Job ID = 16439171 SRX = SRX15206454 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:42:45 prefetch.2.10.7: 1) Downloading 'SRR19139352'... 2022-08-02T05:42:45 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:43:17 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:43:18 prefetch.2.10.7: 'SRR19139352' is valid 2022-08-02T05:43:18 prefetch.2.10.7: 1) 'SRR19139352' was downloaded successfully 2022-08-02T05:43:18 prefetch.2.10.7: 'SRR19139352' has 0 unresolved dependencies Read 16316366 spots for SRR19139352/SRR19139352.sra Written 16316366 spots for SRR19139352/SRR19139352.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439327 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:51 16316366 reads; of these: 16316366 (100.00%) were unpaired; of these: 621028 (3.81%) aligned 0 times 8899652 (54.54%) aligned exactly 1 time 6795686 (41.65%) aligned >1 times 96.19% overall alignment rate Time searching: 00:07:52 Overall time: 00:07:52 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5331950 / 15695338 = 0.3397 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 14:58:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.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 14:58:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:58:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:58:12: 1000000 INFO @ Tue, 02 Aug 2022 14:58:21: 2000000 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 14:58:31: 3000000 INFO @ Tue, 02 Aug 2022 14:58:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.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 14:58:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:58:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:58:42: 4000000 INFO @ Tue, 02 Aug 2022 14:58:45: 1000000 INFO @ Tue, 02 Aug 2022 14:58:52: 5000000 INFO @ Tue, 02 Aug 2022 14:58:58: 2000000 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 14:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.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 14:59:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:59:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:59:02: 6000000 INFO @ Tue, 02 Aug 2022 14:59:12: 3000000 INFO @ Tue, 02 Aug 2022 14:59:12: 1000000 INFO @ Tue, 02 Aug 2022 14:59:12: 7000000 INFO @ Tue, 02 Aug 2022 14:59:22: 2000000 INFO @ Tue, 02 Aug 2022 14:59:22: 8000000 INFO @ Tue, 02 Aug 2022 14:59:25: 4000000 INFO @ Tue, 02 Aug 2022 14:59:33: 3000000 INFO @ Tue, 02 Aug 2022 14:59:33: 9000000 INFO @ Tue, 02 Aug 2022 14:59:38: 5000000 INFO @ Tue, 02 Aug 2022 14:59:43: 10000000 INFO @ Tue, 02 Aug 2022 14:59:43: 4000000 INFO @ Tue, 02 Aug 2022 14:59:46: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:59:46: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:59:46: #1 total tags in treatment: 10363388 INFO @ Tue, 02 Aug 2022 14:59:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:59:46: #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 14:59:47: #1 tags after filtering in treatment: 10363388 INFO @ Tue, 02 Aug 2022 14:59:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:59:47: #1 finished! INFO @ Tue, 02 Aug 2022 14:59:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:59:48: #2 number of paired peaks: 6461 INFO @ Tue, 02 Aug 2022 14:59:48: start model_add_line... INFO @ Tue, 02 Aug 2022 14:59:48: start X-correlation... INFO @ Tue, 02 Aug 2022 14:59:49: end of X-cor INFO @ Tue, 02 Aug 2022 14:59:49: #2 finished! INFO @ Tue, 02 Aug 2022 14:59:49: #2 predicted fragment length is 199 bps INFO @ Tue, 02 Aug 2022 14:59:49: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 02 Aug 2022 14:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.05_model.r INFO @ Tue, 02 Aug 2022 14:59:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:59:52: 6000000 INFO @ Tue, 02 Aug 2022 14:59:54: 5000000 INFO @ Tue, 02 Aug 2022 15:00:04: 6000000 INFO @ Tue, 02 Aug 2022 15:00:05: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:00:15: 7000000 INFO @ Tue, 02 Aug 2022 15:00:19: 8000000 INFO @ Tue, 02 Aug 2022 15:00:26: 8000000 INFO @ Tue, 02 Aug 2022 15:00:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:00:33: 9000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:00:37: 9000000 INFO @ Tue, 02 Aug 2022 15:00:48: 10000000 INFO @ Tue, 02 Aug 2022 15:00:49: 10000000 INFO @ Tue, 02 Aug 2022 15:00:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:00:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:00:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.05_summits.bed INFO @ Tue, 02 Aug 2022 15:00:50: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (9431 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:00:52: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:00:52: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:00:52: #1 total tags in treatment: 10363388 INFO @ Tue, 02 Aug 2022 15:00:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:00:52: #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 15:00:53: #1 tags after filtering in treatment: 10363388 INFO @ Tue, 02 Aug 2022 15:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:00:53: #1 finished! INFO @ Tue, 02 Aug 2022 15:00:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:00:53: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:00:53: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:00:53: #1 total tags in treatment: 10363388 INFO @ Tue, 02 Aug 2022 15:00:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:00:53: #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 15:00:53: #1 tags after filtering in treatment: 10363388 INFO @ Tue, 02 Aug 2022 15:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:00:53: #1 finished! INFO @ Tue, 02 Aug 2022 15:00:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:00:54: #2 number of paired peaks: 6461 INFO @ Tue, 02 Aug 2022 15:00:54: start model_add_line... INFO @ Tue, 02 Aug 2022 15:00:54: start X-correlation... INFO @ Tue, 02 Aug 2022 15:00:54: end of X-cor INFO @ Tue, 02 Aug 2022 15:00:54: #2 finished! INFO @ Tue, 02 Aug 2022 15:00:54: #2 predicted fragment length is 199 bps INFO @ Tue, 02 Aug 2022 15:00:54: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 02 Aug 2022 15:00:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.10_model.r INFO @ Tue, 02 Aug 2022 15:00:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:00:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:00:55: #2 number of paired peaks: 6461 INFO @ Tue, 02 Aug 2022 15:00:55: start model_add_line... INFO @ Tue, 02 Aug 2022 15:00:55: start X-correlation... INFO @ Tue, 02 Aug 2022 15:00:55: end of X-cor INFO @ Tue, 02 Aug 2022 15:00:55: #2 finished! INFO @ Tue, 02 Aug 2022 15:00:55: #2 predicted fragment length is 199 bps INFO @ Tue, 02 Aug 2022 15:00:55: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 02 Aug 2022 15:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.20_model.r INFO @ Tue, 02 Aug 2022 15:00:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:01:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:01:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.10_summits.bed INFO @ Tue, 02 Aug 2022 15:01:54: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6368 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:01:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:01:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:01:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206454/SRX15206454.20_summits.bed INFO @ Tue, 02 Aug 2022 15:01:56: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3830 records, 4 fields): 23 millis CompletedMACS2peakCalling