Job ID = 14172388 SRX = SRX9281776 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2965673 spots for SRR12813313/SRR12813313.sra Written 2965673 spots for SRR12813313/SRR12813313.sra Read 2965000 spots for SRR12813314/SRR12813314.sra Written 2965000 spots for SRR12813314/SRR12813314.sra Read 3065598 spots for SRR12813315/SRR12813315.sra Written 3065598 spots for SRR12813315/SRR12813315.sra Read 2888594 spots for SRR12813316/SRR12813316.sra Written 2888594 spots for SRR12813316/SRR12813316.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172832 ("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: 00:03:28 11884865 reads; of these: 11884865 (100.00%) were paired; of these: 11410667 (96.01%) aligned concordantly 0 times 347488 (2.92%) aligned concordantly exactly 1 time 126710 (1.07%) aligned concordantly >1 times ---- 11410667 pairs aligned concordantly 0 times; of these: 1079 (0.01%) aligned discordantly 1 time ---- 11409588 pairs aligned 0 times concordantly or discordantly; of these: 22819176 mates make up the pairs; of these: 22572793 (98.92%) aligned 0 times 62264 (0.27%) aligned exactly 1 time 184119 (0.81%) aligned >1 times 5.04% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 11029 / 474561 = 0.0232 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 15:20:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.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 15:20:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:20:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:20:17: 1000000 INFO @ Sat, 11 Dec 2021 15:20:18: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:20:18: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:20:18: #1 total tags in treatment: 463180 INFO @ Sat, 11 Dec 2021 15:20:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:20:18: #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 15:20:18: #1 tags after filtering in treatment: 457412 INFO @ Sat, 11 Dec 2021 15:20:18: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:20:18: #1 finished! INFO @ Sat, 11 Dec 2021 15:20:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:20:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:20:18: #2 number of paired peaks: 714 WARNING @ Sat, 11 Dec 2021 15:20:18: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Sat, 11 Dec 2021 15:20:18: start model_add_line... INFO @ Sat, 11 Dec 2021 15:20:18: start X-correlation... INFO @ Sat, 11 Dec 2021 15:20:18: end of X-cor INFO @ Sat, 11 Dec 2021 15:20:18: #2 finished! INFO @ Sat, 11 Dec 2021 15:20:18: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 15:20:18: #2 alternative fragment length(s) may be 96,592 bps INFO @ Sat, 11 Dec 2021 15:20:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.05_model.r INFO @ Sat, 11 Dec 2021 15:20:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:20:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:20:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:20:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:20:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.05_summits.bed INFO @ Sat, 11 Dec 2021 15:20:20: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (99 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 15:20:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.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 15:20:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:20:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:20:48: 1000000 INFO @ Sat, 11 Dec 2021 15:20:49: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:20:49: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:20:49: #1 total tags in treatment: 463180 INFO @ Sat, 11 Dec 2021 15:20:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:20:49: #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 15:20:49: #1 tags after filtering in treatment: 457412 INFO @ Sat, 11 Dec 2021 15:20:49: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:20:49: #1 finished! INFO @ Sat, 11 Dec 2021 15:20:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:20:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:20:49: #2 number of paired peaks: 714 WARNING @ Sat, 11 Dec 2021 15:20:49: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Sat, 11 Dec 2021 15:20:49: start model_add_line... INFO @ Sat, 11 Dec 2021 15:20:49: start X-correlation... INFO @ Sat, 11 Dec 2021 15:20:49: end of X-cor INFO @ Sat, 11 Dec 2021 15:20:49: #2 finished! INFO @ Sat, 11 Dec 2021 15:20:49: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 15:20:49: #2 alternative fragment length(s) may be 96,592 bps INFO @ Sat, 11 Dec 2021 15:20:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.10_model.r INFO @ Sat, 11 Dec 2021 15:20:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:20:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:20:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.10_summits.bed INFO @ Sat, 11 Dec 2021 15:20:50: Done! pass1 - making usageList (4 chroms): 2 millis pass2 - checking and writing primary data (47 records, 4 fields): 3 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 15:21:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.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 15:21:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:21:08: #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 15:21:19: 1000000 INFO @ Sat, 11 Dec 2021 15:21:20: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:21:20: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:21:20: #1 total tags in treatment: 463180 INFO @ Sat, 11 Dec 2021 15:21:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:21:20: #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 15:21:20: #1 tags after filtering in treatment: 457412 INFO @ Sat, 11 Dec 2021 15:21:20: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:21:20: #1 finished! INFO @ Sat, 11 Dec 2021 15:21:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:21:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:21:20: #2 number of paired peaks: 714 WARNING @ Sat, 11 Dec 2021 15:21:20: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Sat, 11 Dec 2021 15:21:20: start model_add_line... INFO @ Sat, 11 Dec 2021 15:21:20: start X-correlation... INFO @ Sat, 11 Dec 2021 15:21:20: end of X-cor INFO @ Sat, 11 Dec 2021 15:21:20: #2 finished! INFO @ Sat, 11 Dec 2021 15:21:20: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 15:21:20: #2 alternative fragment length(s) may be 96,592 bps INFO @ Sat, 11 Dec 2021 15:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.20_model.r INFO @ Sat, 11 Dec 2021 15:21:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:21:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:21:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:21:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:21:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281776/SRX9281776.20_summits.bed INFO @ Sat, 11 Dec 2021 15:21:22: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis CompletedMACS2peakCalling