Job ID = 14167208 SRX = SRX6407576 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8024682 spots for SRR9645767/SRR9645767.sra Written 8024682 spots for SRR9645767/SRR9645767.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167753 ("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: 00:03:36 8024682 reads; of these: 8024682 (100.00%) were unpaired; of these: 415547 (5.18%) aligned 0 times 6061038 (75.53%) aligned exactly 1 time 1548097 (19.29%) aligned >1 times 94.82% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:37 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] 622567 / 7609135 = 0.0818 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:09:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.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 @ Fri, 10 Dec 2021 11:09:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:09:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:09:25: 1000000 INFO @ Fri, 10 Dec 2021 11:09:31: 2000000 INFO @ Fri, 10 Dec 2021 11:09:37: 3000000 INFO @ Fri, 10 Dec 2021 11:09:43: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.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 @ Fri, 10 Dec 2021 11:09:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:09:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:09:49: 5000000 INFO @ Fri, 10 Dec 2021 11:09:56: 6000000 INFO @ Fri, 10 Dec 2021 11:09:56: 1000000 INFO @ Fri, 10 Dec 2021 11:10:03: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 11:10:03: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 11:10:03: #1 total tags in treatment: 6986568 INFO @ Fri, 10 Dec 2021 11:10:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:10:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:10:03: #1 tags after filtering in treatment: 6986568 INFO @ Fri, 10 Dec 2021 11:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:10:03: #1 finished! INFO @ Fri, 10 Dec 2021 11:10:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:10:04: #2 number of paired peaks: 604 WARNING @ Fri, 10 Dec 2021 11:10:04: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Fri, 10 Dec 2021 11:10:04: start model_add_line... INFO @ Fri, 10 Dec 2021 11:10:04: start X-correlation... INFO @ Fri, 10 Dec 2021 11:10:04: end of X-cor INFO @ Fri, 10 Dec 2021 11:10:04: #2 finished! INFO @ Fri, 10 Dec 2021 11:10:04: #2 predicted fragment length is 171 bps INFO @ Fri, 10 Dec 2021 11:10:04: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 10 Dec 2021 11:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.05_model.r WARNING @ Fri, 10 Dec 2021 11:10:04: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:10:04: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Fri, 10 Dec 2021 11:10:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:10:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:10:04: 2000000 INFO @ Fri, 10 Dec 2021 11:10:11: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.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 @ Fri, 10 Dec 2021 11:10:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:10:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:10:19: 4000000 INFO @ Fri, 10 Dec 2021 11:10:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:10:25: 1000000 INFO @ Fri, 10 Dec 2021 11:10:26: 5000000 INFO @ Fri, 10 Dec 2021 11:10:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:10:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:10:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.05_summits.bed INFO @ Fri, 10 Dec 2021 11:10:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1347 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:10:32: 2000000 INFO @ Fri, 10 Dec 2021 11:10:34: 6000000 INFO @ Fri, 10 Dec 2021 11:10:39: 3000000 INFO @ Fri, 10 Dec 2021 11:10:42: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 11:10:42: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 11:10:42: #1 total tags in treatment: 6986568 INFO @ Fri, 10 Dec 2021 11:10:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:10:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:10:42: #1 tags after filtering in treatment: 6986568 INFO @ Fri, 10 Dec 2021 11:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:10:42: #1 finished! INFO @ Fri, 10 Dec 2021 11:10:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:10:42: #2 number of paired peaks: 604 WARNING @ Fri, 10 Dec 2021 11:10:42: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Fri, 10 Dec 2021 11:10:42: start model_add_line... INFO @ Fri, 10 Dec 2021 11:10:42: start X-correlation... INFO @ Fri, 10 Dec 2021 11:10:42: end of X-cor INFO @ Fri, 10 Dec 2021 11:10:42: #2 finished! INFO @ Fri, 10 Dec 2021 11:10:42: #2 predicted fragment length is 171 bps INFO @ Fri, 10 Dec 2021 11:10:42: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 10 Dec 2021 11:10:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.10_model.r WARNING @ Fri, 10 Dec 2021 11:10:42: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:10:42: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Fri, 10 Dec 2021 11:10:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:10:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:10:46: 4000000 INFO @ Fri, 10 Dec 2021 11:10:52: 5000000 INFO @ Fri, 10 Dec 2021 11:10:57: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:10:59: 6000000 INFO @ Fri, 10 Dec 2021 11:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.10_summits.bed INFO @ Fri, 10 Dec 2021 11:11:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (658 records, 4 fields): 71 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:11:05: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 11:11:05: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 11:11:05: #1 total tags in treatment: 6986568 INFO @ Fri, 10 Dec 2021 11:11:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:11:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:11:05: #1 tags after filtering in treatment: 6986568 INFO @ Fri, 10 Dec 2021 11:11:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:11:05: #1 finished! INFO @ Fri, 10 Dec 2021 11:11:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:11:06: #2 number of paired peaks: 604 WARNING @ Fri, 10 Dec 2021 11:11:06: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Fri, 10 Dec 2021 11:11:06: start model_add_line... INFO @ Fri, 10 Dec 2021 11:11:06: start X-correlation... INFO @ Fri, 10 Dec 2021 11:11:06: end of X-cor INFO @ Fri, 10 Dec 2021 11:11:06: #2 finished! INFO @ Fri, 10 Dec 2021 11:11:06: #2 predicted fragment length is 171 bps INFO @ Fri, 10 Dec 2021 11:11:06: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 10 Dec 2021 11:11:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.20_model.r WARNING @ Fri, 10 Dec 2021 11:11:06: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:11:06: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Fri, 10 Dec 2021 11:11:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:11:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:11:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:11:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:11:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:11:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:11:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6407576/SRX6407576.20_summits.bed INFO @ Fri, 10 Dec 2021 11:11:29: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (344 records, 4 fields): 2 millis CompletedMACS2peakCalling