Job ID = 16438983 SRX = SRX15206427 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:19:09 prefetch.2.10.7: 1) Downloading 'SRR19139384'... 2022-08-02T05:19:09 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:19:32 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:19:33 prefetch.2.10.7: 'SRR19139384' is valid 2022-08-02T05:19:33 prefetch.2.10.7: 1) 'SRR19139384' was downloaded successfully 2022-08-02T05:19:33 prefetch.2.10.7: 'SRR19139384' has 0 unresolved dependencies Read 13608661 spots for SRR19139384/SRR19139384.sra Written 13608661 spots for SRR19139384/SRR19139384.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439130 ("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: 00:05:04 13608661 reads; of these: 13608661 (100.00%) were unpaired; of these: 286843 (2.11%) aligned 0 times 8328331 (61.20%) aligned exactly 1 time 4993487 (36.69%) aligned >1 times 97.89% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 4724368 / 13321818 = 0.3546 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 14:28:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.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 14:28:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:28:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:28:55: 1000000 INFO @ Tue, 02 Aug 2022 14:29:01: 2000000 INFO @ Tue, 02 Aug 2022 14:29:06: 3000000 INFO @ Tue, 02 Aug 2022 14:29:12: 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 14:29:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.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 14:29:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:29:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:29:19: 5000000 INFO @ Tue, 02 Aug 2022 14:29:26: 6000000 INFO @ Tue, 02 Aug 2022 14:29:26: 1000000 INFO @ Tue, 02 Aug 2022 14:29:33: 7000000 INFO @ Tue, 02 Aug 2022 14:29:34: 2000000 INFO @ Tue, 02 Aug 2022 14:29:41: 8000000 INFO @ Tue, 02 Aug 2022 14:29:42: 3000000 INFO @ Tue, 02 Aug 2022 14:29:45: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:29:45: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:29:45: #1 total tags in treatment: 8597450 INFO @ Tue, 02 Aug 2022 14:29:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:29:45: #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 14:29:45: #1 tags after filtering in treatment: 8597450 INFO @ Tue, 02 Aug 2022 14:29:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:29:45: #1 finished! INFO @ Tue, 02 Aug 2022 14:29:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:29:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:29:46: #2 number of paired peaks: 3980 INFO @ Tue, 02 Aug 2022 14:29:46: start model_add_line... INFO @ Tue, 02 Aug 2022 14:29:46: start X-correlation... INFO @ Tue, 02 Aug 2022 14:29:46: end of X-cor INFO @ Tue, 02 Aug 2022 14:29:46: #2 finished! INFO @ Tue, 02 Aug 2022 14:29:46: #2 predicted fragment length is 155 bps INFO @ Tue, 02 Aug 2022 14:29:46: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 02 Aug 2022 14:29:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.05_model.r INFO @ Tue, 02 Aug 2022 14:29:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:29:46: #3 Pre-compute pvalue-qvalue table... 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 14:29:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.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 14:29:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:29:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:29:50: 4000000 INFO @ Tue, 02 Aug 2022 14:29:55: 1000000 INFO @ Tue, 02 Aug 2022 14:29:58: 5000000 INFO @ Tue, 02 Aug 2022 14:30:02: 2000000 INFO @ Tue, 02 Aug 2022 14:30:06: 6000000 INFO @ Tue, 02 Aug 2022 14:30:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:30:10: 3000000 INFO @ Tue, 02 Aug 2022 14:30:14: 7000000 INFO @ Tue, 02 Aug 2022 14:30:17: 4000000 INFO @ Tue, 02 Aug 2022 14:30:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:30:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:30:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.05_summits.bed INFO @ Tue, 02 Aug 2022 14:30:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9917 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:30:22: 8000000 INFO @ Tue, 02 Aug 2022 14:30:24: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:30:27: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:30:27: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:30:27: #1 total tags in treatment: 8597450 INFO @ Tue, 02 Aug 2022 14:30:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:30:27: #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 14:30:27: #1 tags after filtering in treatment: 8597450 INFO @ Tue, 02 Aug 2022 14:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:30:27: #1 finished! INFO @ Tue, 02 Aug 2022 14:30:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:30:28: #2 number of paired peaks: 3980 INFO @ Tue, 02 Aug 2022 14:30:28: start model_add_line... INFO @ Tue, 02 Aug 2022 14:30:28: start X-correlation... INFO @ Tue, 02 Aug 2022 14:30:28: end of X-cor INFO @ Tue, 02 Aug 2022 14:30:28: #2 finished! INFO @ Tue, 02 Aug 2022 14:30:28: #2 predicted fragment length is 155 bps INFO @ Tue, 02 Aug 2022 14:30:28: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 02 Aug 2022 14:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.10_model.r INFO @ Tue, 02 Aug 2022 14:30:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:30:31: 6000000 INFO @ Tue, 02 Aug 2022 14:30:37: 7000000 INFO @ Tue, 02 Aug 2022 14:30:44: 8000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:30:47: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:30:47: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:30:47: #1 total tags in treatment: 8597450 INFO @ Tue, 02 Aug 2022 14:30:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:30:47: #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 14:30:47: #1 tags after filtering in treatment: 8597450 INFO @ Tue, 02 Aug 2022 14:30:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:30:47: #1 finished! INFO @ Tue, 02 Aug 2022 14:30:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:30:48: #2 number of paired peaks: 3980 INFO @ Tue, 02 Aug 2022 14:30:48: start model_add_line... INFO @ Tue, 02 Aug 2022 14:30:48: start X-correlation... INFO @ Tue, 02 Aug 2022 14:30:48: end of X-cor INFO @ Tue, 02 Aug 2022 14:30:48: #2 finished! INFO @ Tue, 02 Aug 2022 14:30:48: #2 predicted fragment length is 155 bps INFO @ Tue, 02 Aug 2022 14:30:48: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 02 Aug 2022 14:30:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.20_model.r INFO @ Tue, 02 Aug 2022 14:30:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:30:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:30:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:31:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.10_summits.bed INFO @ Tue, 02 Aug 2022 14:31:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5745 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:31:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:31:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:31:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:31:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206427/SRX15206427.20_summits.bed INFO @ Tue, 02 Aug 2022 14:31:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2901 records, 4 fields): 37 millis CompletedMACS2peakCalling