Job ID = 14172304 SRX = SRX9281761 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2066242 spots for SRR12813523/SRR12813523.sra Written 2066242 spots for SRR12813523/SRR12813523.sra Read 2033316 spots for SRR12813524/SRR12813524.sra Written 2033316 spots for SRR12813524/SRR12813524.sra Read 2108411 spots for SRR12813525/SRR12813525.sra Written 2108411 spots for SRR12813525/SRR12813525.sra Read 2067299 spots for SRR12813526/SRR12813526.sra Written 2067299 spots for SRR12813526/SRR12813526.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172751 ("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: 00:01:24 8275268 reads; of these: 8275268 (100.00%) were paired; of these: 8011538 (96.81%) aligned concordantly 0 times 194133 (2.35%) aligned concordantly exactly 1 time 69597 (0.84%) aligned concordantly >1 times ---- 8011538 pairs aligned concordantly 0 times; of these: 625 (0.01%) aligned discordantly 1 time ---- 8010913 pairs aligned 0 times concordantly or discordantly; of these: 16021826 mates make up the pairs; of these: 15880672 (99.12%) aligned 0 times 41263 (0.26%) aligned exactly 1 time 99891 (0.62%) aligned >1 times 4.05% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 5843 / 263963 = 0.0221 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 15:06:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.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 15:06:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:06:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:06:15: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:06:15: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:06:15: #1 total tags in treatment: 257897 INFO @ Sat, 11 Dec 2021 15:06:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:15: #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 15:06:15: #1 tags after filtering in treatment: 255801 INFO @ Sat, 11 Dec 2021 15:06:15: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:06:15: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:16: #2 number of paired peaks: 1147 INFO @ Sat, 11 Dec 2021 15:06:16: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:16: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:16: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:16: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:16: #2 predicted fragment length is 103 bps INFO @ Sat, 11 Dec 2021 15:06:16: #2 alternative fragment length(s) may be 103,173,206 bps INFO @ Sat, 11 Dec 2021 15:06:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.05_model.r INFO @ Sat, 11 Dec 2021 15:06:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:06:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:06:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:06:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.05_summits.bed INFO @ Sat, 11 Dec 2021 15:06:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (60 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 15:06:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.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 15:06:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:06:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:06:45: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:06:45: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:06:45: #1 total tags in treatment: 257897 INFO @ Sat, 11 Dec 2021 15:06:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:45: #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 15:06:45: #1 tags after filtering in treatment: 255801 INFO @ Sat, 11 Dec 2021 15:06:45: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:06:45: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:45: #2 number of paired peaks: 1147 INFO @ Sat, 11 Dec 2021 15:06:45: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:45: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:45: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:45: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:45: #2 predicted fragment length is 103 bps INFO @ Sat, 11 Dec 2021 15:06:45: #2 alternative fragment length(s) may be 103,173,206 bps INFO @ Sat, 11 Dec 2021 15:06:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.10_model.r INFO @ Sat, 11 Dec 2021 15:06:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:06:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.10_summits.bed INFO @ Sat, 11 Dec 2021 15:06:46: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (38 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 15:07:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.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 15:07:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:07:12: #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 15:07:15: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:07:15: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:07:15: #1 total tags in treatment: 257897 INFO @ Sat, 11 Dec 2021 15:07:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:07:15: #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 15:07:15: #1 tags after filtering in treatment: 255801 INFO @ Sat, 11 Dec 2021 15:07:15: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:07:15: #1 finished! INFO @ Sat, 11 Dec 2021 15:07:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:07:15: #2 number of paired peaks: 1147 INFO @ Sat, 11 Dec 2021 15:07:15: start model_add_line... INFO @ Sat, 11 Dec 2021 15:07:15: start X-correlation... INFO @ Sat, 11 Dec 2021 15:07:15: end of X-cor INFO @ Sat, 11 Dec 2021 15:07:15: #2 finished! INFO @ Sat, 11 Dec 2021 15:07:15: #2 predicted fragment length is 103 bps INFO @ Sat, 11 Dec 2021 15:07:15: #2 alternative fragment length(s) may be 103,173,206 bps INFO @ Sat, 11 Dec 2021 15:07:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.20_model.r INFO @ Sat, 11 Dec 2021 15:07:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:07:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:07:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:07:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:07:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281761/SRX9281761.20_summits.bed INFO @ Sat, 11 Dec 2021 15:07:16: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 1 millis CompletedMACS2peakCalling