Job ID = 16439705 SRX = SRX11499372 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23067906 spots for SRR15192733/SRR15192733.sra Written 23067906 spots for SRR15192733/SRR15192733.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440022 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:34:37 23067906 reads; of these: 23067906 (100.00%) were paired; of these: 6138663 (26.61%) aligned concordantly 0 times 15658597 (67.88%) aligned concordantly exactly 1 time 1270646 (5.51%) aligned concordantly >1 times ---- 6138663 pairs aligned concordantly 0 times; of these: 1714805 (27.93%) aligned discordantly 1 time ---- 4423858 pairs aligned 0 times concordantly or discordantly; of these: 8847716 mates make up the pairs; of these: 7854805 (88.78%) aligned 0 times 700749 (7.92%) aligned exactly 1 time 292162 (3.30%) aligned >1 times 82.97% overall alignment rate Time searching: 00:34:38 Overall time: 00:34:38 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] 2004583 / 17489446 = 0.1146 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 16:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.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 16:52:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:52:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:53:00: 1000000 INFO @ Tue, 02 Aug 2022 16:53:06: 2000000 INFO @ Tue, 02 Aug 2022 16:53:12: 3000000 INFO @ Tue, 02 Aug 2022 16:53:19: 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 16:53:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.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 16:53:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:53:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:53:25: 5000000 INFO @ Tue, 02 Aug 2022 16:53:30: 1000000 INFO @ Tue, 02 Aug 2022 16:53:32: 6000000 INFO @ Tue, 02 Aug 2022 16:53:36: 2000000 INFO @ Tue, 02 Aug 2022 16:53:39: 7000000 INFO @ Tue, 02 Aug 2022 16:53:43: 3000000 INFO @ Tue, 02 Aug 2022 16:53:45: 8000000 INFO @ Tue, 02 Aug 2022 16:53:50: 4000000 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 16:53:52: 9000000 INFO @ Tue, 02 Aug 2022 16:53:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.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 16:53:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:53:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:53:56: 5000000 INFO @ Tue, 02 Aug 2022 16:53:59: 10000000 INFO @ Tue, 02 Aug 2022 16:54:00: 1000000 INFO @ Tue, 02 Aug 2022 16:54:03: 6000000 INFO @ Tue, 02 Aug 2022 16:54:06: 11000000 INFO @ Tue, 02 Aug 2022 16:54:06: 2000000 INFO @ Tue, 02 Aug 2022 16:54:10: 7000000 INFO @ Tue, 02 Aug 2022 16:54:12: 12000000 INFO @ Tue, 02 Aug 2022 16:54:13: 3000000 INFO @ Tue, 02 Aug 2022 16:54:17: 8000000 INFO @ Tue, 02 Aug 2022 16:54:19: 13000000 INFO @ Tue, 02 Aug 2022 16:54:20: 4000000 INFO @ Tue, 02 Aug 2022 16:54:24: 9000000 INFO @ Tue, 02 Aug 2022 16:54:26: 14000000 INFO @ Tue, 02 Aug 2022 16:54:26: 5000000 INFO @ Tue, 02 Aug 2022 16:54:30: 10000000 INFO @ Tue, 02 Aug 2022 16:54:33: 15000000 INFO @ Tue, 02 Aug 2022 16:54:33: 6000000 INFO @ Tue, 02 Aug 2022 16:54:37: 11000000 INFO @ Tue, 02 Aug 2022 16:54:40: 16000000 INFO @ Tue, 02 Aug 2022 16:54:40: 7000000 INFO @ Tue, 02 Aug 2022 16:54:44: 12000000 INFO @ Tue, 02 Aug 2022 16:54:47: 8000000 INFO @ Tue, 02 Aug 2022 16:54:47: 17000000 INFO @ Tue, 02 Aug 2022 16:54:51: 13000000 INFO @ Tue, 02 Aug 2022 16:54:53: 9000000 INFO @ Tue, 02 Aug 2022 16:54:54: 18000000 INFO @ Tue, 02 Aug 2022 16:54:58: 14000000 INFO @ Tue, 02 Aug 2022 16:55:00: 10000000 INFO @ Tue, 02 Aug 2022 16:55:00: 19000000 INFO @ Tue, 02 Aug 2022 16:55:05: 15000000 INFO @ Tue, 02 Aug 2022 16:55:07: 11000000 INFO @ Tue, 02 Aug 2022 16:55:07: 20000000 INFO @ Tue, 02 Aug 2022 16:55:12: 16000000 INFO @ Tue, 02 Aug 2022 16:55:14: 12000000 INFO @ Tue, 02 Aug 2022 16:55:14: 21000000 INFO @ Tue, 02 Aug 2022 16:55:19: 17000000 INFO @ Tue, 02 Aug 2022 16:55:20: 13000000 INFO @ Tue, 02 Aug 2022 16:55:21: 