Job ID = 16436206 SRX = SRX12178857 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:05:43 prefetch.2.10.7: 1) Downloading 'SRR15888057'... 2022-08-02T02:05:43 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:06:33 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:06:33 prefetch.2.10.7: 1) 'SRR15888057' was downloaded successfully 2022-08-02T02:06:33 prefetch.2.10.7: 'SRR15888057' has 0 unresolved dependencies Read 13626280 spots for SRR15888057/SRR15888057.sra Written 13626280 spots for SRR15888057/SRR15888057.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436375 ("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: 00:12:26 13626280 reads; of these: 13626280 (100.00%) were paired; of these: 6050491 (44.40%) aligned concordantly 0 times 5962404 (43.76%) aligned concordantly exactly 1 time 1613385 (11.84%) aligned concordantly >1 times ---- 6050491 pairs aligned concordantly 0 times; of these: 1578418 (26.09%) aligned discordantly 1 time ---- 4472073 pairs aligned 0 times concordantly or discordantly; of these: 8944146 mates make up the pairs; of these: 6559985 (73.34%) aligned 0 times 1550198 (17.33%) aligned exactly 1 time 833963 (9.32%) aligned >1 times 75.93% overall alignment rate Time searching: 00:12:27 Overall time: 00:12:27 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 12 files... [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] 5843939 / 9124473 = 0.6405 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 11:24:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.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 11:24:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:24:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:24:29: 1000000 INFO @ Tue, 02 Aug 2022 11:24:35: 2000000 INFO @ Tue, 02 Aug 2022 11:24:42: 3000000 INFO @ Tue, 02 Aug 2022 11:24:48: 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 11:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.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 11:24:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:24:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:24:54: 5000000 INFO @ Tue, 02 Aug 2022 11:24:59: 1000000 INFO @ Tue, 02 Aug 2022 11:25:00: 6000000 INFO @ Tue, 02 Aug 2022 11:25:04: 2000000 INFO @ Tue, 02 Aug 2022 11:25:06: 7000000 INFO @ Tue, 02 Aug 2022 11:25:10: 3000000 INFO @ Tue, 02 Aug 2022 11:25:13: 8000000 INFO @ Tue, 02 Aug 2022 11:25:16: 4000000 INFO @ Tue, 02 Aug 2022 11:25:19: 9000000 INFO @ Tue, 02 Aug 2022 11:25:19: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:25:19: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:25:19: #1 total tags in treatment: 2635088 INFO @ Tue, 02 Aug 2022 11:25:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:25:19: #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 11:25:19: #1 tags after filtering in treatment: 2219472 INFO @ Tue, 02 Aug 2022 11:25:19: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 11:25:19: #1 finished! INFO @ Tue, 02 Aug 2022 11:25:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:25:19: #2 number of paired peaks: 4018 INFO @ Tue, 02 Aug 2022 11:25:19: start model_add_line... INFO @ Tue, 02 Aug 2022 11:25:19: start X-correlation... INFO @ Tue, 02 Aug 2022 11:25:19: end of X-cor INFO @ Tue, 02 Aug 2022 11:25:19: #2 finished! INFO @ Tue, 02 Aug 2022 11:25:19: #2 predicted fragment length is 155 bps INFO @ Tue, 02 Aug 2022 11:25:19: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 02 Aug 2022 11:25:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.05_model.r INFO @ Tue, 02 Aug 2022 11:25:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:25:19: #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 11:25:21: 5000000 INFO @ Tue, 02 Aug 2022 11:25:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.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 11:25:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:25:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:25:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:25:27: 6000000 INFO @ Tue, 02 Aug 2022 11:25:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:25:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:25:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.05_summits.bed INFO @ Tue, 02 Aug 2022 11:25:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5555 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:25:29: 1000000 INFO @ Tue, 02 Aug 2022 11:25:32: 7000000 INFO @ Tue, 02 Aug 2022 11:25:34: 2000000 INFO @ Tue, 02 Aug 2022 11:25:38: 8000000 INFO @ Tue, 02 Aug 2022 11:25:40: 3000000 INFO @ Tue, 02 Aug 2022 11:25:43: 9000000 INFO @ Tue, 02 Aug 2022 11:25:43: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:25:43: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:25:43: #1 total tags in treatment: 2635088 INFO @ Tue, 02 Aug 2022 11:25:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:25:43: #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 11:25:43: #1 tags after filtering in treatment: 2219472 INFO @ Tue, 02 Aug 2022 11:25:43: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 11:25:43: #1 finished! INFO @ Tue, 02 Aug 2022 11:25:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:25:44: #2 number of paired peaks: 4018 INFO @ Tue, 02 Aug 2022 11:25:44: start model_add_line... INFO @ Tue, 02 Aug 2022 11:25:44: start X-correlation... INFO @ Tue, 02 Aug 2022 11:25:44: end of X-cor INFO @ Tue, 02 Aug 2022 11:25:44: #2 finished! INFO @ Tue, 02 Aug 2022 11:25:44: #2 predicted fragment length is 155 bps INFO @ Tue, 02 Aug 2022 11:25:44: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 02 Aug 2022 11:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.10_model.r INFO @ Tue, 02 Aug 2022 11:25:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:25:45: 4000000 INFO @ Tue, 02 Aug 2022 11:25:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:25:50: 5000000 INFO @ Tue, 02 Aug 2022 11:25:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:25:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:25:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.10_summits.bed INFO @ Tue, 02 Aug 2022 11:25:52: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2569 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:25:55: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:26:01: 7000000 INFO @ Tue, 02 Aug 2022 11:26:06: 8000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:26:11: 9000000 INFO @ Tue, 02 Aug 2022 11:26:11: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:26:11: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:26:11: #1 total tags in treatment: 2635088 INFO @ Tue, 02 Aug 2022 11:26:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:26:11: #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 11:26:11: #1 tags after filtering in treatment: 2219472 INFO @ Tue, 02 Aug 2022 11:26:11: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 11:26:11: #1 finished! INFO @ Tue, 02 Aug 2022 11:26:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:26:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:26:11: #2 number of paired peaks: 4018 INFO @ Tue, 02 Aug 2022 11:26:11: start model_add_line... INFO @ Tue, 02 Aug 2022 11:26:11: start X-correlation... INFO @ Tue, 02 Aug 2022 11:26:11: end of X-cor INFO @ Tue, 02 Aug 2022 11:26:11: #2 finished! INFO @ Tue, 02 Aug 2022 11:26:11: #2 predicted fragment length is 155 bps INFO @ Tue, 02 Aug 2022 11:26:11: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 02 Aug 2022 11:26:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.20_model.r INFO @ Tue, 02 Aug 2022 11:26:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:26:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:26:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:26:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:26:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:26:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178857/SRX12178857.20_summits.bed INFO @ Tue, 02 Aug 2022 11:26:19: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (781 records, 4 fields): 25 millis CompletedMACS2peakCalling