Job ID = 14159366 SRX = SRX3180824 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7645090 spots for SRR6030475/SRR6030475.sra Written 7645090 spots for SRR6030475/SRR6030475.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159551 ("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: 00:01:27 7645090 reads; of these: 7645090 (100.00%) were unpaired; of these: 1991700 (26.05%) aligned 0 times 4733902 (61.92%) aligned exactly 1 time 919488 (12.03%) aligned >1 times 73.95% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 1404464 / 5653390 = 0.2484 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 @ Wed, 08 Dec 2021 21:17:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.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 @ Wed, 08 Dec 2021 21:17:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:17:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:17:31: 1000000 INFO @ Wed, 08 Dec 2021 21:17:36: 2000000 INFO @ Wed, 08 Dec 2021 21:17:41: 3000000 INFO @ Wed, 08 Dec 2021 21:17:46: 4000000 INFO @ Wed, 08 Dec 2021 21:17:47: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:17:47: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:17:47: #1 total tags in treatment: 4248926 INFO @ Wed, 08 Dec 2021 21:17:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:17:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:17:47: #1 tags after filtering in treatment: 4248926 INFO @ Wed, 08 Dec 2021 21:17:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:17:47: #1 finished! INFO @ Wed, 08 Dec 2021 21:17:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:17:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:17:47: #2 number of paired peaks: 427 WARNING @ Wed, 08 Dec 2021 21:17:47: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Wed, 08 Dec 2021 21:17:47: start model_add_line... INFO @ Wed, 08 Dec 2021 21:17:47: start X-correlation... INFO @ Wed, 08 Dec 2021 21:17:47: end of X-cor INFO @ Wed, 08 Dec 2021 21:17:47: #2 finished! INFO @ Wed, 08 Dec 2021 21:17:47: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 21:17:47: #2 alternative fragment length(s) may be 50,196,487 bps INFO @ Wed, 08 Dec 2021 21:17:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.05_model.r WARNING @ Wed, 08 Dec 2021 21:17:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:17:47: #2 You may need to consider one of the other alternative d(s): 50,196,487 WARNING @ Wed, 08 Dec 2021 21:17:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:17:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:17:47: #3 Pre-compute pvalue-qvalue table... 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 @ Wed, 08 Dec 2021 21:17:56: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.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 @ Wed, 08 Dec 2021 21:17:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:17:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:18:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:18:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:18:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.05_summits.bed INFO @ Wed, 08 Dec 2021 21:18:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (512 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:18:01: 1000000 INFO @ Wed, 08 Dec 2021 21:18:07: 2000000 INFO @ Wed, 08 Dec 2021 21:18:12: 3000000 INFO @ Wed, 08 Dec 2021 21:18:17: 4000000 INFO @ Wed, 08 Dec 2021 21:18:18: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:18:18: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:18:18: #1 total tags in treatment: 4248926 INFO @ Wed, 08 Dec 2021 21:18:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:18:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:18:18: #1 tags after filtering in treatment: 4248926 INFO @ Wed, 08 Dec 2021 21:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:18:18: #1 finished! INFO @ Wed, 08 Dec 2021 21:18:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:18:19: #2 number of paired peaks: 427 WARNING @ Wed, 08 Dec 2021 21:18:19: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Wed, 08 Dec 2021 21:18:19: start model_add_line... INFO @ Wed, 08 Dec 2021 21:18:19: start X-correlation... INFO @ Wed, 08 Dec 2021 21:18:19: end of X-cor INFO @ Wed, 08 Dec 2021 21:18:19: #2 finished! INFO @ Wed, 08 Dec 2021 21:18:19: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 21:18:19: #2 alternative fragment length(s) may be 50,196,487 bps INFO @ Wed, 08 Dec 2021 21:18:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.10_model.r WARNING @ Wed, 08 Dec 2021 21:18:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:18:19: #2 You may need to consider one of the other alternative d(s): 50,196,487 WARNING @ Wed, 08 Dec 2021 21:18:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:18:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:18:19: #3 Pre-compute pvalue-qvalue table... 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 @ Wed, 08 Dec 2021 21:18:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.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 @ Wed, 08 Dec 2021 21:18:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:18:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:18:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:18:32: 1000000 INFO @ Wed, 08 Dec 2021 21:18:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:18:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:18:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.10_summits.bed INFO @ Wed, 08 Dec 2021 21:18:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:18:38: 2000000 INFO @ Wed, 08 Dec 2021 21:18:44: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:18:49: 4000000 INFO @ Wed, 08 Dec 2021 21:18:51: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:18:51: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:18:51: #1 total tags in treatment: 4248926 INFO @ Wed, 08 Dec 2021 21:18:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:18:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:18:51: #1 tags after filtering in treatment: 4248926 INFO @ Wed, 08 Dec 2021 21:18:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:18:51: #1 finished! INFO @ Wed, 08 Dec 2021 21:18:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:18:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:18:51: #2 number of paired peaks: 427 WARNING @ Wed, 08 Dec 2021 21:18:51: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Wed, 08 Dec 2021 21:18:51: start model_add_line... INFO @ Wed, 08 Dec 2021 21:18:51: start X-correlation... INFO @ Wed, 08 Dec 2021 21:18:51: end of X-cor INFO @ Wed, 08 Dec 2021 21:18:51: #2 finished! INFO @ Wed, 08 Dec 2021 21:18:51: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 21:18:51: #2 alternative fragment length(s) may be 50,196,487 bps INFO @ Wed, 08 Dec 2021 21:18:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.20_model.r WARNING @ Wed, 08 Dec 2021 21:18:51: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:18:51: #2 You may need to consider one of the other alternative d(s): 50,196,487 WARNING @ Wed, 08 Dec 2021 21:18:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:18:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:18:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:19:00: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:19:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:19:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180824/SRX3180824.20_summits.bed INFO @ Wed, 08 Dec 2021 21:19:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling