Job ID = 14172253 SRX = SRX9281753 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4726878 spots for SRR12813491/SRR12813491.sra Written 4726878 spots for SRR12813491/SRR12813491.sra Read 4729217 spots for SRR12813492/SRR12813492.sra Written 4729217 spots for SRR12813492/SRR12813492.sra Read 4859785 spots for SRR12813493/SRR12813493.sra Written 4859785 spots for SRR12813493/SRR12813493.sra Read 4500112 spots for SRR12813494/SRR12813494.sra Written 4500112 spots for SRR12813494/SRR12813494.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172711 ("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: 00:03:43 18815992 reads; of these: 18815992 (100.00%) were paired; of these: 16369892 (87.00%) aligned concordantly 0 times 2256230 (11.99%) aligned concordantly exactly 1 time 189870 (1.01%) aligned concordantly >1 times ---- 16369892 pairs aligned concordantly 0 times; of these: 14686 (0.09%) aligned discordantly 1 time ---- 16355206 pairs aligned 0 times concordantly or discordantly; of these: 32710412 mates make up the pairs; of these: 32318376 (98.80%) aligned 0 times 229028 (0.70%) aligned exactly 1 time 163008 (0.50%) aligned >1 times 14.12% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 456090 / 2451318 = 0.1861 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 15:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.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 15:00:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:00:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:01:03: 1000000 INFO @ Sat, 11 Dec 2021 15:01:08: 2000000 INFO @ Sat, 11 Dec 2021 15:01:13: 3000000 INFO @ Sat, 11 Dec 2021 15:01:18: 4000000 INFO @ Sat, 11 Dec 2021 15:01:20: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:01:20: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:01:20: #1 total tags in treatment: 1990144 INFO @ Sat, 11 Dec 2021 15:01:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:01:20: #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 15:01:20: #1 tags after filtering in treatment: 1237103 INFO @ Sat, 11 Dec 2021 15:01:20: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:01:20: #1 finished! INFO @ Sat, 11 Dec 2021 15:01:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:01:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:01:20: #2 number of paired peaks: 10383 INFO @ Sat, 11 Dec 2021 15:01:20: start model_add_line... INFO @ Sat, 11 Dec 2021 15:01:20: start X-correlation... INFO @ Sat, 11 Dec 2021 15:01:20: end of X-cor INFO @ Sat, 11 Dec 2021 15:01:20: #2 finished! INFO @ Sat, 11 Dec 2021 15:01:20: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 15:01:20: #2 alternative fragment length(s) may be 154,313 bps INFO @ Sat, 11 Dec 2021 15:01:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.05_model.r INFO @ Sat, 11 Dec 2021 15:01:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:01:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:01:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:01:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.05_summits.bed INFO @ Sat, 11 Dec 2021 15:01:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7431 records, 4 fields): 8 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 15:01:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.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 15:01:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:01:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:01:33: 1000000 INFO @ Sat, 11 Dec 2021 15:01:38: 2000000 INFO @ Sat, 11 Dec 2021 15:01:43: 3000000 INFO @ Sat, 11 Dec 2021 15:01:48: 4000000 INFO @ Sat, 11 Dec 2021 15:01:50: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:01:50: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:01:50: #1 total tags in treatment: 1990144 INFO @ Sat, 11 Dec 2021 15:01:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:01:50: #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 15:01:50: #1 tags after filtering in treatment: 1237103 INFO @ Sat, 11 Dec 2021 15:01:50: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:01:50: #1 finished! INFO @ Sat, 11 Dec 2021 15:01:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:01:50: #2 number of paired peaks: 10383 INFO @ Sat, 11 Dec 2021 15:01:50: start model_add_line... INFO @ Sat, 11 Dec 2021 15:01:50: start X-correlation... INFO @ Sat, 11 Dec 2021 15:01:50: end of X-cor INFO @ Sat, 11 Dec 2021 15:01:50: #2 finished! INFO @ Sat, 11 Dec 2021 15:01:50: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 15:01:50: #2 alternative fragment length(s) may be 154,313 bps INFO @ Sat, 11 Dec 2021 15:01:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.10_model.r INFO @ Sat, 11 Dec 2021 15:01:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:01:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:01:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.10_summits.bed INFO @ Sat, 11 Dec 2021 15:01:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5732 records, 4 fields): 7 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 15:01:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.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 15:01:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:01:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:02:03: 1000000 INFO @ Sat, 11 Dec 2021 15:02:08: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:02:13: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:02:18: 4000000 INFO @ Sat, 11 Dec 2021 15:02:20: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:02:20: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:02:20: #1 total tags in treatment: 1990144 INFO @ Sat, 11 Dec 2021 15:02:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:02:20: #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 15:02:20: #1 tags after filtering in treatment: 1237103 INFO @ Sat, 11 Dec 2021 15:02:20: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:02:20: #1 finished! INFO @ Sat, 11 Dec 2021 15:02:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:02:20: #2 number of paired peaks: 10383 INFO @ Sat, 11 Dec 2021 15:02:20: start model_add_line... INFO @ Sat, 11 Dec 2021 15:02:20: start X-correlation... INFO @ Sat, 11 Dec 2021 15:02:20: end of X-cor INFO @ Sat, 11 Dec 2021 15:02:20: #2 finished! INFO @ Sat, 11 Dec 2021 15:02:20: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 15:02:20: #2 alternative fragment length(s) may be 154,313 bps INFO @ Sat, 11 Dec 2021 15:02:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.20_model.r INFO @ Sat, 11 Dec 2021 15:02:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:02:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:02:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281753/SRX9281753.20_summits.bed INFO @ Sat, 11 Dec 2021 15:02:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2672 records, 4 fields): 4 millis CompletedMACS2peakCalling