Job ID = 14171431 SRX = SRX9555284 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3871966 spots for SRR13110707/SRR13110707.sra Written 3871966 spots for SRR13110707/SRR13110707.sra Read 3743379 spots for SRR13110708/SRR13110708.sra Written 3743379 spots for SRR13110708/SRR13110708.sra Read 3927777 spots for SRR13110709/SRR13110709.sra Written 3927777 spots for SRR13110709/SRR13110709.sra Read 3824969 spots for SRR13110710/SRR13110710.sra Written 3824969 spots for SRR13110710/SRR13110710.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171917 ("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: 00:02:58 15368091 reads; of these: 15368091 (100.00%) were paired; of these: 14969442 (97.41%) aligned concordantly 0 times 286493 (1.86%) aligned concordantly exactly 1 time 112156 (0.73%) aligned concordantly >1 times ---- 14969442 pairs aligned concordantly 0 times; of these: 2482 (0.02%) aligned discordantly 1 time ---- 14966960 pairs aligned 0 times concordantly or discordantly; of these: 29933920 mates make up the pairs; of these: 29400065 (98.22%) aligned 0 times 197693 (0.66%) aligned exactly 1 time 336162 (1.12%) aligned >1 times 4.35% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 9293 / 399142 = 0.0233 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 11:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.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 11:43:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:43:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:43:50: 1000000 INFO @ Sat, 11 Dec 2021 11:43:51: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:43:51: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:43:51: #1 total tags in treatment: 389366 INFO @ Sat, 11 Dec 2021 11:43:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:51: #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 11:43:51: #1 tags after filtering in treatment: 383824 INFO @ Sat, 11 Dec 2021 11:43:51: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:43:51: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:51: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 11:43:51: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 11:43:51: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:51: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:51: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:51: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:51: #2 predicted fragment length is 92 bps INFO @ Sat, 11 Dec 2021 11:43:51: #2 alternative fragment length(s) may be 92,566 bps INFO @ Sat, 11 Dec 2021 11:43:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.05_model.r INFO @ Sat, 11 Dec 2021 11:43:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.05_summits.bed INFO @ Sat, 11 Dec 2021 11:43:52: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (112 records, 4 fields): 1 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 11:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.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 11:44:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:44:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:44:19: 1000000 INFO @ Sat, 11 Dec 2021 11:44:20: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:44:20: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:44:20: #1 total tags in treatment: 389366 INFO @ Sat, 11 Dec 2021 11:44:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:44:20: #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 11:44:20: #1 tags after filtering in treatment: 383824 INFO @ Sat, 11 Dec 2021 11:44:20: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:44:20: #1 finished! INFO @ Sat, 11 Dec 2021 11:44:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:44:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:44:20: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 11:44:20: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 11:44:20: start model_add_line... INFO @ Sat, 11 Dec 2021 11:44:20: start X-correlation... INFO @ Sat, 11 Dec 2021 11:44:20: end of X-cor INFO @ Sat, 11 Dec 2021 11:44:20: #2 finished! INFO @ Sat, 11 Dec 2021 11:44:20: #2 predicted fragment length is 92 bps INFO @ Sat, 11 Dec 2021 11:44:20: #2 alternative fragment length(s) may be 92,566 bps INFO @ Sat, 11 Dec 2021 11:44:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.10_model.r INFO @ Sat, 11 Dec 2021 11:44:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:44:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:44:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:44:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:44:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:44:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.10_summits.bed INFO @ Sat, 11 Dec 2021 11:44:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (56 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 11:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.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 11:44:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:44:45: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:44:49: 1000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:44:51: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:44:51: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:44:51: #1 total tags in treatment: 389366 INFO @ Sat, 11 Dec 2021 11:44:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:44:51: #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 11:44:51: #1 tags after filtering in treatment: 383824 INFO @ Sat, 11 Dec 2021 11:44:51: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 11:44:51: #1 finished! INFO @ Sat, 11 Dec 2021 11:44:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:44:51: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 11:44:51: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 11:44:51: start model_add_line... INFO @ Sat, 11 Dec 2021 11:44:51: start X-correlation... INFO @ Sat, 11 Dec 2021 11:44:51: end of X-cor INFO @ Sat, 11 Dec 2021 11:44:51: #2 finished! INFO @ Sat, 11 Dec 2021 11:44:51: #2 predicted fragment length is 92 bps INFO @ Sat, 11 Dec 2021 11:44:51: #2 alternative fragment length(s) may be 92,566 bps INFO @ Sat, 11 Dec 2021 11:44:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.20_model.r INFO @ Sat, 11 Dec 2021 11:44:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:44:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:44:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:44:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:44:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:44:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555284/SRX9555284.20_summits.bed INFO @ Sat, 11 Dec 2021 11:44:52: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (35 records, 4 fields): 18 millis CompletedMACS2peakCalling