Job ID = 6626491 SRX = SRX5736471 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4164073 spots for SRR8956882/SRR8956882.sra Written 4164073 spots for SRR8956882/SRR8956882.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626622 ("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: 00:08:37 4164073 reads; of these: 4164073 (100.00%) were paired; of these: 972751 (23.36%) aligned concordantly 0 times 2417192 (58.05%) aligned concordantly exactly 1 time 774130 (18.59%) aligned concordantly >1 times ---- 972751 pairs aligned concordantly 0 times; of these: 56792 (5.84%) aligned discordantly 1 time ---- 915959 pairs aligned 0 times concordantly or discordantly; of these: 1831918 mates make up the pairs; of these: 1597584 (87.21%) aligned 0 times 85416 (4.66%) aligned exactly 1 time 148918 (8.13%) aligned >1 times 80.82% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 509220 / 3237310 = 0.1573 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:18:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.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 @ Tue, 14 Jul 2020 07:18:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:18:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:18:59: 1000000 INFO @ Tue, 14 Jul 2020 07:19:05: 2000000 INFO @ Tue, 14 Jul 2020 07:19:10: 3000000 INFO @ Tue, 14 Jul 2020 07:19:15: 4000000 INFO @ Tue, 14 Jul 2020 07:19:20: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:19:23: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:19:23: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:19:23: #1 total tags in treatment: 2686674 INFO @ Tue, 14 Jul 2020 07:19:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:19:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:19:23: #1 tags after filtering in treatment: 2570112 INFO @ Tue, 14 Jul 2020 07:19:23: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 07:19:23: #1 finished! INFO @ Tue, 14 Jul 2020 07:19:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:19:24: #2 number of paired peaks: 521 WARNING @ Tue, 14 Jul 2020 07:19:24: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Tue, 14 Jul 2020 07:19:24: start model_add_line... INFO @ Tue, 14 Jul 2020 07:19:24: start X-correlation... INFO @ Tue, 14 Jul 2020 07:19:24: end of X-cor INFO @ Tue, 14 Jul 2020 07:19:24: #2 finished! INFO @ Tue, 14 Jul 2020 07:19:24: #2 predicted fragment length is 192 bps INFO @ Tue, 14 Jul 2020 07:19:24: #2 alternative fragment length(s) may be 192 bps INFO @ Tue, 14 Jul 2020 07:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.05_model.r INFO @ Tue, 14 Jul 2020 07:19:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:19:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.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 @ Tue, 14 Jul 2020 07:19:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:19:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:19:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:19:29: 1000000 INFO @ Tue, 14 Jul 2020 07:19:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:19:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:19:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.05_summits.bed INFO @ Tue, 14 Jul 2020 07:19:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1810 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:19:34: 2000000 INFO @ Tue, 14 Jul 2020 07:19:39: 3000000 INFO @ Tue, 14 Jul 2020 07:19:44: 4000000 INFO @ Tue, 14 Jul 2020 07:19:49: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:19:53: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:19:53: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:19:53: #1 total tags in treatment: 2686674 INFO @ Tue, 14 Jul 2020 07:19:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:19:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:19:53: #1 tags after filtering in treatment: 2570112 INFO @ Tue, 14 Jul 2020 07:19:53: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 07:19:53: #1 finished! INFO @ Tue, 14 Jul 2020 07:19:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:19:53: #2 number of paired peaks: 521 WARNING @ Tue, 14 Jul 2020 07:19:53: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Tue, 14 Jul 2020 07:19:53: start model_add_line... INFO @ Tue, 14 Jul 2020 07:19:53: start X-correlation... INFO @ Tue, 14 Jul 2020 07:19:53: end of X-cor INFO @ Tue, 14 Jul 2020 07:19:53: #2 finished! INFO @ Tue, 14 Jul 2020 07:19:53: #2 predicted fragment length is 192 bps INFO @ Tue, 14 Jul 2020 07:19:53: #2 alternative fragment length(s) may be 192 bps INFO @ Tue, 14 Jul 2020 07:19:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.10_model.r INFO @ Tue, 14 Jul 2020 07:19:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:19:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:19:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.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 @ Tue, 14 Jul 2020 07:19:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:19:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:19:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:19:59: 1000000 INFO @ Tue, 14 Jul 2020 07:20:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:20:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:20:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.10_summits.bed INFO @ Tue, 14 Jul 2020 07:20:01: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (559 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:20:04: 2000000 INFO @ Tue, 14 Jul 2020 07:20:09: 3000000 INFO @ Tue, 14 Jul 2020 07:20:14: 4000000 INFO @ Tue, 14 Jul 2020 07:20:20: 5000000 INFO @ Tue, 14 Jul 2020 07:20:23: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:20:23: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:20:23: #1 total tags in treatment: 2686674 INFO @ Tue, 14 Jul 2020 07:20:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:20:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:20:23: #1 tags after filtering in treatment: 2570112 INFO @ Tue, 14 Jul 2020 07:20:23: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 07:20:23: #1 finished! INFO @ Tue, 14 Jul 2020 07:20:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:20:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:20:23: #2 number of paired peaks: 521 WARNING @ Tue, 14 Jul 2020 07:20:23: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Tue, 14 Jul 2020 07:20:23: start model_add_line... INFO @ Tue, 14 Jul 2020 07:20:23: start X-correlation... INFO @ Tue, 14 Jul 2020 07:20:23: end of X-cor INFO @ Tue, 14 Jul 2020 07:20:23: #2 finished! INFO @ Tue, 14 Jul 2020 07:20:23: #2 predicted fragment length is 192 bps INFO @ Tue, 14 Jul 2020 07:20:23: #2 alternative fragment length(s) may be 192 bps INFO @ Tue, 14 Jul 2020 07:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.20_model.r INFO @ Tue, 14 Jul 2020 07:20:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:20:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:20:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:20:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:20:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736471/SRX5736471.20_summits.bed INFO @ Tue, 14 Jul 2020 07:20:32: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (121 records, 4 fields): 41 millis CompletedMACS2peakCalling BigWig に変換しました。