for SRR14022398/SRR14022398.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160682 ("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: 00:01:45 7765878 reads; of these: 7765878 (100.00%) were unpaired; of these: 119067 (1.53%) aligned 0 times 6433175 (82.84%) aligned exactly 1 time 1213636 (15.63%) aligned >1 times 98.47% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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] 392703 / 7646811 = 0.0514 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 03:16:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.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 03:16:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:16:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:16:47: 1000000 INFO @ Thu, 09 Dec 2021 03:16:52: 2000000 INFO @ Thu, 09 Dec 2021 03:16:57: 3000000 INFO @ Thu, 09 Dec 2021 03:17:02: 4000000 INFO @ Thu, 09 Dec 2021 03:17:07: 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 03:17:12: 6000000 INFO @ Thu, 09 Dec 2021 03:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.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 03:17:12: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:17:12: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:17:17: 7000000 INFO @ Thu, 09 Dec 2021 03:17:18: 1000000 INFO @ Thu, 09 Dec 2021 03:17:19: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:17:19: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:17:19: #1 total tags in treatment: 7254108 INFO @ Thu, 09 Dec 2021 03:17:19: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:17:19: #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 03:17:19: #1 tags after filtering in treatment: 7254108 INFO @ Thu, 09 Dec 2021 03:17:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:17:19: #1 finished! INFO @ Thu, 09 Dec 2021 03:17:19: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:17:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:17:19: #2 number of paired peaks: 285 WARNING @ Thu, 09 Dec 2021 03:17:19: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 09 Dec 2021 03:17:19: start model_add_line... INFO @ Thu, 09 Dec 2021 03:17:19: start X-correlation... INFO @ Thu, 09 Dec 2021 03:17:19: end of X-cor INFO @ Thu, 09 Dec 2021 03:17:19: #2 finished! INFO @ Thu, 09 Dec 2021 03:17:19: #2 predicted fragment length is 51 bps INFO @ Thu, 09 Dec 2021 03:17:19: #2 alternative fragment length(s) may be 4,51,561 bps INFO @ Thu, 09 Dec 2021 03:17:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.05_model.r WARNING @ Thu, 09 Dec 2021 03:17:19: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:17:19: #2 You may need to consider one of the other alternative d(s): 4,51,561 WARNING @ Thu, 09 Dec 2021 03:17:19: #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 03:17:19: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:17:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:17:25: 2000000 INFO @ Thu, 09 Dec 2021 03:17:31: 3000000 INFO @ Thu, 09 Dec 2021 03:17:34: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:17:37: 4000000 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 03:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.05_summits.bed INFO @ Thu, 09 Dec 2021 03:17:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.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 03:17:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:17:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:17:43: 5000000 INFO @ Thu, 09 Dec 2021 03:17:48: 1000000 INFO @ Thu, 09 Dec 2021 03:17:49: 6000000 INFO @ Thu, 09 Dec 2021 03:17:55: 2000000 INFO @ Thu, 09 Dec 2021 03:17:56: 7000000 INFO @ Thu, 09 Dec 2021 03:17:57: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:17:57: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:17:57: #1 total tags in treatment: 7254108 INFO @ Thu, 09 Dec 2021 03:17:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:17:57: #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 03:17:57: #1 tags after filtering in treatment: 7254108 INFO @ Thu, 09 Dec 2021 03:17:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:17:57: #1 finished! INFO @ Thu, 09 Dec 2021 03:17:57: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:17:58: #2 number of paired peaks: 285 WARNING @ Thu, 09 Dec 2021 03:17:58: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 09 Dec 2021 03:17:58: start model_add_line... INFO @ Thu, 09 Dec 2021 03:17:58: start X-correlation... INFO @ Thu, 09 Dec 2021 03:17:58: end of X-cor INFO @ Thu, 09 Dec 2021 03:17:58: #2 finished! INFO @ Thu, 09 Dec 2021 03:17:58: #2 predicted fragment length is 51 bps INFO @ Thu, 09 Dec 2021 03:17:58: #2 alternative fragment length(s) may be 4,51,561 bps INFO @ Thu, 09 Dec 2021 03:17:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.10_model.r WARNING @ Thu, 09 Dec 2021 03:17:58: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:17:58: #2 You may need to consider one of the other alternative d(s): 4,51,561 WARNING @ Thu, 09 Dec 2021 03:17:58: #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 03:17:58: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:17:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:18:01: 3000000 INFO @ Thu, 09 Dec 2021 03:18:07: 4000000 INFO @ Thu, 09 Dec 2021 03:18:12: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:18:13: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:18:19: 6000000 INFO @ Thu, 09 Dec 2021 03:18:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:18:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:18:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.10_summits.bed INFO @ Thu, 09 Dec 2021 03:18:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:18:25: 7000000 INFO @ Thu, 09 Dec 2021 03:18:27: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:18:27: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:18:27: #1 total tags in treatment: 7254108 INFO @ Thu, 09 Dec 2021 03:18:27: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:18:27: #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 03:18:27: #1 tags after filtering in treatment: 7254108 INFO @ Thu, 09 Dec 2021 03:18:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:18:27: #1 finished! INFO @ Thu, 09 Dec 2021 03:18:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:18:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:18:27: #2 number of paired peaks: 285 WARNING @ Thu, 09 Dec 2021 03:18:27: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 09 Dec 2021 03:18:27: start model_add_line... INFO @ Thu, 09 Dec 2021 03:18:27: start X-correlation... INFO @ Thu, 09 Dec 2021 03:18:27: end of X-cor INFO @ Thu, 09 Dec 2021 03:18:27: #2 finished! INFO @ Thu, 09 Dec 2021 03:18:27: #2 predicted fragment length is 51 bps INFO @ Thu, 09 Dec 2021 03:18:27: #2 alternative fragment length(s) may be 4,51,561 bps INFO @ Thu, 09 Dec 2021 03:18:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.20_model.r WARNING @ Thu, 09 Dec 2021 03:18:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:18:27: #2 You may need to consider one of the other alternative d(s): 4,51,561 WARNING @ Thu, 09 Dec 2021 03:18:27: #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 03:18:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:18:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:18:41: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:18:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:18:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:18:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399010/SRX10399010.20_summits.bed INFO @ Thu, 09 Dec 2021 03:18:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis CompletedMACS2peakCalling