Job ID = 12265792 SRX = SRX7282558 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16582 spots for SRR10603253/SRR10603253.sra Written 16582 spots for SRR10603253/SRR10603253.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265900 ("srTdm6") 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: 00:00:01 16582 reads; of these: 16582 (100.00%) were unpaired; of these: 2990 (18.03%) aligned 0 times 3831 (23.10%) aligned exactly 1 time 9761 (58.87%) aligned >1 times 81.97% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 9233 / 13592 = 0.6793 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 03 Apr 2021 08:25:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:25:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:25:11: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:25:11: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:25:11: #1 total tags in treatment: 4359 INFO @ Sat, 03 Apr 2021 08:25:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:25:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:25:11: #1 tags after filtering in treatment: 4357 INFO @ Sat, 03 Apr 2021 08:25:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:25:11: #1 finished! INFO @ Sat, 03 Apr 2021 08:25:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:25:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:25:11: #2 number of paired peaks: 115 WARNING @ Sat, 03 Apr 2021 08:25:11: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 03 Apr 2021 08:25:11: start model_add_line... INFO @ Sat, 03 Apr 2021 08:25:11: start X-correlation... INFO @ Sat, 03 Apr 2021 08:25:11: end of X-cor INFO @ Sat, 03 Apr 2021 08:25:11: #2 finished! INFO @ Sat, 03 Apr 2021 08:25:11: #2 predicted fragment length is 11 bps INFO @ Sat, 03 Apr 2021 08:25:11: #2 alternative fragment length(s) may be 11,25,62,77,121,141,169,193,227,246,296,343,351,403,461,512,560,574 bps INFO @ Sat, 03 Apr 2021 08:25:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.05_model.r WARNING @ Sat, 03 Apr 2021 08:25:11: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:25:11: #2 You may need to consider one of the other alternative d(s): 11,25,62,77,121,141,169,193,227,246,296,343,351,403,461,512,560,574 WARNING @ Sat, 03 Apr 2021 08:25:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:25:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:25:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:25:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:25:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:25:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:25:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.05_summits.bed INFO @ Sat, 03 Apr 2021 08:25:11: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 03 Apr 2021 08:25:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:25:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:25:41: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:25:41: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:25:41: #1 total tags in treatment: 4359 INFO @ Sat, 03 Apr 2021 08:25:41: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:25:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:25:41: #1 tags after filtering in treatment: 4357 INFO @ Sat, 03 Apr 2021 08:25:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:25:41: #1 finished! INFO @ Sat, 03 Apr 2021 08:25:41: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:25:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:25:41: #2 number of paired peaks: 115 WARNING @ Sat, 03 Apr 2021 08:25:41: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 03 Apr 2021 08:25:41: start model_add_line... INFO @ Sat, 03 Apr 2021 08:25:41: start X-correlation... INFO @ Sat, 03 Apr 2021 08:25:41: end of X-cor INFO @ Sat, 03 Apr 2021 08:25:41: #2 finished! INFO @ Sat, 03 Apr 2021 08:25:41: #2 predicted fragment length is 11 bps INFO @ Sat, 03 Apr 2021 08:25:41: #2 alternative fragment length(s) may be 11,25,62,77,121,141,169,193,227,246,296,343,351,403,461,512,560,574 bps INFO @ Sat, 03 Apr 2021 08:25:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.10_model.r WARNING @ Sat, 03 Apr 2021 08:25:41: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:25:41: #2 You may need to consider one of the other alternative d(s): 11,25,62,77,121,141,169,193,227,246,296,343,351,403,461,512,560,574 WARNING @ Sat, 03 Apr 2021 08:25:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:25:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:25:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:25:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:25:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:25:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:25:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.10_summits.bed INFO @ Sat, 03 Apr 2021 08:25:41: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 0 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:26:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 03 Apr 2021 08:26:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:26:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:26:12: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:26:12: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:26:12: #1 total tags in treatment: 4359 INFO @ Sat, 03 Apr 2021 08:26:12: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:26:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:26:12: #1 tags after filtering in treatment: 4357 INFO @ Sat, 03 Apr 2021 08:26:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:26:12: #1 finished! INFO @ Sat, 03 Apr 2021 08:26:12: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:26:12: #2 number of paired peaks: 115 WARNING @ Sat, 03 Apr 2021 08:26:12: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 03 Apr 2021 08:26:12: start model_add_line... INFO @ Sat, 03 Apr 2021 08:26:12: start X-correlation... INFO @ Sat, 03 Apr 2021 08:26:12: end of X-cor INFO @ Sat, 03 Apr 2021 08:26:12: #2 finished! INFO @ Sat, 03 Apr 2021 08:26:12: #2 predicted fragment length is 11 bps INFO @ Sat, 03 Apr 2021 08:26:12: #2 alternative fragment length(s) may be 11,25,62,77,121,141,169,193,227,246,296,343,351,403,461,512,560,574 bps INFO @ Sat, 03 Apr 2021 08:26:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.20_model.r WARNING @ Sat, 03 Apr 2021 08:26:12: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:26:12: #2 You may need to consider one of the other alternative d(s): 11,25,62,77,121,141,169,193,227,246,296,343,351,403,461,512,560,574 WARNING @ Sat, 03 Apr 2021 08:26:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:26:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:26:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:26:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:26:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:26:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:26:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282558/SRX7282558.20_summits.bed INFO @ Sat, 03 Apr 2021 08:26:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling