Job ID = 12265757 SRX = SRX7282540 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16264 spots for SRR10603123/SRR10603123.sra Written 16264 spots for SRR10603123/SRR10603123.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265875 ("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: 00:00:00 16264 reads; of these: 16264 (100.00%) were unpaired; of these: 2591 (15.93%) aligned 0 times 4425 (27.21%) aligned exactly 1 time 9248 (56.86%) aligned >1 times 84.07% 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] 9598 / 13673 = 0.7020 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 08:22:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.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 08:22:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:22:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:22:56: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:22:56: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:22:56: #1 total tags in treatment: 4075 INFO @ Sat, 03 Apr 2021 08:22:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:22:56: #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 08:22:56: #1 tags after filtering in treatment: 4073 INFO @ Sat, 03 Apr 2021 08:22:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:22:56: #1 finished! INFO @ Sat, 03 Apr 2021 08:22:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:22:56: #2 number of paired peaks: 105 WARNING @ Sat, 03 Apr 2021 08:22:56: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 03 Apr 2021 08:22:56: start model_add_line... INFO @ Sat, 03 Apr 2021 08:22:56: start X-correlation... INFO @ Sat, 03 Apr 2021 08:22:56: end of X-cor INFO @ Sat, 03 Apr 2021 08:22:56: #2 finished! INFO @ Sat, 03 Apr 2021 08:22:56: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:22:56: #2 alternative fragment length(s) may be 9,33,62,96,116,132,160,214,259,286,338,366,413,461,493,535,560 bps INFO @ Sat, 03 Apr 2021 08:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.05_model.r WARNING @ Sat, 03 Apr 2021 08:22:56: #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 08:22:56: #2 You may need to consider one of the other alternative d(s): 9,33,62,96,116,132,160,214,259,286,338,366,413,461,493,535,560 WARNING @ Sat, 03 Apr 2021 08:22:56: #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 08:22:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:22:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:22:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:22:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:22:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.05_summits.bed INFO @ Sat, 03 Apr 2021 08:22:56: 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 08:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.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 08:23:26: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:23:26: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:23:26: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:23:26: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:23:26: #1 total tags in treatment: 4075 INFO @ Sat, 03 Apr 2021 08:23:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:23:26: #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 08:23:26: #1 tags after filtering in treatment: 4073 INFO @ Sat, 03 Apr 2021 08:23:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:23:26: #1 finished! INFO @ Sat, 03 Apr 2021 08:23:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:23:26: #2 number of paired peaks: 105 WARNING @ Sat, 03 Apr 2021 08:23:26: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 03 Apr 2021 08:23:26: start model_add_line... INFO @ Sat, 03 Apr 2021 08:23:26: start X-correlation... INFO @ Sat, 03 Apr 2021 08:23:26: end of X-cor INFO @ Sat, 03 Apr 2021 08:23:26: #2 finished! INFO @ Sat, 03 Apr 2021 08:23:26: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:23:26: #2 alternative fragment length(s) may be 9,33,62,96,116,132,160,214,259,286,338,366,413,461,493,535,560 bps INFO @ Sat, 03 Apr 2021 08:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.10_model.r WARNING @ Sat, 03 Apr 2021 08:23:26: #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 08:23:26: #2 You may need to consider one of the other alternative d(s): 9,33,62,96,116,132,160,214,259,286,338,366,413,461,493,535,560 WARNING @ Sat, 03 Apr 2021 08:23:26: #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 08:23:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:23:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.10_summits.bed INFO @ Sat, 03 Apr 2021 08:23:26: Done! pass1 - making usageList (1 chroms): 0 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 08:23:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.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 08:23:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:23:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:23:56: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:23:56: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:23:56: #1 total tags in treatment: 4075 INFO @ Sat, 03 Apr 2021 08:23:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:23:56: #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 08:23:56: #1 tags after filtering in treatment: 4073 INFO @ Sat, 03 Apr 2021 08:23:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:23:56: #1 finished! INFO @ Sat, 03 Apr 2021 08:23:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:23:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:23:56: #2 number of paired peaks: 105 WARNING @ Sat, 03 Apr 2021 08:23:56: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 03 Apr 2021 08:23:56: start model_add_line... INFO @ Sat, 03 Apr 2021 08:23:56: start X-correlation... INFO @ Sat, 03 Apr 2021 08:23:56: end of X-cor INFO @ Sat, 03 Apr 2021 08:23:56: #2 finished! INFO @ Sat, 03 Apr 2021 08:23:56: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:23:56: #2 alternative fragment length(s) may be 9,33,62,96,116,132,160,214,259,286,338,366,413,461,493,535,560 bps INFO @ Sat, 03 Apr 2021 08:23:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.20_model.r WARNING @ Sat, 03 Apr 2021 08:23:56: #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 08:23:56: #2 You may need to consider one of the other alternative d(s): 9,33,62,96,116,132,160,214,259,286,338,366,413,461,493,535,560 WARNING @ Sat, 03 Apr 2021 08:23:56: #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 08:23:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:23:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:23:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282540/SRX7282540.20_summits.bed INFO @ Sat, 03 Apr 2021 08:23:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling