Job ID = 14171418 SRX = SRX9555275 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11926454 spots for SRR13110671/SRR13110671.sra Written 11926454 spots for SRR13110671/SRR13110671.sra Read 14329043 spots for SRR13110672/SRR13110672.sra Written 14329043 spots for SRR13110672/SRR13110672.sra Read 14400146 spots for SRR13110673/SRR13110673.sra Written 14400146 spots for SRR13110673/SRR13110673.sra Read 14374630 spots for SRR13110674/SRR13110674.sra Written 14374630 spots for SRR13110674/SRR13110674.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171973 ("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: 00:13:23 55030273 reads; of these: 55030273 (100.00%) were paired; of these: 53770233 (97.71%) aligned concordantly 0 times 1001632 (1.82%) aligned concordantly exactly 1 time 258408 (0.47%) aligned concordantly >1 times ---- 53770233 pairs aligned concordantly 0 times; of these: 11335 (0.02%) aligned discordantly 1 time ---- 53758898 pairs aligned 0 times concordantly or discordantly; of these: 107517796 mates make up the pairs; of these: 106332501 (98.90%) aligned 0 times 164699 (0.15%) aligned exactly 1 time 1020596 (0.95%) aligned >1 times 3.39% overall alignment rate Time searching: 00:13:23 Overall time: 00:13:23 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] 69023 / 1269651 = 0.0544 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 11:56:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.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 11:56:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:56:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:57:01: 1000000 INFO @ Sat, 11 Dec 2021 11:57:09: 2000000 INFO @ Sat, 11 Dec 2021 11:57:15: 3000000 INFO @ Sat, 11 Dec 2021 11:57:19: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:57:19: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:57:19: #1 total tags in treatment: 1191461 INFO @ Sat, 11 Dec 2021 11:57:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:57:19: #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 11:57:19: #1 tags after filtering in treatment: 1152144 INFO @ Sat, 11 Dec 2021 11:57:19: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:57:19: #1 finished! INFO @ Sat, 11 Dec 2021 11:57:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:57:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:57:19: #2 number of paired peaks: 4226 INFO @ Sat, 11 Dec 2021 11:57:19: start model_add_line... INFO @ Sat, 11 Dec 2021 11:57:19: start X-correlation... INFO @ Sat, 11 Dec 2021 11:57:19: end of X-cor INFO @ Sat, 11 Dec 2021 11:57:19: #2 finished! INFO @ Sat, 11 Dec 2021 11:57:19: #2 predicted fragment length is 283 bps INFO @ Sat, 11 Dec 2021 11:57:19: #2 alternative fragment length(s) may be 3,283 bps INFO @ Sat, 11 Dec 2021 11:57:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.05_model.r INFO @ Sat, 11 Dec 2021 11:57:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:57:19: #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 11:57:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:57:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:57:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:57:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.05_summits.bed INFO @ Sat, 11 Dec 2021 11:57:23: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:57:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.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 11:57:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:57:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:57:31: 1000000 INFO @ Sat, 11 Dec 2021 11:57:39: 2000000 INFO @ Sat, 11 Dec 2021 11:57:46: 3000000 INFO @ Sat, 11 Dec 2021 11:57:49: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:57:49: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:57:49: #1 total tags in treatment: 1191461 INFO @ Sat, 11 Dec 2021 11:57:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:57:49: #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 11:57:49: #1 tags after filtering in treatment: 1152144 INFO @ Sat, 11 Dec 2021 11:57:49: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:57:49: #1 finished! INFO @ Sat, 11 Dec 2021 11:57:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:57:50: #2 number of paired peaks: 4226 INFO @ Sat, 11 Dec 2021 11:57:50: start model_add_line... INFO @ Sat, 11 Dec 2021 11:57:50: start X-correlation... INFO @ Sat, 11 Dec 2021 11:57:50: end of X-cor INFO @ Sat, 11 Dec 2021 11:57:50: #2 finished! INFO @ Sat, 11 Dec 2021 11:57:50: #2 predicted fragment length is 283 bps INFO @ Sat, 11 Dec 2021 11:57:50: #2 alternative fragment length(s) may be 3,283 bps INFO @ Sat, 11 Dec 2021 11:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.10_model.r INFO @ Sat, 11 Dec 2021 11:57:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:57:50: #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 11:57:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.10_summits.bed INFO @ Sat, 11 Dec 2021 11:57:54: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:57:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.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 11:57:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:57:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:58:01: 1000000 INFO @ Sat, 11 Dec 2021 11:58:09: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:58:16: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:58:19: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:58:19: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:58:19: #1 total tags in treatment: 1191461 INFO @ Sat, 11 Dec 2021 11:58:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:58:19: #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 11:58:19: #1 tags after filtering in treatment: 1152144 INFO @ Sat, 11 Dec 2021 11:58:19: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:58:19: #1 finished! INFO @ Sat, 11 Dec 2021 11:58:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:58:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:58:20: #2 number of paired peaks: 4226 INFO @ Sat, 11 Dec 2021 11:58:20: start model_add_line... INFO @ Sat, 11 Dec 2021 11:58:20: start X-correlation... INFO @ Sat, 11 Dec 2021 11:58:20: end of X-cor INFO @ Sat, 11 Dec 2021 11:58:20: #2 finished! INFO @ Sat, 11 Dec 2021 11:58:20: #2 predicted fragment length is 283 bps INFO @ Sat, 11 Dec 2021 11:58:20: #2 alternative fragment length(s) may be 3,283 bps INFO @ Sat, 11 Dec 2021 11:58:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.20_model.r INFO @ Sat, 11 Dec 2021 11:58:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:58:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:58:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555275/SRX9555275.20_summits.bed INFO @ Sat, 11 Dec 2021 11:58:24: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (52 records, 4 fields): 2 millis CompletedMACS2peakCalling