Job ID = 12264922 SRX = SRX3088373 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15126 spots for SRR5928051/SRR5928051.sra Written 15126 spots for SRR5928051/SRR5928051.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265057 ("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 15126 reads; of these: 15126 (100.00%) were unpaired; of these: 7627 (50.42%) aligned 0 times 6083 (40.22%) aligned exactly 1 time 1416 (9.36%) aligned >1 times 49.58% 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] 2238 / 7499 = 0.2984 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 05:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.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 05:59:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:59:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 05:59:31: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 05:59:31: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 05:59:31: #1 total tags in treatment: 5261 INFO @ Sat, 03 Apr 2021 05:59:31: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 05:59:31: #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 05:59:31: #1 tags after filtering in treatment: 5259 INFO @ Sat, 03 Apr 2021 05:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 05:59:31: #1 finished! INFO @ Sat, 03 Apr 2021 05:59:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 05:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 05:59:31: #2 number of paired peaks: 164 WARNING @ Sat, 03 Apr 2021 05:59:31: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 03 Apr 2021 05:59:31: start model_add_line... INFO @ Sat, 03 Apr 2021 05:59:31: start X-correlation... INFO @ Sat, 03 Apr 2021 05:59:31: end of X-cor INFO @ Sat, 03 Apr 2021 05:59:31: #2 finished! INFO @ Sat, 03 Apr 2021 05:59:31: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 05:59:31: #2 alternative fragment length(s) may be 9,41,78,104,135,162,208,217,253,291,366,414,445,490,530,583 bps INFO @ Sat, 03 Apr 2021 05:59:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.05_model.r WARNING @ Sat, 03 Apr 2021 05:59:31: #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 05:59:31: #2 You may need to consider one of the other alternative d(s): 9,41,78,104,135,162,208,217,253,291,366,414,445,490,530,583 WARNING @ Sat, 03 Apr 2021 05:59:31: #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 05:59:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 05:59:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 05:59:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 05:59:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.05_peaks.xls INFO @ Sat, 03 Apr 2021 05:59:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 05:59:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.05_summits.bed INFO @ Sat, 03 Apr 2021 05:59:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) 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 06:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.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 06:00:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:01: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:00:01: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:00:01: #1 total tags in treatment: 5261 INFO @ Sat, 03 Apr 2021 06:00:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:01: #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 06:00:01: #1 tags after filtering in treatment: 5259 INFO @ Sat, 03 Apr 2021 06:00:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:01: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:00:01: #2 number of paired peaks: 164 WARNING @ Sat, 03 Apr 2021 06:00:01: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 03 Apr 2021 06:00:01: start model_add_line... INFO @ Sat, 03 Apr 2021 06:00:01: start X-correlation... INFO @ Sat, 03 Apr 2021 06:00:01: end of X-cor INFO @ Sat, 03 Apr 2021 06:00:01: #2 finished! INFO @ Sat, 03 Apr 2021 06:00:01: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 06:00:01: #2 alternative fragment length(s) may be 9,41,78,104,135,162,208,217,253,291,366,414,445,490,530,583 bps INFO @ Sat, 03 Apr 2021 06:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.10_model.r WARNING @ Sat, 03 Apr 2021 06:00:01: #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 06:00:01: #2 You may need to consider one of the other alternative d(s): 9,41,78,104,135,162,208,217,253,291,366,414,445,490,530,583 WARNING @ Sat, 03 Apr 2021 06:00:01: #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 06:00:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:00:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:00:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:00:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.10_summits.bed INFO @ Sat, 03 Apr 2021 06:00:01: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) 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 06:00:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.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 06:00:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:31: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:00:31: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:00:31: #1 total tags in treatment: 5261 INFO @ Sat, 03 Apr 2021 06:00:31: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:31: #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 06:00:31: #1 tags after filtering in treatment: 5259 INFO @ Sat, 03 Apr 2021 06:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:31: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:00:31: #2 number of paired peaks: 164 WARNING @ Sat, 03 Apr 2021 06:00:31: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 03 Apr 2021 06:00:31: start model_add_line... INFO @ Sat, 03 Apr 2021 06:00:31: start X-correlation... INFO @ Sat, 03 Apr 2021 06:00:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:00:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:00:31: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 06:00:31: #2 alternative fragment length(s) may be 9,41,78,104,135,162,208,217,253,291,366,414,445,490,530,583 bps INFO @ Sat, 03 Apr 2021 06:00:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.20_model.r WARNING @ Sat, 03 Apr 2021 06:00:31: #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 06:00:31: #2 You may need to consider one of the other alternative d(s): 9,41,78,104,135,162,208,217,253,291,366,414,445,490,530,583 WARNING @ Sat, 03 Apr 2021 06:00:31: #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 06:00:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:00:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:00:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:00:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:00:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088373/SRX3088373.20_summits.bed INFO @ Sat, 03 Apr 2021 06:00:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling