Job ID = 16438990 SRX = SRX15206433 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:20:09 prefetch.2.10.7: 1) Downloading 'SRR19139378'... 2022-08-02T05:20:09 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:20:20 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:20:20 prefetch.2.10.7: 'SRR19139378' is valid 2022-08-02T05:20:20 prefetch.2.10.7: 1) 'SRR19139378' was downloaded successfully 2022-08-02T05:20:20 prefetch.2.10.7: 'SRR19139378' has 0 unresolved dependencies Read 8530639 spots for SRR19139378/SRR19139378.sra Written 8530639 spots for SRR19139378/SRR19139378.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439025 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:03:02 8530639 reads; of these: 8530639 (100.00%) were unpaired; of these: 230454 (2.70%) aligned 0 times 3418296 (40.07%) aligned exactly 1 time 4881889 (57.23%) aligned >1 times 97.30% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 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] 1132283 / 8300185 = 0.1364 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 14:25:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.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 14:25:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:25:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:25:54: 1000000 INFO @ Tue, 02 Aug 2022 14:26:00: 2000000 INFO @ Tue, 02 Aug 2022 14:26:05: 3000000 INFO @ Tue, 02 Aug 2022 14:26:11: 4000000 INFO @ Tue, 02 Aug 2022 14:26:16: 5000000 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 14:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.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 14:26:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:26:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:26:22: 6000000 INFO @ Tue, 02 Aug 2022 14:26:25: 1000000 INFO @ Tue, 02 Aug 2022 14:26:29: 7000000 INFO @ Tue, 02 Aug 2022 14:26:30: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:26:30: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:26:30: #1 total tags in treatment: 7167902 INFO @ Tue, 02 Aug 2022 14:26:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:26:30: #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 14:26:30: #1 tags after filtering in treatment: 7167902 INFO @ Tue, 02 Aug 2022 14:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:26:30: #1 finished! INFO @ Tue, 02 Aug 2022 14:26:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:26:31: #2 number of paired peaks: 4628 INFO @ Tue, 02 Aug 2022 14:26:31: start model_add_line... INFO @ Tue, 02 Aug 2022 14:26:31: start X-correlation... INFO @ Tue, 02 Aug 2022 14:26:31: end of X-cor INFO @ Tue, 02 Aug 2022 14:26:31: #2 finished! INFO @ Tue, 02 Aug 2022 14:26:31: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 14:26:31: #2 alternative fragment length(s) may be 4,236 bps INFO @ Tue, 02 Aug 2022 14:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.05_model.r INFO @ Tue, 02 Aug 2022 14:26:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:26:32: 2000000 INFO @ Tue, 02 Aug 2022 14:26:39: 3000000 BedGraph に変換中... INFO @ Tue, 02 Aug 2022 14:26:46: 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 14:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.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 14:26:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:26:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:26:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:26:53: 5000000 INFO @ Tue, 02 Aug 2022 14:26:55: 1000000 INFO @ Tue, 02 Aug 2022 14:26:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:26:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:26:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.05_summits.bed INFO @ Tue, 02 Aug 2022 14:26:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5483 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:27:01: 6000000 INFO @ Tue, 02 Aug 2022 14:27:01: 2000000 INFO @ Tue, 02 Aug 2022 14:27:08: 7000000 INFO @ Tue, 02 Aug 2022 14:27:08: 3000000 INFO @ Tue, 02 Aug 2022 14:27:09: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:27:09: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:27:09: #1 total tags in treatment: 7167902 INFO @ Tue, 02 Aug 2022 14:27:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:27:09: #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 14:27:09: #1 tags after filtering in treatment: 7167902 INFO @ Tue, 02 Aug 2022 14:27:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:27:09: #1 finished! INFO @ Tue, 02 Aug 2022 14:27:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:27:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:27:10: #2 number of paired peaks: 4628 INFO @ Tue, 02 Aug 2022 14:27:10: start model_add_line... INFO @ Tue, 02 Aug 2022 14:27:10: start X-correlation... INFO @ Tue, 02 Aug 2022 14:27:10: end of X-cor INFO @ Tue, 02 Aug 2022 14:27:10: #2 finished! INFO @ Tue, 02 Aug 2022 14:27:10: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 14:27:10: #2 alternative fragment length(s) may be 4,236 bps INFO @ Tue, 02 Aug 2022 14:27:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.10_model.r INFO @ Tue, 02 Aug 2022 14:27:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:27:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:27:14: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:27:20: 5000000 INFO @ Tue, 02 Aug 2022 14:27:25: 6000000 INFO @ Tue, 02 Aug 2022 14:27:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:27:31: 7000000 INFO @ Tue, 02 Aug 2022 14:27:32: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:27:32: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:27:32: #1 total tags in treatment: 7167902 INFO @ Tue, 02 Aug 2022 14:27:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:27:32: #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 14:27:32: #1 tags after filtering in treatment: 7167902 INFO @ Tue, 02 Aug 2022 14:27:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:27:32: #1 finished! INFO @ Tue, 02 Aug 2022 14:27:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:27:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:27:33: #2 number of paired peaks: 4628 INFO @ Tue, 02 Aug 2022 14:27:33: start model_add_line... INFO @ Tue, 02 Aug 2022 14:27:33: start X-correlation... INFO @ Tue, 02 Aug 2022 14:27:33: end of X-cor INFO @ Tue, 02 Aug 2022 14:27:33: #2 finished! INFO @ Tue, 02 Aug 2022 14:27:33: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 14:27:33: #2 alternative fragment length(s) may be 4,236 bps INFO @ Tue, 02 Aug 2022 14:27:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.20_model.r INFO @ Tue, 02 Aug 2022 14:27:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:27:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:27:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:27:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:27:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.10_summits.bed INFO @ Tue, 02 Aug 2022 14:27:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2415 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:27:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:27:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:27:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:27:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206433/SRX15206433.20_summits.bed INFO @ Tue, 02 Aug 2022 14:28:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (843 records, 4 fields): 31 millis CompletedMACS2peakCalling