Job ID = 16438674 SRX = SRX14748153 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2457732 spots for SRR18645010/SRR18645010.sra Written 2457732 spots for SRR18645010/SRR18645010.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438912 ("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: 00:03:25 2457732 reads; of these: 2457732 (100.00%) were paired; of these: 679111 (27.63%) aligned concordantly 0 times 1292529 (52.59%) aligned concordantly exactly 1 time 486092 (19.78%) aligned concordantly >1 times ---- 679111 pairs aligned concordantly 0 times; of these: 6713 (0.99%) aligned discordantly 1 time ---- 672398 pairs aligned 0 times concordantly or discordantly; of these: 1344796 mates make up the pairs; of these: 1164985 (86.63%) aligned 0 times 112453 (8.36%) aligned exactly 1 time 67358 (5.01%) aligned >1 times 76.30% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 64861 / 1783753 = 0.0364 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:07:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.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 @ Tue, 02 Aug 2022 14:07:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:07:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:07:19: 1000000 INFO @ Tue, 02 Aug 2022 14:07:25: 2000000 INFO @ Tue, 02 Aug 2022 14:07:30: 3000000 INFO @ Tue, 02 Aug 2022 14:07:34: #1 tag size is determined as 65 bps INFO @ Tue, 02 Aug 2022 14:07:34: #1 tag size = 65 INFO @ Tue, 02 Aug 2022 14:07:34: #1 total tags in treatment: 1713822 INFO @ Tue, 02 Aug 2022 14:07:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:07:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:07:34: #1 tags after filtering in treatment: 1667240 INFO @ Tue, 02 Aug 2022 14:07:34: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 14:07:34: #1 finished! INFO @ Tue, 02 Aug 2022 14:07:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:07:34: #2 number of paired peaks: 1710 INFO @ Tue, 02 Aug 2022 14:07:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:07:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:07:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:07:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:07:34: #2 predicted fragment length is 212 bps INFO @ Tue, 02 Aug 2022 14:07:34: #2 alternative fragment length(s) may be 212 bps INFO @ Tue, 02 Aug 2022 14:07:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.05_model.r INFO @ Tue, 02 Aug 2022 14:07:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:07:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:07:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:07:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:07:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:07:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.05_summits.bed INFO @ Tue, 02 Aug 2022 14:07:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1100 records, 4 fields): 99 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:07:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.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 @ Tue, 02 Aug 2022 14:07:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:07:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:07:50: 1000000 INFO @ Tue, 02 Aug 2022 14:07:57: 2000000 INFO @ Tue, 02 Aug 2022 14:08:03: 3000000 INFO @ Tue, 02 Aug 2022 14:08:07: #1 tag size is determined as 65 bps INFO @ Tue, 02 Aug 2022 14:08:07: #1 tag size = 65 INFO @ Tue, 02 Aug 2022 14:08:07: #1 total tags in treatment: 1713822 INFO @ Tue, 02 Aug 2022 14:08:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:08:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:08:07: #1 tags after filtering in treatment: 1667240 INFO @ Tue, 02 Aug 2022 14:08:07: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 14:08:07: #1 finished! INFO @ Tue, 02 Aug 2022 14:08:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:08:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:08:07: #2 number of paired peaks: 1710 INFO @ Tue, 02 Aug 2022 14:08:07: start model_add_line... INFO @ Tue, 02 Aug 2022 14:08:07: start X-correlation... INFO @ Tue, 02 Aug 2022 14:08:07: end of X-cor INFO @ Tue, 02 Aug 2022 14:08:07: #2 finished! INFO @ Tue, 02 Aug 2022 14:08:07: #2 predicted fragment length is 212 bps INFO @ Tue, 02 Aug 2022 14:08:07: #2 alternative fragment length(s) may be 212 bps INFO @ Tue, 02 Aug 2022 14:08:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.10_model.r INFO @ Tue, 02 Aug 2022 14:08:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:08:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:08:11: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:08:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:08:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:08:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.10_summits.bed INFO @ Tue, 02 Aug 2022 14:08:13: Done! INFO @ Tue, 02 Aug 2022 14:08:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.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 @ Tue, 02 Aug 2022 14:08:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:08:13: #1 read treatment tags... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 209 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:08:19: 1000000 INFO @ Tue, 02 Aug 2022 14:08:24: 2000000 INFO @ Tue, 02 Aug 2022 14:08:30: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:08:33: #1 tag size is determined as 65 bps INFO @ Tue, 02 Aug 2022 14:08:33: #1 tag size = 65 INFO @ Tue, 02 Aug 2022 14:08:33: #1 total tags in treatment: 1713822 INFO @ Tue, 02 Aug 2022 14:08:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:08:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:08:33: #1 tags after filtering in treatment: 1667240 INFO @ Tue, 02 Aug 2022 14:08:33: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 14:08:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:08:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:08:34: #2 number of paired peaks: 1710 INFO @ Tue, 02 Aug 2022 14:08:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:08:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:08:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:08:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:08:34: #2 predicted fragment length is 212 bps INFO @ Tue, 02 Aug 2022 14:08:34: #2 alternative fragment length(s) may be 212 bps INFO @ Tue, 02 Aug 2022 14:08:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.20_model.r INFO @ Tue, 02 Aug 2022 14:08:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:08:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:08:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:08:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:08:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:08:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748153/SRX14748153.20_summits.bed INFO @ Tue, 02 Aug 2022 14:08:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (249 records, 4 fields): 33 millis CompletedMACS2peakCalling