Job ID = 12266281 SRX = SRX7282770 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17727 spots for SRR10603161/SRR10603161.sra Written 17727 spots for SRR10603161/SRR10603161.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266384 ("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 17727 reads; of these: 17727 (100.00%) were unpaired; of these: 2436 (13.74%) aligned 0 times 6051 (34.13%) aligned exactly 1 time 9240 (52.12%) aligned >1 times 86.26% 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] 10368 / 15291 = 0.6780 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 08:54:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.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 08:54:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:54:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:54:16: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:54:16: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:54:16: #1 total tags in treatment: 4923 INFO @ Sat, 03 Apr 2021 08:54:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:54:16: #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 08:54:16: #1 tags after filtering in treatment: 4922 INFO @ Sat, 03 Apr 2021 08:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:54:16: #1 finished! INFO @ Sat, 03 Apr 2021 08:54:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:54:16: #2 number of paired peaks: 117 WARNING @ Sat, 03 Apr 2021 08:54:16: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sat, 03 Apr 2021 08:54:16: start model_add_line... INFO @ Sat, 03 Apr 2021 08:54:16: start X-correlation... INFO @ Sat, 03 Apr 2021 08:54:16: end of X-cor INFO @ Sat, 03 Apr 2021 08:54:16: #2 finished! INFO @ Sat, 03 Apr 2021 08:54:16: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:54:16: #2 alternative fragment length(s) may be 9,26,55,68,98,116,131,146,174,201,231,256,282,339,365,390,422,475,504 bps INFO @ Sat, 03 Apr 2021 08:54:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.05_model.r WARNING @ Sat, 03 Apr 2021 08:54:16: #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 08:54:16: #2 You may need to consider one of the other alternative d(s): 9,26,55,68,98,116,131,146,174,201,231,256,282,339,365,390,422,475,504 WARNING @ Sat, 03 Apr 2021 08:54:16: #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 08:54:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:54:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:54:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:54:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:54:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.05_summits.bed INFO @ Sat, 03 Apr 2021 08:54:16: 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 08:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.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 08:54:46: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:54:46: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:54:46: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:54:46: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:54:46: #1 total tags in treatment: 4923 INFO @ Sat, 03 Apr 2021 08:54:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:54:46: #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 08:54:46: #1 tags after filtering in treatment: 4922 INFO @ Sat, 03 Apr 2021 08:54:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:54:46: #1 finished! INFO @ Sat, 03 Apr 2021 08:54:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:54:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:54:46: #2 number of paired peaks: 117 WARNING @ Sat, 03 Apr 2021 08:54:46: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sat, 03 Apr 2021 08:54:46: start model_add_line... INFO @ Sat, 03 Apr 2021 08:54:46: start X-correlation... INFO @ Sat, 03 Apr 2021 08:54:46: end of X-cor INFO @ Sat, 03 Apr 2021 08:54:46: #2 finished! INFO @ Sat, 03 Apr 2021 08:54:46: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:54:46: #2 alternative fragment length(s) may be 9,26,55,68,98,116,131,146,174,201,231,256,282,339,365,390,422,475,504 bps INFO @ Sat, 03 Apr 2021 08:54:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.10_model.r WARNING @ Sat, 03 Apr 2021 08:54:46: #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 08:54:46: #2 You may need to consider one of the other alternative d(s): 9,26,55,68,98,116,131,146,174,201,231,256,282,339,365,390,422,475,504 WARNING @ Sat, 03 Apr 2021 08:54:46: #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 08:54:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:54:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:54:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:54:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.10_summits.bed INFO @ Sat, 03 Apr 2021 08:54:46: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 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 08:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.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 08:55:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:55:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:55:16: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:55:16: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:55:16: #1 total tags in treatment: 4923 INFO @ Sat, 03 Apr 2021 08:55:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:55:16: #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 08:55:16: #1 tags after filtering in treatment: 4922 INFO @ Sat, 03 Apr 2021 08:55:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:55:16: #1 finished! INFO @ Sat, 03 Apr 2021 08:55:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:55:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:55:16: #2 number of paired peaks: 117 WARNING @ Sat, 03 Apr 2021 08:55:16: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Sat, 03 Apr 2021 08:55:16: start model_add_line... INFO @ Sat, 03 Apr 2021 08:55:16: start X-correlation... INFO @ Sat, 03 Apr 2021 08:55:16: end of X-cor INFO @ Sat, 03 Apr 2021 08:55:16: #2 finished! INFO @ Sat, 03 Apr 2021 08:55:16: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:55:16: #2 alternative fragment length(s) may be 9,26,55,68,98,116,131,146,174,201,231,256,282,339,365,390,422,475,504 bps INFO @ Sat, 03 Apr 2021 08:55:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.20_model.r WARNING @ Sat, 03 Apr 2021 08:55:16: #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 08:55:16: #2 You may need to consider one of the other alternative d(s): 9,26,55,68,98,116,131,146,174,201,231,256,282,339,365,390,422,475,504 WARNING @ Sat, 03 Apr 2021 08:55:16: #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 08:55:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:55:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:55:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:55:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:55:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:55:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282770/SRX7282770.20_summits.bed INFO @ Sat, 03 Apr 2021 08:55:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling