Job ID = 12266207 SRX = SRX7282724 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15555 spots for SRR10603155/SRR10603155.sra Written 15555 spots for SRR10603155/SRR10603155.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266315 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:01 15555 reads; of these: 15555 (100.00%) were unpaired; of these: 2162 (13.90%) aligned 0 times 4795 (30.83%) aligned exactly 1 time 8598 (55.27%) aligned >1 times 86.10% overall alignment rate Time searching: 00:00:02 Overall time: 00:00:02 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] 7421 / 13393 = 0.5541 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 08:51:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.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 08:51:46: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:51:46: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:51:46: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:51:46: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:51:46: #1 total tags in treatment: 5972 INFO @ Sat, 03 Apr 2021 08:51:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:51:46: #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 08:51:46: #1 tags after filtering in treatment: 5971 INFO @ Sat, 03 Apr 2021 08:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:51:46: #1 finished! INFO @ Sat, 03 Apr 2021 08:51:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:51:46: #2 number of paired peaks: 154 WARNING @ Sat, 03 Apr 2021 08:51:46: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Sat, 03 Apr 2021 08:51:46: start model_add_line... INFO @ Sat, 03 Apr 2021 08:51:46: start X-correlation... INFO @ Sat, 03 Apr 2021 08:51:46: end of X-cor INFO @ Sat, 03 Apr 2021 08:51:46: #2 finished! INFO @ Sat, 03 Apr 2021 08:51:46: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Apr 2021 08:51:46: #2 alternative fragment length(s) may be 11,29,59,89,109,146,170,193,220,245,294,341,367,374,421,487,527,563 bps INFO @ Sat, 03 Apr 2021 08:51:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.05_model.r WARNING @ Sat, 03 Apr 2021 08:51:46: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:51:46: #2 You may need to consider one of the other alternative d(s): 11,29,59,89,109,146,170,193,220,245,294,341,367,374,421,487,527,563 WARNING @ Sat, 03 Apr 2021 08:51:46: #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 08:51:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:51:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:51:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:51:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:51:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:51:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.05_summits.bed INFO @ Sat, 03 Apr 2021 08:51:46: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (5 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 08:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.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 08:52:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:52:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:52:16: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:52:16: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:52:16: #1 total tags in treatment: 5972 INFO @ Sat, 03 Apr 2021 08:52:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:52:16: #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 08:52:16: #1 tags after filtering in treatment: 5971 INFO @ Sat, 03 Apr 2021 08:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:52:16: #1 finished! INFO @ Sat, 03 Apr 2021 08:52:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:52:16: #2 number of paired peaks: 154 WARNING @ Sat, 03 Apr 2021 08:52:16: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Sat, 03 Apr 2021 08:52:16: start model_add_line... INFO @ Sat, 03 Apr 2021 08:52:16: start X-correlation... INFO @ Sat, 03 Apr 2021 08:52:16: end of X-cor INFO @ Sat, 03 Apr 2021 08:52:16: #2 finished! INFO @ Sat, 03 Apr 2021 08:52:16: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Apr 2021 08:52:16: #2 alternative fragment length(s) may be 11,29,59,89,109,146,170,193,220,245,294,341,367,374,421,487,527,563 bps INFO @ Sat, 03 Apr 2021 08:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.10_model.r WARNING @ Sat, 03 Apr 2021 08:52:16: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:52:16: #2 You may need to consider one of the other alternative d(s): 11,29,59,89,109,146,170,193,220,245,294,341,367,374,421,487,527,563 WARNING @ Sat, 03 Apr 2021 08:52:16: #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 08:52:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:52:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:52:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:52:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:52:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.10_summits.bed INFO @ Sat, 03 Apr 2021 08:52:16: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 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 08:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.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 08:52:46: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:52:46: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:52:46: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:52:46: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:52:46: #1 total tags in treatment: 5972 INFO @ Sat, 03 Apr 2021 08:52:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:52:46: #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 08:52:46: #1 tags after filtering in treatment: 5971 INFO @ Sat, 03 Apr 2021 08:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:52:46: #1 finished! INFO @ Sat, 03 Apr 2021 08:52:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:52:46: #2 number of paired peaks: 154 WARNING @ Sat, 03 Apr 2021 08:52:46: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Sat, 03 Apr 2021 08:52:46: start model_add_line... INFO @ Sat, 03 Apr 2021 08:52:46: start X-correlation... INFO @ Sat, 03 Apr 2021 08:52:46: end of X-cor INFO @ Sat, 03 Apr 2021 08:52:46: #2 finished! INFO @ Sat, 03 Apr 2021 08:52:46: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Apr 2021 08:52:46: #2 alternative fragment length(s) may be 11,29,59,89,109,146,170,193,220,245,294,341,367,374,421,487,527,563 bps INFO @ Sat, 03 Apr 2021 08:52:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.20_model.r WARNING @ Sat, 03 Apr 2021 08:52:46: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:52:46: #2 You may need to consider one of the other alternative d(s): 11,29,59,89,109,146,170,193,220,245,294,341,367,374,421,487,527,563 WARNING @ Sat, 03 Apr 2021 08:52:46: #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 08:52:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:52:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:52:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:52:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:52:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282724/SRX7282724.20_summits.bed INFO @ Sat, 03 Apr 2021 08:52:46: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling