Job ID = 14171417 SRX = SRX9555274 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10092590 spots for SRR13110667/SRR13110667.sra Written 10092590 spots for SRR13110667/SRR13110667.sra Read 9842523 spots for SRR13110668/SRR13110668.sra Written 9842523 spots for SRR13110668/SRR13110668.sra Read 10415779 spots for SRR13110669/SRR13110669.sra Written 10415779 spots for SRR13110669/SRR13110669.sra Read 10122099 spots for SRR13110670/SRR13110670.sra Written 10122099 spots for SRR13110670/SRR13110670.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171932 ("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: 00:06:59 40472991 reads; of these: 40472991 (100.00%) were paired; of these: 38847604 (95.98%) aligned concordantly 0 times 1266668 (3.13%) aligned concordantly exactly 1 time 358719 (0.89%) aligned concordantly >1 times ---- 38847604 pairs aligned concordantly 0 times; of these: 12990 (0.03%) aligned discordantly 1 time ---- 38834614 pairs aligned 0 times concordantly or discordantly; of these: 77669228 mates make up the pairs; of these: 76938572 (99.06%) aligned 0 times 166064 (0.21%) aligned exactly 1 time 564592 (0.73%) aligned >1 times 4.95% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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] 70486 / 1635859 = 0.0431 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 11:46:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.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 11:46:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:46:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:47:03: 1000000 INFO @ Sat, 11 Dec 2021 11:47:10: 2000000 INFO @ Sat, 11 Dec 2021 11:47:17: 3000000 INFO @ Sat, 11 Dec 2021 11:47:22: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:47:22: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:47:22: #1 total tags in treatment: 1555284 INFO @ Sat, 11 Dec 2021 11:47:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:47:22: #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 11:47:22: #1 tags after filtering in treatment: 1504182 INFO @ Sat, 11 Dec 2021 11:47:22: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:47:22: #1 finished! INFO @ Sat, 11 Dec 2021 11:47:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:47:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:47:23: #2 number of paired peaks: 2395 INFO @ Sat, 11 Dec 2021 11:47:23: start model_add_line... INFO @ Sat, 11 Dec 2021 11:47:23: start X-correlation... INFO @ Sat, 11 Dec 2021 11:47:23: end of X-cor INFO @ Sat, 11 Dec 2021 11:47:23: #2 finished! INFO @ Sat, 11 Dec 2021 11:47:23: #2 predicted fragment length is 282 bps INFO @ Sat, 11 Dec 2021 11:47:23: #2 alternative fragment length(s) may be 257,263,282 bps INFO @ Sat, 11 Dec 2021 11:47:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.05_model.r INFO @ Sat, 11 Dec 2021 11:47:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:47:23: #3 Pre-compute pvalue-qvalue table... 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 11:47:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:47:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.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 11:47:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:47:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.05_summits.bed INFO @ Sat, 11 Dec 2021 11:47:28: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (273 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:47:33: 1000000 INFO @ Sat, 11 Dec 2021 11:47:40: 2000000 INFO @ Sat, 11 Dec 2021 11:47:47: 3000000 INFO @ Sat, 11 Dec 2021 11:47:52: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:47:52: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:47:52: #1 total tags in treatment: 1555284 INFO @ Sat, 11 Dec 2021 11:47:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:47:52: #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 11:47:52: #1 tags after filtering in treatment: 1504182 INFO @ Sat, 11 Dec 2021 11:47:52: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:47:52: #1 finished! INFO @ Sat, 11 Dec 2021 11:47:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:47:53: #2 number of paired peaks: 2395 INFO @ Sat, 11 Dec 2021 11:47:53: start model_add_line... INFO @ Sat, 11 Dec 2021 11:47:53: start X-correlation... INFO @ Sat, 11 Dec 2021 11:47:53: end of X-cor INFO @ Sat, 11 Dec 2021 11:47:53: #2 finished! INFO @ Sat, 11 Dec 2021 11:47:53: #2 predicted fragment length is 282 bps INFO @ Sat, 11 Dec 2021 11:47:53: #2 alternative fragment length(s) may be 257,263,282 bps INFO @ Sat, 11 Dec 2021 11:47:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.10_model.r INFO @ Sat, 11 Dec 2021 11:47:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:47:53: #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 11:47:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.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 11:47:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:47:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.10_summits.bed INFO @ Sat, 11 Dec 2021 11:47:58: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (121 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:48:02: 1000000 INFO @ Sat, 11 Dec 2021 11:48:07: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:48:12: 3000000 INFO @ Sat, 11 Dec 2021 11:48:17: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:48:17: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:48:17: #1 total tags in treatment: 1555284 INFO @ Sat, 11 Dec 2021 11:48:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:48:17: #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 11:48:17: #1 tags after filtering in treatment: 1504182 INFO @ Sat, 11 Dec 2021 11:48:17: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:48:17: #1 finished! INFO @ Sat, 11 Dec 2021 11:48:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:48:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:48:17: #2 number of paired peaks: 2395 INFO @ Sat, 11 Dec 2021 11:48:17: start model_add_line... INFO @ Sat, 11 Dec 2021 11:48:17: start X-correlation... INFO @ Sat, 11 Dec 2021 11:48:17: end of X-cor INFO @ Sat, 11 Dec 2021 11:48:17: #2 finished! INFO @ Sat, 11 Dec 2021 11:48:17: #2 predicted fragment length is 282 bps INFO @ Sat, 11 Dec 2021 11:48:17: #2 alternative fragment length(s) may be 257,263,282 bps INFO @ Sat, 11 Dec 2021 11:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.20_model.r INFO @ Sat, 11 Dec 2021 11:48:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:48:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:48:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:48:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:48:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:48:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555274/SRX9555274.20_summits.bed INFO @ Sat, 11 Dec 2021 11:48:22: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 5 millis CompletedMACS2peakCalling