Job ID = 14171144 SRX = SRX9555316 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1355299 spots for SRR13110451/SRR13110451.sra Written 1355299 spots for SRR13110451/SRR13110451.sra Read 1339570 spots for SRR13110452/SRR13110452.sra Written 1339570 spots for SRR13110452/SRR13110452.sra Read 1373415 spots for SRR13110453/SRR13110453.sra Written 1373415 spots for SRR13110453/SRR13110453.sra Read 1357626 spots for SRR13110454/SRR13110454.sra Written 1357626 spots for SRR13110454/SRR13110454.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171607 ("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: 00:00:51 5425910 reads; of these: 5425910 (100.00%) were paired; of these: 5205913 (95.95%) aligned concordantly 0 times 157784 (2.91%) aligned concordantly exactly 1 time 62213 (1.15%) aligned concordantly >1 times ---- 5205913 pairs aligned concordantly 0 times; of these: 518 (0.01%) aligned discordantly 1 time ---- 5205395 pairs aligned 0 times concordantly or discordantly; of these: 10410790 mates make up the pairs; of these: 10379763 (99.70%) aligned 0 times 11582 (0.11%) aligned exactly 1 time 19445 (0.19%) aligned >1 times 4.35% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 5088 / 220365 = 0.0231 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 @ Sat, 11 Dec 2021 10:07:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.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, 11 Dec 2021 10:07:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:07:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:07:40: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 10:07:40: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 10:07:40: #1 total tags in treatment: 214920 INFO @ Sat, 11 Dec 2021 10:07:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:07:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 10:07:40: #1 tags after filtering in treatment: 212465 INFO @ Sat, 11 Dec 2021 10:07:40: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 10:07:40: #1 finished! INFO @ Sat, 11 Dec 2021 10:07:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:07:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:07:40: #2 number of paired peaks: 756 WARNING @ Sat, 11 Dec 2021 10:07:40: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Sat, 11 Dec 2021 10:07:40: start model_add_line... INFO @ Sat, 11 Dec 2021 10:07:40: start X-correlation... INFO @ Sat, 11 Dec 2021 10:07:40: end of X-cor INFO @ Sat, 11 Dec 2021 10:07:40: #2 finished! INFO @ Sat, 11 Dec 2021 10:07:40: #2 predicted fragment length is 85 bps INFO @ Sat, 11 Dec 2021 10:07:40: #2 alternative fragment length(s) may be 85,152,231,277 bps INFO @ Sat, 11 Dec 2021 10:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.05_model.r INFO @ Sat, 11 Dec 2021 10:07:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:07:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:07:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:07:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.05_summits.bed INFO @ Sat, 11 Dec 2021 10:07:41: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (50 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 10:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.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, 11 Dec 2021 10:08:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:08:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:08:10: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 10:08:10: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 10:08:10: #1 total tags in treatment: 214920 INFO @ Sat, 11 Dec 2021 10:08:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:08:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 10:08:10: #1 tags after filtering in treatment: 212465 INFO @ Sat, 11 Dec 2021 10:08:10: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 10:08:10: #1 finished! INFO @ Sat, 11 Dec 2021 10:08:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:08:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:08:10: #2 number of paired peaks: 756 WARNING @ Sat, 11 Dec 2021 10:08:10: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Sat, 11 Dec 2021 10:08:10: start model_add_line... INFO @ Sat, 11 Dec 2021 10:08:10: start X-correlation... INFO @ Sat, 11 Dec 2021 10:08:10: end of X-cor INFO @ Sat, 11 Dec 2021 10:08:10: #2 finished! INFO @ Sat, 11 Dec 2021 10:08:10: #2 predicted fragment length is 85 bps INFO @ Sat, 11 Dec 2021 10:08:10: #2 alternative fragment length(s) may be 85,152,231,277 bps INFO @ Sat, 11 Dec 2021 10:08:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.10_model.r INFO @ Sat, 11 Dec 2021 10:08:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:08:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:08:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:08:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:08:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.10_summits.bed INFO @ Sat, 11 Dec 2021 10:08:11: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 10:08:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.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, 11 Dec 2021 10:08:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:08:38: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:08:40: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 10:08:40: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 10:08:40: #1 total tags in treatment: 214920 INFO @ Sat, 11 Dec 2021 10:08:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:08:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 10:08:40: #1 tags after filtering in treatment: 212465 INFO @ Sat, 11 Dec 2021 10:08:40: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 10:08:40: #1 finished! INFO @ Sat, 11 Dec 2021 10:08:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:08:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:08:40: #2 number of paired peaks: 756 WARNING @ Sat, 11 Dec 2021 10:08:40: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Sat, 11 Dec 2021 10:08:40: start model_add_line... INFO @ Sat, 11 Dec 2021 10:08:40: start X-correlation... INFO @ Sat, 11 Dec 2021 10:08:40: end of X-cor INFO @ Sat, 11 Dec 2021 10:08:40: #2 finished! INFO @ Sat, 11 Dec 2021 10:08:40: #2 predicted fragment length is 85 bps INFO @ Sat, 11 Dec 2021 10:08:40: #2 alternative fragment length(s) may be 85,152,231,277 bps INFO @ Sat, 11 Dec 2021 10:08:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.20_model.r INFO @ Sat, 11 Dec 2021 10:08:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:08:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:08:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:08:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:08:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:08:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555316/SRX9555316.20_summits.bed INFO @ Sat, 11 Dec 2021 10:08:41: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (29 records, 4 fields): 1 millis CompletedMACS2peakCalling