Job ID = 12266401 SRX = SRX7282809 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31902 spots for SRR10603104/SRR10603104.sra Written 31902 spots for SRR10603104/SRR10603104.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266511 ("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 31902 reads; of these: 31902 (100.00%) were unpaired; of these: 4425 (13.87%) aligned 0 times 16168 (50.68%) aligned exactly 1 time 11309 (35.45%) aligned >1 times 86.13% 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] 16579 / 27477 = 0.6034 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 08:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.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 08:57:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:57:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:57:50: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:57:50: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:57:50: #1 total tags in treatment: 10898 INFO @ Sat, 03 Apr 2021 08:57:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:57:50: #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 08:57:50: #1 tags after filtering in treatment: 10897 INFO @ Sat, 03 Apr 2021 08:57:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:57:50: #1 finished! INFO @ Sat, 03 Apr 2021 08:57:50: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:57:50: #2 number of paired peaks: 456 WARNING @ Sat, 03 Apr 2021 08:57:50: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sat, 03 Apr 2021 08:57:50: start model_add_line... INFO @ Sat, 03 Apr 2021 08:57:50: start X-correlation... INFO @ Sat, 03 Apr 2021 08:57:50: end of X-cor INFO @ Sat, 03 Apr 2021 08:57:50: #2 finished! INFO @ Sat, 03 Apr 2021 08:57:50: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:57:50: #2 alternative fragment length(s) may be 9,29,71,94,135,173,209,270,294,334,453,578 bps INFO @ Sat, 03 Apr 2021 08:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.05_model.r WARNING @ Sat, 03 Apr 2021 08:57:50: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:57:50: #2 You may need to consider one of the other alternative d(s): 9,29,71,94,135,173,209,270,294,334,453,578 WARNING @ Sat, 03 Apr 2021 08:57:50: #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 08:57:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:57:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:57:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:57:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:57:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:57:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.05_summits.bed INFO @ Sat, 03 Apr 2021 08:57:50: Done! pass1 - making usageList (1 chroms): 0 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 08:58:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.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 08:58:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:58:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:58:20: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:58:20: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:58:20: #1 total tags in treatment: 10898 INFO @ Sat, 03 Apr 2021 08:58:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:58:20: #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 08:58:20: #1 tags after filtering in treatment: 10897 INFO @ Sat, 03 Apr 2021 08:58:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:58:20: #1 finished! INFO @ Sat, 03 Apr 2021 08:58:20: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:58:20: #2 number of paired peaks: 456 WARNING @ Sat, 03 Apr 2021 08:58:20: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sat, 03 Apr 2021 08:58:20: start model_add_line... INFO @ Sat, 03 Apr 2021 08:58:20: start X-correlation... INFO @ Sat, 03 Apr 2021 08:58:20: end of X-cor INFO @ Sat, 03 Apr 2021 08:58:20: #2 finished! INFO @ Sat, 03 Apr 2021 08:58:20: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:58:20: #2 alternative fragment length(s) may be 9,29,71,94,135,173,209,270,294,334,453,578 bps INFO @ Sat, 03 Apr 2021 08:58:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.10_model.r WARNING @ Sat, 03 Apr 2021 08:58:20: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:58:20: #2 You may need to consider one of the other alternative d(s): 9,29,71,94,135,173,209,270,294,334,453,578 WARNING @ Sat, 03 Apr 2021 08:58:20: #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 08:58:20: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:58:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:58:20: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.10_summits.bed INFO @ Sat, 03 Apr 2021 08:58:20: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 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 08:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.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 08:58:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:58:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:58:50: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:58:50: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:58:50: #1 total tags in treatment: 10898 INFO @ Sat, 03 Apr 2021 08:58:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:58:50: #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 08:58:50: #1 tags after filtering in treatment: 10897 INFO @ Sat, 03 Apr 2021 08:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:58:50: #1 finished! INFO @ Sat, 03 Apr 2021 08:58:50: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:58:50: #2 number of paired peaks: 456 WARNING @ Sat, 03 Apr 2021 08:58:50: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sat, 03 Apr 2021 08:58:50: start model_add_line... INFO @ Sat, 03 Apr 2021 08:58:50: start X-correlation... INFO @ Sat, 03 Apr 2021 08:58:50: end of X-cor INFO @ Sat, 03 Apr 2021 08:58:50: #2 finished! INFO @ Sat, 03 Apr 2021 08:58:50: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:58:50: #2 alternative fragment length(s) may be 9,29,71,94,135,173,209,270,294,334,453,578 bps INFO @ Sat, 03 Apr 2021 08:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.20_model.r WARNING @ Sat, 03 Apr 2021 08:58:50: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:58:50: #2 You may need to consider one of the other alternative d(s): 9,29,71,94,135,173,209,270,294,334,453,578 WARNING @ Sat, 03 Apr 2021 08:58:50: #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 08:58:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:58:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:58:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:58:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:58:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282809/SRX7282809.20_summits.bed INFO @ Sat, 03 Apr 2021 08:58:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling