Job ID = 14171479 SRX = SRX10971115 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:47:08 prefetch.2.10.7: 1) Downloading 'SRR14631239'... 2021-12-11T02:47:08 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:48:14 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:48:14 prefetch.2.10.7: 1) 'SRR14631239' was downloaded successfully 2021-12-11T02:48:14 prefetch.2.10.7: 'SRR14631239' has 0 unresolved dependencies Read 15419212 spots for SRR14631239/SRR14631239.sra Written 15419212 spots for SRR14631239/SRR14631239.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172105 ("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: 00:41:02 15419212 reads; of these: 15419212 (100.00%) were paired; of these: 2235417 (14.50%) aligned concordantly 0 times 11438970 (74.19%) aligned concordantly exactly 1 time 1744825 (11.32%) aligned concordantly >1 times ---- 2235417 pairs aligned concordantly 0 times; of these: 273754 (12.25%) aligned discordantly 1 time ---- 1961663 pairs aligned 0 times concordantly or discordantly; of these: 3923326 mates make up the pairs; of these: 2882500 (73.47%) aligned 0 times 674391 (17.19%) aligned exactly 1 time 366435 (9.34%) aligned >1 times 90.65% overall alignment rate Time searching: 00:41:02 Overall time: 00:41:02 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] 1761415 / 13374376 = 0.1317 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 12:40:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.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 12:40:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:40:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:40:11: 1000000 INFO @ Sat, 11 Dec 2021 12:40:17: 2000000 INFO @ Sat, 11 Dec 2021 12:40:23: 3000000 INFO @ Sat, 11 Dec 2021 12:40:28: 4000000 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 12:40:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.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 12:40:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:40:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:40:34: 5000000 INFO @ Sat, 11 Dec 2021 12:40:41: 1000000 INFO @ Sat, 11 Dec 2021 12:40:41: 6000000 INFO @ Sat, 11 Dec 2021 12:40:48: 2000000 INFO @ Sat, 11 Dec 2021 12:40:48: 7000000 INFO @ Sat, 11 Dec 2021 12:40:55: 3000000 INFO @ Sat, 11 Dec 2021 12:40:55: 8000000 INFO @ Sat, 11 Dec 2021 12:41:02: 4000000 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 12:41:02: 9000000 INFO @ Sat, 11 Dec 2021 12:41:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.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 12:41:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:41:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:41:09: 5000000 INFO @ Sat, 11 Dec 2021 12:41:09: 10000000 INFO @ Sat, 11 Dec 2021 12:41:11: 1000000 INFO @ Sat, 11 Dec 2021 12:41:16: 6000000 INFO @ Sat, 11 Dec 2021 12:41:16: 11000000 INFO @ Sat, 11 Dec 2021 12:41:18: 2000000 INFO @ Sat, 11 Dec 2021 12:41:23: 7000000 INFO @ Sat, 11 Dec 2021 12:41:24: 12000000 INFO @ Sat, 11 Dec 2021 12:41:26: 3000000 INFO @ Sat, 11 Dec 2021 12:41:30: 8000000 INFO @ Sat, 11 Dec 2021 12:41:31: 13000000 INFO @ Sat, 11 Dec 2021 12:41:33: 4000000 INFO @ Sat, 11 Dec 2021 12:41:37: 9000000 INFO @ Sat, 11 Dec 2021 12:41:38: 14000000 INFO @ Sat, 11 Dec 2021 12:41:40: 5000000 INFO @ Sat, 11 Dec 2021 12:41:44: 10000000 INFO @ Sat, 11 Dec 2021 12:41:45: 15000000 INFO @ Sat, 11 Dec 2021 12:41:47: 6000000 INFO @ Sat, 11 Dec 2021 12:41:51: 11000000 INFO @ Sat, 11 Dec 2021 12:41:52: 16000000 INFO @ Sat, 11 Dec 2021 12:41:54: 7000000 INFO @ Sat, 11 Dec 2021 12:41:58: 12000000 INFO @ Sat, 11 Dec 2021 12:41:59: 17000000 INFO @ Sat, 11 Dec 2021 12:42:00: 8000000 INFO @ Sat, 11 Dec 2021 12:42:05: 13000000 INFO @ Sat, 11 Dec 2021 12:42:06: 18000000 INFO @ Sat, 11 Dec 2021 12:42:07: 9000000 INFO @ Sat, 11 Dec 2021 12:42:12: 14000000 INFO @ Sat, 11 Dec 2021 12:42:13: 19000000 INFO @ Sat, 11 Dec 2021 12:42:14: 10000000 INFO @ Sat, 11 Dec 2021 12:42:19: 15000000 INFO @ Sat, 11 Dec 2021 12:42:20: 20000000 INFO @ Sat, 11 Dec 2021 12:42:21: 11000000 INFO @ Sat, 11 Dec 2021 12:42:26: 16000000 INFO @ Sat, 11 Dec 2021 12:42:27: 21000000 INFO @ Sat, 11 Dec 2021 12:42:28: 12000000 INFO @ Sat, 11 Dec 2021 12:42:33: 17000000 INFO @ Sat, 11 Dec 2021 12:42:34: 22000000 INFO @ Sat, 11 Dec 2021 12:42:35: 13000000 INFO @ Sat, 11 Dec 2021 12:42:40: 18000000 INFO @ Sat, 11 Dec 2021 12:42:41: 23000000 INFO @ Sat, 11 Dec 2021 12:42:41: 14000000 INFO @ Sat, 11 Dec 2021 12:42:47: 19000000 INFO @ Sat, 11 Dec 2021 12:42:48: 24000000 INFO @ Sat, 11 Dec 2021 12:42:48: 15000000 INFO @ Sat, 11 Dec 2021 12:42:51: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 12:42:51: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 12:42:51: #1 total tags in treatment: 11439781 INFO @ Sat, 11 Dec 2021 12:42:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:42:51: #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 12:42:51: #1 tags after filtering in treatment: 10536391 INFO @ Sat, 11 Dec 2021 12:42:51: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 12:42:51: #1 finished! INFO @ Sat, 11 Dec 2021 12:42:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:42:52: #2 number of paired peaks: 1320 INFO @ Sat, 11 Dec 2021 12:42:52: start model_add_line... INFO @ Sat, 11 Dec 2021 12:42:52: start X-correlation... INFO @ Sat, 11 Dec 2021 12:42:52: end of X-cor INFO @ Sat, 11 Dec 2021 12:42:52: #2 finished! INFO @ Sat, 11 Dec 2021 12:42:52: #2 predicted fragment length is 240 bps INFO @ Sat, 11 Dec 2021 12:42:52: #2 alternative fragment length(s) may be 240 bps INFO @ Sat, 11 Dec 2021 12:42:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.05_model.r INFO @ Sat, 11 Dec 2021 12:42:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:42:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:42:54: 20000000 INFO @ Sat, 11 Dec 2021 12:42:55: 16000000 INFO @ Sat, 11 Dec 2021 12:43:00: 21000000 INFO @ Sat, 11 Dec 2021 12:43:02: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:43:07: 22000000 INFO @ Sat, 11 Dec 2021 12:43:08: 18000000 INFO @ Sat, 11 Dec 2021 12:43:14: 23000000 INFO @ Sat, 11 Dec 2021 12:43:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:43:15: 19000000 INFO @ Sat, 11 Dec 2021 12:43:20: 24000000 INFO @ Sat, 11 Dec 2021 12:43:22: 20000000 INFO @ Sat, 11 Dec 2021 12:43:23: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 12:43:23: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 12:43:23: #1 total tags in treatment: 11439781 INFO @ Sat, 11 Dec 2021 12:43:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:43:23: #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 12:43:23: #1 tags after filtering in treatment: 10536391 INFO @ Sat, 11 Dec 2021 12:43:23: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 12:43:23: #1 finished! INFO @ Sat, 11 Dec 2021 12:43:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:43:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:43:24: #2 number of paired peaks: 1320 INFO @ Sat, 11 Dec 2021 12:43:24: start model_add_line... INFO @ Sat, 11 Dec 2021 12:43:24: start X-correlation... INFO @ Sat, 11 Dec 2021 12:43:24: end of X-cor INFO @ Sat, 11 Dec 2021 12:43:24: #2 finished! INFO @ Sat, 11 Dec 2021 12:43:24: #2 predicted fragment length is 240 bps INFO @ Sat, 11 Dec 2021 12:43:24: #2 alternative fragment length(s) may be 240 bps INFO @ Sat, 11 Dec 2021 12:43:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.10_model.r INFO @ Sat, 11 Dec 2021 12:43:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:43:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:43:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:43:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:43:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.05_summits.bed INFO @ Sat, 11 Dec 2021 12:43:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3538 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:43:28: 21000000 INFO @ Sat, 11 Dec 2021 12:43:35: 22000000 INFO @ Sat, 11 Dec 2021 12:43:41: 23000000 INFO @ Sat, 11 Dec 2021 12:43:46: 24000000 INFO @ Sat, 11 Dec 2021 12:43:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:43:49: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 12:43:49: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 12:43:49: #1 total tags in treatment: 11439781 INFO @ Sat, 11 Dec 2021 12:43:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:43:49: #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 12:43:49: #1 tags after filtering in treatment: 10536391 INFO @ Sat, 11 Dec 2021 12:43:49: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 12:43:49: #1 finished! INFO @ Sat, 11 Dec 2021 12:43:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:43:50: #2 number of paired peaks: 1320 INFO @ Sat, 11 Dec 2021 12:43:50: start model_add_line... INFO @ Sat, 11 Dec 2021 12:43:50: start X-correlation... INFO @ Sat, 11 Dec 2021 12:43:50: end of X-cor INFO @ Sat, 11 Dec 2021 12:43:50: #2 finished! INFO @ Sat, 11 Dec 2021 12:43:50: #2 predicted fragment length is 240 bps INFO @ Sat, 11 Dec 2021 12:43:50: #2 alternative fragment length(s) may be 240 bps INFO @ Sat, 11 Dec 2021 12:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.20_model.r INFO @ Sat, 11 Dec 2021 12:43:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:43:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:43:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:43:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.10_summits.bed INFO @ Sat, 11 Dec 2021 12:43:58: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2632 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:44:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971115/SRX10971115.20_summits.bed INFO @ Sat, 11 Dec 2021 12:44:24: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1926 records, 4 fields): 4 millis CompletedMACS2peakCalling