Job ID = 14172313 SRX = SRX9281763 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2506548 spots for SRR12813531/SRR12813531.sra Written 2506548 spots for SRR12813531/SRR12813531.sra Read 2458095 spots for SRR12813532/SRR12813532.sra Written 2458095 spots for SRR12813532/SRR12813532.sra Read 2566033 spots for SRR12813533/SRR12813533.sra Written 2566033 spots for SRR12813533/SRR12813533.sra Read 2512805 spots for SRR12813534/SRR12813534.sra Written 2512805 spots for SRR12813534/SRR12813534.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172780 ("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: 00:02:40 10043481 reads; of these: 10043481 (100.00%) were paired; of these: 9734871 (96.93%) aligned concordantly 0 times 221918 (2.21%) aligned concordantly exactly 1 time 86692 (0.86%) aligned concordantly >1 times ---- 9734871 pairs aligned concordantly 0 times; of these: 1030 (0.01%) aligned discordantly 1 time ---- 9733841 pairs aligned 0 times concordantly or discordantly; of these: 19467682 mates make up the pairs; of these: 19309119 (99.19%) aligned 0 times 37941 (0.19%) aligned exactly 1 time 120622 (0.62%) aligned >1 times 3.87% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 7084 / 309225 = 0.0229 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 15:10:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.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 15:10:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:10:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:10:18: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:10:18: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:10:18: #1 total tags in treatment: 301535 INFO @ Sat, 11 Dec 2021 15:10:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:10:18: #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 15:10:18: #1 tags after filtering in treatment: 297518 INFO @ Sat, 11 Dec 2021 15:10:18: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:10:18: #1 finished! INFO @ Sat, 11 Dec 2021 15:10:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:10:18: #2 number of paired peaks: 784 WARNING @ Sat, 11 Dec 2021 15:10:18: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Sat, 11 Dec 2021 15:10:18: start model_add_line... INFO @ Sat, 11 Dec 2021 15:10:18: start X-correlation... INFO @ Sat, 11 Dec 2021 15:10:18: end of X-cor INFO @ Sat, 11 Dec 2021 15:10:18: #2 finished! INFO @ Sat, 11 Dec 2021 15:10:18: #2 predicted fragment length is 104 bps INFO @ Sat, 11 Dec 2021 15:10:18: #2 alternative fragment length(s) may be 104,263 bps INFO @ Sat, 11 Dec 2021 15:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.05_model.r INFO @ Sat, 11 Dec 2021 15:10:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:10:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:10:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.05_summits.bed INFO @ Sat, 11 Dec 2021 15:10:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (77 records, 4 fields): 3 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 15:10:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.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 15:10:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:10:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:10:48: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:10:48: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:10:48: #1 total tags in treatment: 301535 INFO @ Sat, 11 Dec 2021 15:10:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:10:48: #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 15:10:48: #1 tags after filtering in treatment: 297518 INFO @ Sat, 11 Dec 2021 15:10:48: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:10:48: #1 finished! INFO @ Sat, 11 Dec 2021 15:10:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:10:48: #2 number of paired peaks: 784 WARNING @ Sat, 11 Dec 2021 15:10:48: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Sat, 11 Dec 2021 15:10:48: start model_add_line... INFO @ Sat, 11 Dec 2021 15:10:48: start X-correlation... INFO @ Sat, 11 Dec 2021 15:10:48: end of X-cor INFO @ Sat, 11 Dec 2021 15:10:48: #2 finished! INFO @ Sat, 11 Dec 2021 15:10:48: #2 predicted fragment length is 104 bps INFO @ Sat, 11 Dec 2021 15:10:48: #2 alternative fragment length(s) may be 104,263 bps INFO @ Sat, 11 Dec 2021 15:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.10_model.r INFO @ Sat, 11 Dec 2021 15:10:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:10:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.10_summits.bed INFO @ Sat, 11 Dec 2021 15:10:49: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (42 records, 4 fields): 2 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 15:11:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.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 15:11:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:11:14: #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 15:11:18: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:11:18: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:11:18: #1 total tags in treatment: 301535 INFO @ Sat, 11 Dec 2021 15:11:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:11:18: #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 15:11:18: #1 tags after filtering in treatment: 297518 INFO @ Sat, 11 Dec 2021 15:11:18: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:11:18: #1 finished! INFO @ Sat, 11 Dec 2021 15:11:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:11:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:11:18: #2 number of paired peaks: 784 WARNING @ Sat, 11 Dec 2021 15:11:18: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Sat, 11 Dec 2021 15:11:18: start model_add_line... INFO @ Sat, 11 Dec 2021 15:11:18: start X-correlation... INFO @ Sat, 11 Dec 2021 15:11:18: end of X-cor INFO @ Sat, 11 Dec 2021 15:11:18: #2 finished! INFO @ Sat, 11 Dec 2021 15:11:18: #2 predicted fragment length is 104 bps INFO @ Sat, 11 Dec 2021 15:11:18: #2 alternative fragment length(s) may be 104,263 bps INFO @ Sat, 11 Dec 2021 15:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.20_model.r INFO @ Sat, 11 Dec 2021 15:11:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:11:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:11:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:11:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:11:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281763/SRX9281763.20_summits.bed INFO @ Sat, 11 Dec 2021 15:11:20: Done! pass1 - making usageList (3 chroms): 2 millis pass2 - checking and writing primary data (34 records, 4 fields): 1 millis CompletedMACS2peakCalling