Job ID = 12264987 SRX = SRX3088431 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12266 spots for SRR5928109/SRR5928109.sra Written 12266 spots for SRR5928109/SRR5928109.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265146 ("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: 00:00:00 12266 reads; of these: 12266 (100.00%) were unpaired; of these: 5070 (41.33%) aligned 0 times 5558 (45.31%) aligned exactly 1 time 1638 (13.35%) aligned >1 times 58.67% overall alignment rate Time searching: 00:00:00 Overall time: 00:00:00 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] 2011 / 7196 = 0.2795 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 06:03:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.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 06:03:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:03:59: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:03:59: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:03:59: #1 total tags in treatment: 5185 INFO @ Sat, 03 Apr 2021 06:03:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:59: #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 06:03:59: #1 tags after filtering in treatment: 5185 INFO @ Sat, 03 Apr 2021 06:03:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:59: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:59: #2 number of paired peaks: 198 WARNING @ Sat, 03 Apr 2021 06:03:59: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Sat, 03 Apr 2021 06:03:59: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:59: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:59: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:59: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:59: #2 predicted fragment length is 10 bps INFO @ Sat, 03 Apr 2021 06:03:59: #2 alternative fragment length(s) may be 10,36,52,69,87,109,131,152,167,187,209,212,220,266,288,363,522 bps INFO @ Sat, 03 Apr 2021 06:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.05_model.r WARNING @ Sat, 03 Apr 2021 06:03:59: #2 Since the d (10) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:03:59: #2 You may need to consider one of the other alternative d(s): 10,36,52,69,87,109,131,152,167,187,209,212,220,266,288,363,522 WARNING @ Sat, 03 Apr 2021 06:03:59: #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 06:03:59: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:03:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:03:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:03:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:03:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.05_summits.bed INFO @ Sat, 03 Apr 2021 06:03:59: 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 06:04:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.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 06:04:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:04:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:04:29: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:04:29: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:04:29: #1 total tags in treatment: 5185 INFO @ Sat, 03 Apr 2021 06:04:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:29: #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 06:04:29: #1 tags after filtering in treatment: 5185 INFO @ Sat, 03 Apr 2021 06:04:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:29: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:29: #2 number of paired peaks: 198 WARNING @ Sat, 03 Apr 2021 06:04:29: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Sat, 03 Apr 2021 06:04:29: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:29: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:29: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:29: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:29: #2 predicted fragment length is 10 bps INFO @ Sat, 03 Apr 2021 06:04:29: #2 alternative fragment length(s) may be 10,36,52,69,87,109,131,152,167,187,209,212,220,266,288,363,522 bps INFO @ Sat, 03 Apr 2021 06:04:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.10_model.r WARNING @ Sat, 03 Apr 2021 06:04:29: #2 Since the d (10) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:29: #2 You may need to consider one of the other alternative d(s): 10,36,52,69,87,109,131,152,167,187,209,212,220,266,288,363,522 WARNING @ Sat, 03 Apr 2021 06:04:29: #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 06:04:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:04:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.10_summits.bed INFO @ Sat, 03 Apr 2021 06:04:29: Done! pass1 - making usageList (0 chroms): 1 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 06:04:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.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 06:04:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:04:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:04:59: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:04:59: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:04:59: #1 total tags in treatment: 5185 INFO @ Sat, 03 Apr 2021 06:04:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:59: #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 06:04:59: #1 tags after filtering in treatment: 5185 INFO @ Sat, 03 Apr 2021 06:04:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:59: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:59: #2 number of paired peaks: 198 WARNING @ Sat, 03 Apr 2021 06:04:59: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Sat, 03 Apr 2021 06:04:59: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:59: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:59: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:59: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:59: #2 predicted fragment length is 10 bps INFO @ Sat, 03 Apr 2021 06:04:59: #2 alternative fragment length(s) may be 10,36,52,69,87,109,131,152,167,187,209,212,220,266,288,363,522 bps INFO @ Sat, 03 Apr 2021 06:04:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.20_model.r WARNING @ Sat, 03 Apr 2021 06:04:59: #2 Since the d (10) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:59: #2 You may need to consider one of the other alternative d(s): 10,36,52,69,87,109,131,152,167,187,209,212,220,266,288,363,522 WARNING @ Sat, 03 Apr 2021 06:04:59: #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 06:04:59: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:04:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088431/SRX3088431.20_summits.bed INFO @ Sat, 03 Apr 2021 06:04:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling