Job ID = 14160562 SRX = SRX10399009 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9288481 spots for SRR14022397/SRR14022397.sra Written 9288481 spots for SRR14022397/SRR14022397.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160681 ("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: 00:01:59 9288481 reads; of these: 9288481 (100.00%) were unpaired; of these: 129450 (1.39%) aligned 0 times 7690333 (82.79%) aligned exactly 1 time 1468698 (15.81%) aligned >1 times 98.61% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 577165 / 9159031 = 0.0630 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 03:16:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.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 03:16:54: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:16:54: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:16:59: 1000000 INFO @ Thu, 09 Dec 2021 03:17:05: 2000000 INFO @ Thu, 09 Dec 2021 03:17:10: 3000000 INFO @ Thu, 09 Dec 2021 03:17:15: 4000000 INFO @ Thu, 09 Dec 2021 03:17:20: 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 03:17:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.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 03:17:23: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:17:23: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:17:25: 6000000 INFO @ Thu, 09 Dec 2021 03:17:30: 1000000 INFO @ Thu, 09 Dec 2021 03:17:31: 7000000 INFO @ Thu, 09 Dec 2021 03:17:36: 2000000 INFO @ Thu, 09 Dec 2021 03:17:37: 8000000 INFO @ Thu, 09 Dec 2021 03:17:40: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:17:40: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:17:40: #1 total tags in treatment: 8581866 INFO @ Thu, 09 Dec 2021 03:17:40: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:17:40: #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 03:17:40: #1 tags after filtering in treatment: 8581866 INFO @ Thu, 09 Dec 2021 03:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:17:40: #1 finished! INFO @ Thu, 09 Dec 2021 03:17:40: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:17:41: #2 number of paired peaks: 280 WARNING @ Thu, 09 Dec 2021 03:17:41: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Thu, 09 Dec 2021 03:17:41: start model_add_line... INFO @ Thu, 09 Dec 2021 03:17:41: start X-correlation... INFO @ Thu, 09 Dec 2021 03:17:41: end of X-cor INFO @ Thu, 09 Dec 2021 03:17:41: #2 finished! INFO @ Thu, 09 Dec 2021 03:17:41: #2 predicted fragment length is 51 bps INFO @ Thu, 09 Dec 2021 03:17:41: #2 alternative fragment length(s) may be 4,51,549,566 bps INFO @ Thu, 09 Dec 2021 03:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.05_model.r WARNING @ Thu, 09 Dec 2021 03:17:41: #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 03:17:41: #2 You may need to consider one of the other alternative d(s): 4,51,549,566 WARNING @ Thu, 09 Dec 2021 03:17:41: #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 03:17:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:17:42: 3000000 INFO @ Thu, 09 Dec 2021 03:17:49: 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 03:17:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.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 03:17:54: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:17:54: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:17:55: 5000000 INFO @ Thu, 09 Dec 2021 03:17:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:18:00: 1000000 INFO @ Thu, 09 Dec 2021 03:18:01: 6000000 INFO @ Thu, 09 Dec 2021 03:18:07: 2000000 INFO @ Thu, 09 Dec 2021 03:18:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:18:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:18:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.05_summits.bed INFO @ Thu, 09 Dec 2021 03:18:07: Done! INFO @ Thu, 09 Dec 2021 03:18:08: 7000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (475 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:18:13: 3000000 INFO @ Thu, 09 Dec 2021 03:18:14: 8000000 INFO @ Thu, 09 Dec 2021 03:18:18: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:18:18: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:18:18: #1 total tags in treatment: 8581866 INFO @ Thu, 09 Dec 2021 03:18:18: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:18:18: #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 03:18:18: #1 tags after filtering in treatment: 8581866 INFO @ Thu, 09 Dec 2021 03:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:18:18: #1 finished! INFO @ Thu, 09 Dec 2021 03:18:18: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:18:18: #2 number of paired peaks: 280 WARNING @ Thu, 09 Dec 2021 03:18:18: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Thu, 09 Dec 2021 03:18:18: start model_add_line... INFO @ Thu, 09 Dec 2021 03:18:18: start X-correlation... INFO @ Thu, 09 Dec 2021 03:18:18: end of X-cor INFO @ Thu, 09 Dec 2021 03:18:18: #2 finished! INFO @ Thu, 09 Dec 2021 03:18:18: #2 predicted fragment length is 51 bps INFO @ Thu, 09 Dec 2021 03:18:18: #2 alternative fragment length(s) may be 4,51,549,566 bps INFO @ Thu, 09 Dec 2021 03:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.10_model.r WARNING @ Thu, 09 Dec 2021 03:18:18: #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 03:18:18: #2 You may need to consider one of the other alternative d(s): 4,51,549,566 WARNING @ Thu, 09 Dec 2021 03:18:18: #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 03:18:18: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:18:19: 4000000 INFO @ Thu, 09 Dec 2021 03:18:26: 5000000 INFO @ Thu, 09 Dec 2021 03:18:32: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:18:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:18:38: 7000000 INFO @ Thu, 09 Dec 2021 03:18:44: 8000000 INFO @ Thu, 09 Dec 2021 03:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.10_summits.bed INFO @ Thu, 09 Dec 2021 03:18:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:18:47: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:18:47: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:18:47: #1 total tags in treatment: 8581866 INFO @ Thu, 09 Dec 2021 03:18:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:18:47: #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 03:18:47: #1 tags after filtering in treatment: 8581866 INFO @ Thu, 09 Dec 2021 03:18:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:18:47: #1 finished! INFO @ Thu, 09 Dec 2021 03:18:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:18:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:18:48: #2 number of paired peaks: 280 WARNING @ Thu, 09 Dec 2021 03:18:48: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Thu, 09 Dec 2021 03:18:48: start model_add_line... INFO @ Thu, 09 Dec 2021 03:18:48: start X-correlation... INFO @ Thu, 09 Dec 2021 03:18:48: end of X-cor INFO @ Thu, 09 Dec 2021 03:18:48: #2 finished! INFO @ Thu, 09 Dec 2021 03:18:48: #2 predicted fragment length is 51 bps INFO @ Thu, 09 Dec 2021 03:18:48: #2 alternative fragment length(s) may be 4,51,549,566 bps INFO @ Thu, 09 Dec 2021 03:18:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.20_model.r WARNING @ Thu, 09 Dec 2021 03:18:48: #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 03:18:48: #2 You may need to consider one of the other alternative d(s): 4,51,549,566 WARNING @ Thu, 09 Dec 2021 03:18:48: #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 03:18:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:18:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:19:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:19:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:19:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:19:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399009/SRX10399009.20_summits.bed INFO @ Thu, 09 Dec 2021 03:19:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 1 millis CompletedMACS2peakCalling