Job ID = 14170400 SRX = SRX11760554 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T21:42:06 prefetch.2.10.7: 1) Downloading 'SRR15461256'... 2021-12-10T21:42:06 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T21:43:44 prefetch.2.10.7: HTTPS download succeed 2021-12-10T21:43:44 prefetch.2.10.7: 1) 'SRR15461256' was downloaded successfully 2021-12-10T21:43:44 prefetch.2.10.7: 'SRR15461256' has 0 unresolved dependencies Read 44983103 spots for SRR15461256/SRR15461256.sra Written 44983103 spots for SRR15461256/SRR15461256.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170974 ("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: 00:31:23 44983103 reads; of these: 44983103 (100.00%) were paired; of these: 10269201 (22.83%) aligned concordantly 0 times 9256916 (20.58%) aligned concordantly exactly 1 time 25456986 (56.59%) aligned concordantly >1 times ---- 10269201 pairs aligned concordantly 0 times; of these: 110995 (1.08%) aligned discordantly 1 time ---- 10158206 pairs aligned 0 times concordantly or discordantly; of these: 20316412 mates make up the pairs; of these: 10587431 (52.11%) aligned 0 times 4129137 (20.32%) aligned exactly 1 time 5599844 (27.56%) aligned >1 times 88.23% overall alignment rate Time searching: 00:31:24 Overall time: 00:31:24 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 28 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] 21564720 / 34738446 = 0.6208 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 07:31:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.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 07:31:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:31:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:31:32: 1000000 INFO @ Sat, 11 Dec 2021 07:31:37: 2000000 INFO @ Sat, 11 Dec 2021 07:31:42: 3000000 INFO @ Sat, 11 Dec 2021 07:31:46: 4000000 INFO @ Sat, 11 Dec 2021 07:31:51: 5000000 INFO @ Sat, 11 Dec 2021 07:31:56: 6000000 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 07:31:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.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 07:31:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:31:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:32:01: 7000000 INFO @ Sat, 11 Dec 2021 07:32:04: 1000000 INFO @ Sat, 11 Dec 2021 07:32:06: 8000000 INFO @ Sat, 11 Dec 2021 07:32:10: 2000000 INFO @ Sat, 11 Dec 2021 07:32:12: 9000000 INFO @ Sat, 11 Dec 2021 07:32:16: 3000000 INFO @ Sat, 11 Dec 2021 07:32:17: 10000000 INFO @ Sat, 11 Dec 2021 07:32:23: 11000000 INFO @ Sat, 11 Dec 2021 07:32:23: 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 07:32:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.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 07:32:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:32:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:32:28: 12000000 INFO @ Sat, 11 Dec 2021 07:32:29: 5000000 INFO @ Sat, 11 Dec 2021 07:32:34: 13000000 INFO @ Sat, 11 Dec 2021 07:32:34: 1000000 INFO @ Sat, 11 Dec 2021 07:32:35: 6000000 INFO @ Sat, 11 Dec 2021 07:32:39: 14000000 INFO @ Sat, 11 Dec 2021 07:32:40: 2000000 INFO @ Sat, 11 Dec 2021 07:32:41: 7000000 INFO @ Sat, 11 Dec 2021 07:32:45: 15000000 INFO @ Sat, 11 Dec 2021 07:32:46: 3000000 INFO @ Sat, 11 Dec 2021 07:32:48: 8000000 INFO @ Sat, 11 Dec 2021 07:32:50: 16000000 INFO @ Sat, 11 Dec 2021 07:32:52: 4000000 INFO @ Sat, 11 Dec 2021 07:32:54: 9000000 INFO @ Sat, 11 Dec 2021 07:32:56: 17000000 INFO @ Sat, 11 Dec 2021 07:32:58: 5000000 INFO @ Sat, 11 Dec 2021 07:33:00: 10000000 INFO @ Sat, 11 Dec 2021 07:33:01: 18000000 INFO @ Sat, 11 Dec 2021 07:33:04: 6000000 INFO @ Sat, 11 Dec 2021 07:33:07: 11000000 INFO @ Sat, 11 Dec 2021 07:33:07: 19000000 INFO @ Sat, 11 Dec 2021 07:33:11: 7000000 INFO @ Sat, 11 Dec 2021 07:33:12: 20000000 INFO @ Sat, 11 Dec 2021 07:33:13: 12000000 INFO @ Sat, 11 Dec 2021 07:33:17: 8000000 INFO @ Sat, 11 Dec 2021 07:33:17: 21000000 INFO @ Sat, 11 Dec 2021 07:33:19: 13000000 INFO @ Sat, 11 Dec 2021 07:33:22: 22000000 INFO @ Sat, 11 Dec 2021 07:33:23: 9000000 INFO @ Sat, 11 Dec 2021 07:33:26: 14000000 INFO @ Sat, 11 Dec 2021 07:33:27: 23000000 INFO @ Sat, 11 Dec 2021 07:33:29: 10000000 INFO @ Sat, 11 Dec 2021 07:33:32: 15000000 INFO @ Sat, 11 Dec 2021 07:33:32: 24000000 INFO @ Sat, 11 Dec 2021 07:33:35: 11000000 INFO @ Sat, 11 Dec 2021 07:33:38: 25000000 INFO @ Sat, 11 Dec 2021 07:33:39: 16000000 INFO @ Sat, 11 Dec 2021 07:33:41: 12000000 INFO @ Sat, 11 Dec 2021 07:33:43: 26000000 INFO @ Sat, 11 Dec 2021 07:33:45: 17000000 INFO @ Sat, 11 Dec 2021 07:33:47: 13000000 INFO @ Sat, 11 Dec 2021 07:33:48: 27000000 INFO @ Sat, 11 Dec 2021 07:33:51: 18000000 INFO @ Sat, 11 Dec 2021 07:33:53: 14000000 INFO @ Sat, 11 Dec 2021 07:33:53: 28000000 INFO @ Sat, 11 Dec 2021 07:33:58: 19000000 INFO @ Sat, 11 Dec 2021 07:33:58: 29000000 INFO @ Sat, 11 Dec 2021 07:33:59: 15000000 INFO @ Sat, 11 Dec 2021 07:34:04: 20000000 INFO @ Sat, 11 Dec 2021 07:34:04: 30000000 INFO @ Sat, 11 Dec 2021 07:34:05: 16000000 INFO @ Sat, 11 Dec 2021 07:34:10: 31000000 INFO @ Sat, 11 Dec 2021 07:34:10: 21000000 INFO @ Sat, 11 Dec 2021 07:34:12: 17000000 INFO @ Sat, 11 Dec 2021 07:34:15: 32000000 INFO @ Sat, 11 Dec 2021 07:34:15: 22000000 INFO @ Sat, 11 Dec 2021 07:34:18: 18000000 INFO @ Sat, 11 Dec 2021 07:34:21: 33000000 INFO @ Sat, 11 Dec 2021 07:34:21: 23000000 INFO @ Sat, 11 Dec 2021 07:34:24: 19000000 INFO @ Sat, 11 Dec 2021 07:34:26: 34000000 INFO @ Sat, 11 Dec 2021 07:34:27: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:34:30: 20000000 INFO @ Sat, 11 Dec 2021 07:34:32: 35000000 INFO @ Sat, 11 Dec 2021 07:34:33: 25000000 INFO @ Sat, 11 Dec 2021 07:34:35: 21000000 INFO @ Sat, 11 Dec 2021 07:34:37: 36000000 INFO @ Sat, 11 Dec 2021 07:34:39: #1 tag size is determined as 37 bps INFO @ Sat, 11 Dec 2021 07:34:39: #1 tag size = 37 INFO @ Sat, 11 Dec 2021 07:34:39: #1 total tags in treatment: 13151100 INFO @ Sat, 11 Dec 2021 07:34:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:34:39: #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 07:34:39: #1 tags after filtering in treatment: 8661268 INFO @ Sat, 11 Dec 2021 07:34:39: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 07:34:39: #1 finished! INFO @ Sat, 11 Dec 2021 07:34:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:34:39: 26000000 INFO @ Sat, 11 Dec 2021 07:34:40: #2 number of paired peaks: 1592 INFO @ Sat, 11 Dec 2021 07:34:40: start model_add_line... INFO @ Sat, 11 Dec 2021 07:34:40: start X-correlation... INFO @ Sat, 11 Dec 2021 07:34:40: end of X-cor INFO @ Sat, 11 Dec 2021 07:34:40: #2 finished! INFO @ Sat, 11 Dec 2021 07:34:40: #2 predicted fragment length is 86 bps INFO @ Sat, 11 Dec 2021 07:34:40: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 11 Dec 2021 07:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.05_model.r INFO @ Sat, 11 Dec 2021 07:34:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:34:41: 22000000 INFO @ Sat, 11 Dec 2021 07:34:45: 27000000 INFO @ Sat, 11 Dec 2021 07:34:47: 23000000 INFO @ Sat, 11 Dec 2021 07:34:51: 28000000 INFO @ Sat, 11 Dec 2021 07:34:52: 24000000 INFO @ Sat, 11 Dec 2021 07:34:57: 29000000 INFO @ Sat, 11 Dec 2021 07:34:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:34:58: 25000000 INFO @ Sat, 11 Dec 2021 07:35:03: 30000000 INFO @ Sat, 11 Dec 2021 07:35:04: 26000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:35:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:35:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:35:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.05_summits.bed INFO @ Sat, 11 Dec 2021 07:35:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10930 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:35:09: 31000000 INFO @ Sat, 11 Dec 2021 07:35:10: 27000000 INFO @ Sat, 11 Dec 2021 07:35:15: 32000000 INFO @ Sat, 11 Dec 2021 07:35:15: 28000000 INFO @ Sat, 11 Dec 2021 07:35:21: 29000000 INFO @ Sat, 11 Dec 2021 07:35:21: 33000000 INFO @ Sat, 11 Dec 2021 07:35:27: 30000000 INFO @ Sat, 11 Dec 2021 07:35:28: 34000000 INFO @ Sat, 11 Dec 2021 07:35:33: 31000000 INFO @ Sat, 11 Dec 2021 07:35:34: 35000000 INFO @ Sat, 11 Dec 2021 07:35:39: 32000000 INFO @ Sat, 11 Dec 2021 07:35:40: 36000000 INFO @ Sat, 11 Dec 2021 07:35:41: #1 tag size is determined as 37 bps INFO @ Sat, 11 Dec 2021 07:35:41: #1 tag size = 37 INFO @ Sat, 11 Dec 2021 07:35:41: #1 total tags in treatment: 13151100 INFO @ Sat, 11 Dec 2021 07:35:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:35:41: #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 07:35:41: #1 tags after filtering in treatment: 8661268 INFO @ Sat, 11 Dec 2021 07:35:41: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 07:35:41: #1 finished! INFO @ Sat, 11 Dec 2021 07:35:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:35:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:35:42: #2 number of paired peaks: 1592 INFO @ Sat, 11 Dec 2021 07:35:42: start model_add_line... INFO @ Sat, 11 Dec 2021 07:35:42: start X-correlation... INFO @ Sat, 11 Dec 2021 07:35:42: end of X-cor INFO @ Sat, 11 Dec 2021 07:35:42: #2 finished! INFO @ Sat, 11 Dec 2021 07:35:42: #2 predicted fragment length is 86 bps INFO @ Sat, 11 Dec 2021 07:35:42: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 11 Dec 2021 07:35:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.10_model.r INFO @ Sat, 11 Dec 2021 07:35:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:35:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:35:45: 33000000 INFO @ Sat, 11 Dec 2021 07:35:51: 34000000 INFO @ Sat, 11 Dec 2021 07:35:56: 35000000 INFO @ Sat, 11 Dec 2021 07:36:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:36:02: 36000000 INFO @ Sat, 11 Dec 2021 07:36:03: #1 tag size is determined as 37 bps INFO @ Sat, 11 Dec 2021 07:36:03: #1 tag size = 37 INFO @ Sat, 11 Dec 2021 07:36:03: #1 total tags in treatment: 13151100 INFO @ Sat, 11 Dec 2021 07:36:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:36:03: #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 07:36:04: #1 tags after filtering in treatment: 8661268 INFO @ Sat, 11 Dec 2021 07:36:04: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 07:36:04: #1 finished! INFO @ Sat, 11 Dec 2021 07:36:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:36:04: #2 number of paired peaks: 1592 INFO @ Sat, 11 Dec 2021 07:36:04: start model_add_line... INFO @ Sat, 11 Dec 2021 07:36:04: start X-correlation... INFO @ Sat, 11 Dec 2021 07:36:04: end of X-cor INFO @ Sat, 11 Dec 2021 07:36:04: #2 finished! INFO @ Sat, 11 Dec 2021 07:36:04: #2 predicted fragment length is 86 bps INFO @ Sat, 11 Dec 2021 07:36:04: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 11 Dec 2021 07:36:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.20_model.r INFO @ Sat, 11 Dec 2021 07:36:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:36:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:36:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:36:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:36:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.10_summits.bed INFO @ Sat, 11 Dec 2021 07:36:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4869 records, 4 fields): 287 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:36:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:36:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:36:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:36:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11760554/SRX11760554.20_summits.bed INFO @ Sat, 11 Dec 2021 07:36:34: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (974 records, 4 fields): 3 millis CompletedMACS2peakCalling