Job ID = 12265743 SRX = SRX7282529 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21048 spots for SRR10603056/SRR10603056.sra Written 21048 spots for SRR10603056/SRR10603056.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265860 ("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 21048 reads; of these: 21048 (100.00%) were unpaired; of these: 2206 (10.48%) aligned 0 times 7929 (37.67%) aligned exactly 1 time 10913 (51.85%) aligned >1 times 89.52% 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] 11503 / 18842 = 0.6105 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 08:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.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 08:21:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:21:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:21:36: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:21:36: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:21:36: #1 total tags in treatment: 7339 INFO @ Sat, 03 Apr 2021 08:21:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:21:36: #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 08:21:36: #1 tags after filtering in treatment: 7336 INFO @ Sat, 03 Apr 2021 08:21:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:21:36: #1 finished! INFO @ Sat, 03 Apr 2021 08:21:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:21:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:21:36: #2 number of paired peaks: 178 WARNING @ Sat, 03 Apr 2021 08:21:36: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 03 Apr 2021 08:21:36: start model_add_line... INFO @ Sat, 03 Apr 2021 08:21:36: start X-correlation... INFO @ Sat, 03 Apr 2021 08:21:36: end of X-cor INFO @ Sat, 03 Apr 2021 08:21:36: #2 finished! INFO @ Sat, 03 Apr 2021 08:21:36: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:21:36: #2 alternative fragment length(s) may be 9,56,85,128,154,192,224,263,293,401,490 bps INFO @ Sat, 03 Apr 2021 08:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.05_model.r WARNING @ Sat, 03 Apr 2021 08:21:36: #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 08:21:36: #2 You may need to consider one of the other alternative d(s): 9,56,85,128,154,192,224,263,293,401,490 WARNING @ Sat, 03 Apr 2021 08:21:36: #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 08:21:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:21:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.05_summits.bed INFO @ Sat, 03 Apr 2021 08:21:36: 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 08:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.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 08:22:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:22:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:22:06: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:22:06: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:22:06: #1 total tags in treatment: 7339 INFO @ Sat, 03 Apr 2021 08:22:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:22:06: #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 08:22:06: #1 tags after filtering in treatment: 7336 INFO @ Sat, 03 Apr 2021 08:22:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:22:06: #1 finished! INFO @ Sat, 03 Apr 2021 08:22:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:22:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:22:06: #2 number of paired peaks: 178 WARNING @ Sat, 03 Apr 2021 08:22:06: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 03 Apr 2021 08:22:06: start model_add_line... INFO @ Sat, 03 Apr 2021 08:22:06: start X-correlation... INFO @ Sat, 03 Apr 2021 08:22:06: end of X-cor INFO @ Sat, 03 Apr 2021 08:22:06: #2 finished! INFO @ Sat, 03 Apr 2021 08:22:06: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:22:06: #2 alternative fragment length(s) may be 9,56,85,128,154,192,224,263,293,401,490 bps INFO @ Sat, 03 Apr 2021 08:22:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.10_model.r WARNING @ Sat, 03 Apr 2021 08:22:06: #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 08:22:06: #2 You may need to consider one of the other alternative d(s): 9,56,85,128,154,192,224,263,293,401,490 WARNING @ Sat, 03 Apr 2021 08:22:06: #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 08:22:06: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:22:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:22:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:22:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:22:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:22:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.10_summits.bed INFO @ Sat, 03 Apr 2021 08:22:06: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 0 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 08:22:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.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 08:22:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:22:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:22:36: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:22:36: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:22:36: #1 total tags in treatment: 7339 INFO @ Sat, 03 Apr 2021 08:22:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:22:36: #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 08:22:36: #1 tags after filtering in treatment: 7336 INFO @ Sat, 03 Apr 2021 08:22:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:22:36: #1 finished! INFO @ Sat, 03 Apr 2021 08:22:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:22:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:22:36: #2 number of paired peaks: 178 WARNING @ Sat, 03 Apr 2021 08:22:36: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 03 Apr 2021 08:22:36: start model_add_line... INFO @ Sat, 03 Apr 2021 08:22:36: start X-correlation... INFO @ Sat, 03 Apr 2021 08:22:36: end of X-cor INFO @ Sat, 03 Apr 2021 08:22:36: #2 finished! INFO @ Sat, 03 Apr 2021 08:22:36: #2 predicted fragment length is 9 bps INFO @ Sat, 03 Apr 2021 08:22:36: #2 alternative fragment length(s) may be 9,56,85,128,154,192,224,263,293,401,490 bps INFO @ Sat, 03 Apr 2021 08:22:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.20_model.r WARNING @ Sat, 03 Apr 2021 08:22:36: #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 08:22:36: #2 You may need to consider one of the other alternative d(s): 9,56,85,128,154,192,224,263,293,401,490 WARNING @ Sat, 03 Apr 2021 08:22:36: #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 08:22:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:22:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:22:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:22:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:22:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:22:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282529/SRX7282529.20_summits.bed INFO @ Sat, 03 Apr 2021 08:22:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling