Job ID = 14172236 SRX = SRX9281744 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11513952 spots for SRR12813265/SRR12813265.sra Written 11513952 spots for SRR12813265/SRR12813265.sra Read 11499419 spots for SRR12813266/SRR12813266.sra Written 11499419 spots for SRR12813266/SRR12813266.sra Read 11670539 spots for SRR12813267/SRR12813267.sra Written 11670539 spots for SRR12813267/SRR12813267.sra Read 11444213 spots for SRR12813268/SRR12813268.sra Written 11444213 spots for SRR12813268/SRR12813268.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172787 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:57 46128123 reads; of these: 46128123 (100.00%) were paired; of these: 43513634 (94.33%) aligned concordantly 0 times 1949712 (4.23%) aligned concordantly exactly 1 time 664777 (1.44%) aligned concordantly >1 times ---- 43513634 pairs aligned concordantly 0 times; of these: 7813 (0.02%) aligned discordantly 1 time ---- 43505821 pairs aligned 0 times concordantly or discordantly; of these: 87011642 mates make up the pairs; of these: 86285189 (99.17%) aligned 0 times 294948 (0.34%) aligned exactly 1 time 431505 (0.50%) aligned >1 times 6.47% overall alignment rate Time searching: 00:12:58 Overall time: 00:12:58 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] 121864 / 2618061 = 0.0465 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 15:12:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.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 15:12:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:12:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:12:17: 1000000 INFO @ Sat, 11 Dec 2021 15:12:27: 2000000 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 15:12:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.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 15:12:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:12:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:12:38: 3000000 INFO @ Sat, 11 Dec 2021 15:12:46: 1000000 INFO @ Sat, 11 Dec 2021 15:12:47: 4000000 INFO @ Sat, 11 Dec 2021 15:12:56: 2000000 INFO @ Sat, 11 Dec 2021 15:12:57: 5000000 INFO @ Sat, 11 Dec 2021 15:13:04: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:13:04: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:13:04: #1 total tags in treatment: 2492755 INFO @ Sat, 11 Dec 2021 15:13:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:13:04: #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 15:13:04: #1 tags after filtering in treatment: 2383827 INFO @ Sat, 11 Dec 2021 15:13:04: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:13:04: #1 finished! INFO @ Sat, 11 Dec 2021 15:13:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:13:04: #2 number of paired peaks: 927 WARNING @ Sat, 11 Dec 2021 15:13:04: Fewer paired peaks (927) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 927 pairs to build model! INFO @ Sat, 11 Dec 2021 15:13:04: start model_add_line... INFO @ Sat, 11 Dec 2021 15:13:04: start X-correlation... INFO @ Sat, 11 Dec 2021 15:13:04: end of X-cor INFO @ Sat, 11 Dec 2021 15:13:04: #2 finished! INFO @ Sat, 11 Dec 2021 15:13:04: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 15:13:04: #2 alternative fragment length(s) may be 101,129,140 bps INFO @ Sat, 11 Dec 2021 15:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.05_model.r INFO @ Sat, 11 Dec 2021 15:13:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:13:04: #3 Pre-compute pvalue-qvalue table... 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 15:13:05: 3000000 INFO @ Sat, 11 Dec 2021 15:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.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 15:13:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:13:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:13:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:13:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:13:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:13:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.05_summits.bed INFO @ Sat, 11 Dec 2021 15:13:12: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (385 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:13:14: 4000000 INFO @ Sat, 11 Dec 2021 15:13:16: 1000000 INFO @ Sat, 11 Dec 2021 15:13:24: 5000000 INFO @ Sat, 11 Dec 2021 15:13:25: 2000000 INFO @ Sat, 11 Dec 2021 15:13:30: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:13:30: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:13:30: #1 total tags in treatment: 2492755 INFO @ Sat, 11 Dec 2021 15:13:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:13:30: #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 15:13:30: #1 tags after filtering in treatment: 2383827 INFO @ Sat, 11 Dec 2021 15:13:30: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:13:30: #1 finished! INFO @ Sat, 11 Dec 2021 15:13:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:13:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:13:31: #2 number of paired peaks: 927 WARNING @ Sat, 11 Dec 2021 15:13:31: Fewer paired peaks (927) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 927 pairs to build model! INFO @ Sat, 11 Dec 2021 15:13:31: start model_add_line... INFO @ Sat, 11 Dec 2021 15:13:31: start X-correlation... INFO @ Sat, 11 Dec 2021 15:13:31: end of X-cor INFO @ Sat, 11 Dec 2021 15:13:31: #2 finished! INFO @ Sat, 11 Dec 2021 15:13:31: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 15:13:31: #2 alternative fragment length(s) may be 101,129,140 bps INFO @ Sat, 11 Dec 2021 15:13:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.10_model.r INFO @ Sat, 11 Dec 2021 15:13:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:13:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:13:33: 3000000 INFO @ Sat, 11 Dec 2021 15:13:36: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:13:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:13:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:13:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.10_summits.bed INFO @ Sat, 11 Dec 2021 15:13:39: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (185 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:13:41: 4000000 INFO @ Sat, 11 Dec 2021 15:13:50: 5000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:13:56: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:13:56: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:13:56: #1 total tags in treatment: 2492755 INFO @ Sat, 11 Dec 2021 15:13:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:13:56: #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 15:13:56: #1 tags after filtering in treatment: 2383827 INFO @ Sat, 11 Dec 2021 15:13:56: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:13:56: #1 finished! INFO @ Sat, 11 Dec 2021 15:13:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:13:56: #2 number of paired peaks: 927 WARNING @ Sat, 11 Dec 2021 15:13:56: Fewer paired peaks (927) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 927 pairs to build model! INFO @ Sat, 11 Dec 2021 15:13:56: start model_add_line... INFO @ Sat, 11 Dec 2021 15:13:56: start X-correlation... INFO @ Sat, 11 Dec 2021 15:13:56: end of X-cor INFO @ Sat, 11 Dec 2021 15:13:56: #2 finished! INFO @ Sat, 11 Dec 2021 15:13:56: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 15:13:56: #2 alternative fragment length(s) may be 101,129,140 bps INFO @ Sat, 11 Dec 2021 15:13:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.20_model.r INFO @ Sat, 11 Dec 2021 15:13:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:13:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:14:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281744/SRX9281744.20_summits.bed INFO @ Sat, 11 Dec 2021 15:14:04: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (88 records, 4 fields): 2 millis CompletedMACS2peakCalling