Job ID = 14171389 SRX = SRX9555263 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8618545 spots for SRR13110406/SRR13110406.sra Written 8618545 spots for SRR13110406/SRR13110406.sra Read 8670422 spots for SRR13110407/SRR13110407.sra Written 8670422 spots for SRR13110407/SRR13110407.sra Read 8818334 spots for SRR13110408/SRR13110408.sra Written 8818334 spots for SRR13110408/SRR13110408.sra Read 8785774 spots for SRR13110409/SRR13110409.sra Written 8785774 spots for SRR13110409/SRR13110409.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171879 ("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: 00:04:05 34893075 reads; of these: 34893075 (100.00%) were paired; of these: 34370962 (98.50%) aligned concordantly 0 times 420225 (1.20%) aligned concordantly exactly 1 time 101888 (0.29%) aligned concordantly >1 times ---- 34370962 pairs aligned concordantly 0 times; of these: 2079 (0.01%) aligned discordantly 1 time ---- 34368883 pairs aligned 0 times concordantly or discordantly; of these: 68737766 mates make up the pairs; of these: 68544776 (99.72%) aligned 0 times 57925 (0.08%) aligned exactly 1 time 135065 (0.20%) aligned >1 times 1.78% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 13389 / 523529 = 0.0256 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 11:38:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.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 11:38:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:38:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:38:34: 1000000 INFO @ Sat, 11 Dec 2021 11:38:35: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:38:35: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:38:35: #1 total tags in treatment: 508767 INFO @ Sat, 11 Dec 2021 11:38:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:38:35: #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 11:38:35: #1 tags after filtering in treatment: 499663 INFO @ Sat, 11 Dec 2021 11:38:35: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:38:35: #1 finished! INFO @ Sat, 11 Dec 2021 11:38:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:38:35: #2 number of paired peaks: 2022 INFO @ Sat, 11 Dec 2021 11:38:35: start model_add_line... INFO @ Sat, 11 Dec 2021 11:38:35: start X-correlation... INFO @ Sat, 11 Dec 2021 11:38:35: end of X-cor INFO @ Sat, 11 Dec 2021 11:38:35: #2 finished! INFO @ Sat, 11 Dec 2021 11:38:35: #2 predicted fragment length is 178 bps INFO @ Sat, 11 Dec 2021 11:38:35: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 11 Dec 2021 11:38:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.05_model.r INFO @ Sat, 11 Dec 2021 11:38:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:38:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:38:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:38:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:38:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:38:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.05_summits.bed INFO @ Sat, 11 Dec 2021 11:38:37: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (167 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 11:38:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.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 11:38:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:38:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:39:04: 1000000 INFO @ Sat, 11 Dec 2021 11:39:05: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:39:05: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:39:05: #1 total tags in treatment: 508767 INFO @ Sat, 11 Dec 2021 11:39:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:39:05: #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 11:39:05: #1 tags after filtering in treatment: 499663 INFO @ Sat, 11 Dec 2021 11:39:05: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:39:05: #1 finished! INFO @ Sat, 11 Dec 2021 11:39:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:39:05: #2 number of paired peaks: 2022 INFO @ Sat, 11 Dec 2021 11:39:05: start model_add_line... INFO @ Sat, 11 Dec 2021 11:39:05: start X-correlation... INFO @ Sat, 11 Dec 2021 11:39:05: end of X-cor INFO @ Sat, 11 Dec 2021 11:39:05: #2 finished! INFO @ Sat, 11 Dec 2021 11:39:05: #2 predicted fragment length is 178 bps INFO @ Sat, 11 Dec 2021 11:39:05: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 11 Dec 2021 11:39:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.10_model.r INFO @ Sat, 11 Dec 2021 11:39:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:39:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:39:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:39:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:39:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:39:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.10_summits.bed INFO @ Sat, 11 Dec 2021 11:39:07: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (74 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 11:39:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.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 11:39:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:39:29: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:39:34: 1000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:39:35: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:39:35: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:39:35: #1 total tags in treatment: 508767 INFO @ Sat, 11 Dec 2021 11:39:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:39:35: #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 11:39:35: #1 tags after filtering in treatment: 499663 INFO @ Sat, 11 Dec 2021 11:39:35: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:39:35: #1 finished! INFO @ Sat, 11 Dec 2021 11:39:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:39:35: #2 number of paired peaks: 2022 INFO @ Sat, 11 Dec 2021 11:39:35: start model_add_line... INFO @ Sat, 11 Dec 2021 11:39:35: start X-correlation... INFO @ Sat, 11 Dec 2021 11:39:35: end of X-cor INFO @ Sat, 11 Dec 2021 11:39:35: #2 finished! INFO @ Sat, 11 Dec 2021 11:39:35: #2 predicted fragment length is 178 bps INFO @ Sat, 11 Dec 2021 11:39:35: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 11 Dec 2021 11:39:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.20_model.r INFO @ Sat, 11 Dec 2021 11:39:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:39:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:39:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:39:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:39:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:39:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555263/SRX9555263.20_summits.bed INFO @ Sat, 11 Dec 2021 11:39:36: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling