Job ID = 14171480 SRX = SRX10971116 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:47:24 prefetch.2.10.7: 1) Downloading 'SRR14631240'... 2021-12-11T02:47:24 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:48:24 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:48:24 prefetch.2.10.7: 1) 'SRR14631240' was downloaded successfully 2021-12-11T02:48:24 prefetch.2.10.7: 'SRR14631240' has 0 unresolved dependencies Read 14337242 spots for SRR14631240/SRR14631240.sra Written 14337242 spots for SRR14631240/SRR14631240.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172188 ("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: 00:58:09 14337242 reads; of these: 14337242 (100.00%) were paired; of these: 2215648 (15.45%) aligned concordantly 0 times 10511394 (73.32%) aligned concordantly exactly 1 time 1610200 (11.23%) aligned concordantly >1 times ---- 2215648 pairs aligned concordantly 0 times; of these: 294213 (13.28%) aligned discordantly 1 time ---- 1921435 pairs aligned 0 times concordantly or discordantly; of these: 3842870 mates make up the pairs; of these: 2877680 (74.88%) aligned 0 times 513398 (13.36%) aligned exactly 1 time 451792 (11.76%) aligned >1 times 89.96% overall alignment rate Time searching: 00:58:10 Overall time: 00:58:10 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] 1743570 / 12307749 = 0.1417 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:59:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.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 @ Sat, 11 Dec 2021 12:59:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:59:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:00:00: 1000000 INFO @ Sat, 11 Dec 2021 13:00:11: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.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 @ Sat, 11 Dec 2021 13:00:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:00:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:00:22: 3000000 INFO @ Sat, 11 Dec 2021 13:00:28: 1000000 INFO @ Sat, 11 Dec 2021 13:00:33: 4000000 INFO @ Sat, 11 Dec 2021 13:00:38: 2000000 INFO @ Sat, 11 Dec 2021 13:00:44: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:00:48: 3000000 INFO @ Sat, 11 Dec 2021 13:00:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.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 @ Sat, 11 Dec 2021 13:00:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:00:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:00:55: 6000000 INFO @ Sat, 11 Dec 2021 13:00:57: 4000000 INFO @ Sat, 11 Dec 2021 13:00:59: 1000000 INFO @ Sat, 11 Dec 2021 13:01:06: 7000000 INFO @ Sat, 11 Dec 2021 13:01:07: 5000000 INFO @ Sat, 11 Dec 2021 13:01:10: 2000000 INFO @ Sat, 11 Dec 2021 13:01:16: 8000000 INFO @ Sat, 11 Dec 2021 13:01:16: 6000000 INFO @ Sat, 11 Dec 2021 13:01:21: 3000000 INFO @ Sat, 11 Dec 2021 13:01:26: 7000000 INFO @ Sat, 11 Dec 2021 13:01:27: 9000000 INFO @ Sat, 11 Dec 2021 13:01:32: 4000000 INFO @ Sat, 11 Dec 2021 13:01:36: 8000000 INFO @ Sat, 11 Dec 2021 13:01:38: 10000000 INFO @ Sat, 11 Dec 2021 13:01:43: 5000000 INFO @ Sat, 11 Dec 2021 13:01:46: 9000000 INFO @ Sat, 11 Dec 2021 13:01:49: 11000000 INFO @ Sat, 11 Dec 2021 13:01:54: 6000000 INFO @ Sat, 11 Dec 2021 13:01:55: 10000000 INFO @ Sat, 11 Dec 2021 13:02:00: 12000000 INFO @ Sat, 11 Dec 2021 13:02:05: 11000000 INFO @ Sat, 11 Dec 2021 13:02:05: 7000000 INFO @ Sat, 11 Dec 2021 13:02:10: 13000000 INFO @ Sat, 11 Dec 2021 13:02:14: 12000000 INFO @ Sat, 11 Dec 2021 13:02:16: 8000000 INFO @ Sat, 11 Dec 2021 13:02:21: 14000000 INFO @ Sat, 11 Dec 2021 13:02:23: 13000000 INFO @ Sat, 11 Dec 2021 13:02:27: 9000000 INFO @ Sat, 11 Dec 2021 13:02:32: 15000000 INFO @ Sat, 11 Dec 2021 13:02:33: 14000000 INFO @ Sat, 11 Dec 2021 13:02:38: 10000000 INFO @ Sat, 11 Dec 2021 13:02:42: 15000000 INFO @ Sat, 11 Dec 2021 13:02:43: 16000000 INFO @ Sat, 11 Dec 2021 13:02:49: 11000000 INFO @ Sat, 11 Dec 2021 13:02:51: 16000000 INFO @ Sat, 11 Dec 2021 13:02:53: 17000000 INFO @ Sat, 11 Dec 2021 13:02:59: 12000000 INFO @ Sat, 11 Dec 2021 13:03:01: 17000000 INFO @ Sat, 11 Dec 2021 13:03:04: 18000000 INFO @ Sat, 11 Dec 2021 13:03:10: 18000000 INFO @ Sat, 11 Dec 2021 13:03:10: 13000000 INFO @ Sat, 11 Dec 2021 13:03:15: 19000000 INFO @ Sat, 11 Dec 2021 13:03:20: 19000000 INFO @ Sat, 11 Dec 2021 13:03:21: 14000000 INFO @ Sat, 11 Dec 2021 13:03:26: 20000000 INFO @ Sat, 11 Dec 2021 13:03:29: 20000000 INFO @ Sat, 11 Dec 2021 13:03:32: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:03:37: 21000000 INFO @ Sat, 11 Dec 2021 13:03:38: 21000000 INFO @ Sat, 11 Dec 2021 13:03:43: 16000000 INFO @ Sat, 11 Dec 2021 13:03:48: 22000000 INFO @ Sat, 11 Dec 2021 13:03:48: 22000000 INFO @ Sat, 11 Dec 2021 13:03:51: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:03:51: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:03:51: #1 total tags in treatment: 10401026 INFO @ Sat, 11 Dec 2021 13:03:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:03:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:03:51: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:03:51: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:03:51: #1 total tags in treatment: 10401026 INFO @ Sat, 11 Dec 2021 13:03:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:03:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:03:51: #1 tags after filtering in treatment: 9614040 INFO @ Sat, 11 Dec 2021 13:03:51: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 13:03:51: #1 finished! INFO @ Sat, 11 Dec 2021 13:03:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:03:51: #1 tags after filtering in treatment: 9614040 INFO @ Sat, 11 Dec 2021 13:03:51: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 13:03:51: #1 finished! INFO @ Sat, 11 Dec 2021 13:03:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:03:52: #2 number of paired peaks: 1439 INFO @ Sat, 11 Dec 2021 13:03:52: start model_add_line... INFO @ Sat, 11 Dec 2021 13:03:52: start X-correlation... INFO @ Sat, 11 Dec 2021 13:03:52: end of X-cor INFO @ Sat, 11 Dec 2021 13:03:52: #2 finished! INFO @ Sat, 11 Dec 2021 13:03:52: #2 predicted fragment length is 242 bps INFO @ Sat, 11 Dec 2021 13:03:52: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 11 Dec 2021 13:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.10_model.r INFO @ Sat, 11 Dec 2021 13:03:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:03:52: #2 number of paired peaks: 1439 INFO @ Sat, 11 Dec 2021 13:03:52: start model_add_line... INFO @ Sat, 11 Dec 2021 13:03:52: start X-correlation... INFO @ Sat, 11 Dec 2021 13:03:52: end of X-cor INFO @ Sat, 11 Dec 2021 13:03:52: #2 finished! INFO @ Sat, 11 Dec 2021 13:03:52: #2 predicted fragment length is 242 bps INFO @ Sat, 11 Dec 2021 13:03:52: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 11 Dec 2021 13:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.05_model.r INFO @ Sat, 11 Dec 2021 13:03:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:03:53: 17000000 INFO @ Sat, 11 Dec 2021 13:04:04: 18000000 INFO @ Sat, 11 Dec 2021 13:04:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:04:15: 19000000 INFO @ Sat, 11 Dec 2021 13:04:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:04:26: 20000000 INFO @ Sat, 11 Dec 2021 13:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.10_summits.bed INFO @ Sat, 11 Dec 2021 13:04:28: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (2577 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.05_summits.bed INFO @ Sat, 11 Dec 2021 13:04:30: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3491 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:04:37: 21000000 INFO @ Sat, 11 Dec 2021 13:04:48: 22000000 INFO @ Sat, 11 Dec 2021 13:04:51: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:04:51: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:04:51: #1 total tags in treatment: 10401026 INFO @ Sat, 11 Dec 2021 13:04:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:04:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:04:51: #1 tags after filtering in treatment: 9614040 INFO @ Sat, 11 Dec 2021 13:04:51: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 13:04:51: #1 finished! INFO @ Sat, 11 Dec 2021 13:04:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:04:52: #2 number of paired peaks: 1439 INFO @ Sat, 11 Dec 2021 13:04:52: start model_add_line... INFO @ Sat, 11 Dec 2021 13:04:52: start X-correlation... INFO @ Sat, 11 Dec 2021 13:04:52: end of X-cor INFO @ Sat, 11 Dec 2021 13:04:52: #2 finished! INFO @ Sat, 11 Dec 2021 13:04:52: #2 predicted fragment length is 242 bps INFO @ Sat, 11 Dec 2021 13:04:52: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 11 Dec 2021 13:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.20_model.r INFO @ Sat, 11 Dec 2021 13:04:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:05:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:05:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:05:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:05:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971116/SRX10971116.20_summits.bed INFO @ Sat, 11 Dec 2021 13:05:30: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1895 records, 4 fields): 6 millis CompletedMACS2peakCalling