Job ID = 16439184 SRX = SRX15206461 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:43:46 prefetch.2.10.7: 1) Downloading 'SRR19139345'... 2022-08-02T05:43:46 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:43:57 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:43:57 prefetch.2.10.7: 'SRR19139345' is valid 2022-08-02T05:43:57 prefetch.2.10.7: 1) 'SRR19139345' was downloaded successfully 2022-08-02T05:43:57 prefetch.2.10.7: 'SRR19139345' has 0 unresolved dependencies Read 7157337 spots for SRR19139345/SRR19139345.sra Written 7157337 spots for SRR19139345/SRR19139345.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439282 ("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: 00:02:32 7157337 reads; of these: 7157337 (100.00%) were unpaired; of these: 169814 (2.37%) aligned 0 times 2870751 (40.11%) aligned exactly 1 time 4116772 (57.52%) aligned >1 times 97.63% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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_rmdupse_core] 847267 / 6987523 = 0.1213 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 14:48:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.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 14:48:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:48:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:48:44: 1000000 INFO @ Tue, 02 Aug 2022 14:48:50: 2000000 INFO @ Tue, 02 Aug 2022 14:48:55: 3000000 INFO @ Tue, 02 Aug 2022 14:49:01: 4000000 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 14:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.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 14:49:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:07: 5000000 INFO @ Tue, 02 Aug 2022 14:49:12: 1000000 INFO @ Tue, 02 Aug 2022 14:49:12: 6000000 INFO @ Tue, 02 Aug 2022 14:49:13: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:49:13: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:49:13: #1 total tags in treatment: 6140256 INFO @ Tue, 02 Aug 2022 14:49:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:49:13: #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 14:49:13: #1 tags after filtering in treatment: 6140256 INFO @ Tue, 02 Aug 2022 14:49:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:49:13: #1 finished! INFO @ Tue, 02 Aug 2022 14:49:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:49:14: #2 number of paired peaks: 5171 INFO @ Tue, 02 Aug 2022 14:49:14: start model_add_line... INFO @ Tue, 02 Aug 2022 14:49:14: start X-correlation... INFO @ Tue, 02 Aug 2022 14:49:14: end of X-cor INFO @ Tue, 02 Aug 2022 14:49:14: #2 finished! INFO @ Tue, 02 Aug 2022 14:49:14: #2 predicted fragment length is 231 bps INFO @ Tue, 02 Aug 2022 14:49:14: #2 alternative fragment length(s) may be 4,217,231 bps INFO @ Tue, 02 Aug 2022 14:49:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.05_model.r INFO @ Tue, 02 Aug 2022 14:49:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:49:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:49:17: 2000000 INFO @ Tue, 02 Aug 2022 14:49:22: 3000000 INFO @ Tue, 02 Aug 2022 14:49:28: 4000000 INFO @ Tue, 02 Aug 2022 14:49:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:49:33: 5000000 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 14:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.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 14:49:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:38: 6000000 INFO @ Tue, 02 Aug 2022 14:49:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:49:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:49:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.05_summits.bed INFO @ Tue, 02 Aug 2022 14:49:39: Done! INFO @ Tue, 02 Aug 2022 14:49:39: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:49:39: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:49:39: #1 total tags in treatment: 6140256 INFO @ Tue, 02 Aug 2022 14:49:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:49:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (14 chroms): 1 millis INFO @ Tue, 02 Aug 2022 14:49:39: #1 tags after filtering in treatment: 6140256 INFO @ Tue, 02 Aug 2022 14:49:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:49:39: #1 finished! INFO @ Tue, 02 Aug 2022 14:49:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:49:39: #2 looking for paired plus/minus strand peaks... pass2 - checking and writing primary data (5637 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:49:40: #2 number of paired peaks: 5171 INFO @ Tue, 02 Aug 2022 14:49:40: start model_add_line... INFO @ Tue, 02 Aug 2022 14:49:40: start X-correlation... INFO @ Tue, 02 Aug 2022 14:49:40: end of X-cor INFO @ Tue, 02 Aug 2022 14:49:40: #2 finished! INFO @ Tue, 02 Aug 2022 14:49:40: #2 predicted fragment length is 231 bps INFO @ Tue, 02 Aug 2022 14:49:40: #2 alternative fragment length(s) may be 4,217,231 bps INFO @ Tue, 02 Aug 2022 14:49:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.10_model.r INFO @ Tue, 02 Aug 2022 14:49:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:49:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:49:42: 1000000 INFO @ Tue, 02 Aug 2022 14:49:47: 2000000 INFO @ Tue, 02 Aug 2022 14:49:52: 3000000 INFO @ Tue, 02 Aug 2022 14:49:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:49:57: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:50:03: 5000000 INFO @ Tue, 02 Aug 2022 14:50:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.10_summits.bed INFO @ Tue, 02 Aug 2022 14:50:04: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2451 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:08: 6000000 INFO @ Tue, 02 Aug 2022 14:50:09: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:50:09: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:50:09: #1 total tags in treatment: 6140256 INFO @ Tue, 02 Aug 2022 14:50:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:09: #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 14:50:09: #1 tags after filtering in treatment: 6140256 INFO @ Tue, 02 Aug 2022 14:50:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:09: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:09: #2 number of paired peaks: 5171 INFO @ Tue, 02 Aug 2022 14:50:09: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:09: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:09: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:09: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:09: #2 predicted fragment length is 231 bps INFO @ Tue, 02 Aug 2022 14:50:09: #2 alternative fragment length(s) may be 4,217,231 bps INFO @ Tue, 02 Aug 2022 14:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.20_model.r INFO @ Tue, 02 Aug 2022 14:50:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:50:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206461/SRX15206461.20_summits.bed INFO @ Tue, 02 Aug 2022 14:50:33: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (865 records, 4 fields): 13 millis CompletedMACS2peakCalling