22000000 INFO @ Tue, 02 Aug 2022 16:55:26: 18000000 INFO @ Tue, 02 Aug 2022 16:55:27: 14000000 INFO @ Tue, 02 Aug 2022 16:55:28: 23000000 INFO @ Tue, 02 Aug 2022 16:55:33: 19000000 INFO @ Tue, 02 Aug 2022 16:55:34: 15000000 INFO @ Tue, 02 Aug 2022 16:55:35: 24000000 INFO @ Tue, 02 Aug 2022 16:55:39: 20000000 INFO @ Tue, 02 Aug 2022 16:55:41: 16000000 INFO @ Tue, 02 Aug 2022 16:55:42: 25000000 INFO @ Tue, 02 Aug 2022 16:55:46: 21000000 INFO @ Tue, 02 Aug 2022 16:55:47: 17000000 INFO @ Tue, 02 Aug 2022 16:55:49: 26000000 INFO @ Tue, 02 Aug 2022 16:55:53: 22000000 INFO @ Tue, 02 Aug 2022 16:55:54: 18000000 INFO @ Tue, 02 Aug 2022 16:55:56: 27000000 INFO @ Tue, 02 Aug 2022 16:56:00: 23000000 INFO @ Tue, 02 Aug 2022 16:56:01: 19000000 INFO @ Tue, 02 Aug 2022 16:56:03: 28000000 INFO @ Tue, 02 Aug 2022 16:56:07: 24000000 INFO @ Tue, 02 Aug 2022 16:56:08: 20000000 INFO @ Tue, 02 Aug 2022 16:56:10: 29000000 INFO @ Tue, 02 Aug 2022 16:56:14: 25000000 INFO @ Tue, 02 Aug 2022 16:56:14: 21000000 INFO @ Tue, 02 Aug 2022 16:56:17: 30000000 INFO @ Tue, 02 Aug 2022 16:56:21: 26000000 INFO @ Tue, 02 Aug 2022 16:56:21: 22000000 INFO @ Tue, 02 Aug 2022 16:56:24: 31000000 INFO @ Tue, 02 Aug 2022 16:56:28: 27000000 INFO @ Tue, 02 Aug 2022 16:56:28: 23000000 INFO @ Tue, 02 Aug 2022 16:56:31: 32000000 INFO @ Tue, 02 Aug 2022 16:56:35: 24000000 INFO @ Tue, 02 Aug 2022 16:56:35: 28000000 INFO @ Tue, 02 Aug 2022 16:56:38: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:56:42: 25000000 INFO @ Tue, 02 Aug 2022 16:56:42: 29000000 INFO @ Tue, 02 Aug 2022 16:56:45: 34000000 INFO @ Tue, 02 Aug 2022 16:56:47: #1 tag size is determined as 128 bps INFO @ Tue, 02 Aug 2022 16:56:47: #1 tag size = 128 INFO @ Tue, 02 Aug 2022 16:56:47: #1 total tags in treatment: 15048523 INFO @ Tue, 02 Aug 2022 16:56:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:56:47: #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 16:56:47: #1 tags after filtering in treatment: 9834522 INFO @ Tue, 02 Aug 2022 16:56:47: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 16:56:47: #1 finished! INFO @ Tue, 02 Aug 2022 16:56:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:56:48: #2 number of paired peaks: 6710 INFO @ Tue, 02 Aug 2022 16:56:48: start model_add_line... INFO @ Tue, 02 Aug 2022 16:56:49: start X-correlation... INFO @ Tue, 02 Aug 2022 16:56:49: 26000000 INFO @ Tue, 02 Aug 2022 16:56:49: end of X-cor INFO @ Tue, 02 Aug 2022 16:56:49: #2 finished! INFO @ Tue, 02 Aug 2022 16:56:49: #2 predicted fragment length is 284 bps INFO @ Tue, 02 Aug 2022 16:56:49: #2 alternative fragment length(s) may be 284 bps INFO @ Tue, 02 Aug 2022 16:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.05_model.r INFO @ Tue, 02 Aug 2022 16:56:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:56:49: 30000000 INFO @ Tue, 02 Aug 2022 16:56:55: 27000000 INFO @ Tue, 02 Aug 2022 16:56:56: 31000000 INFO @ Tue, 02 Aug 2022 16:57:02: 28000000 INFO @ Tue, 02 Aug 2022 16:57:03: 32000000 INFO @ Tue, 02 Aug 2022 16:57:09: 33000000 INFO @ Tue, 02 Aug 2022 16:57:09: 29000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:57:16: 34000000 INFO @ Tue, 02 Aug 2022 16:57:16: 30000000 INFO @ Tue, 02 Aug 2022 16:57:18: #1 tag size is determined as 128 bps INFO @ Tue, 02 Aug 2022 16:57:18: #1 tag size = 128 INFO @ Tue, 02 Aug 2022 16:57:18: #1 total tags in treatment: 15048523 INFO @ Tue, 02 Aug 2022 16:57:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:57:18: #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 16:57:19: #1 tags after filtering in treatment: 9834522 INFO @ Tue, 02 Aug 2022 16:57:19: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 16:57:19: #1 finished! INFO @ Tue, 02 Aug 2022 16:57:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:57:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:57:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:57:20: #2 number of paired peaks: 6710 INFO @ Tue, 02 Aug 2022 16:57:20: start model_add_line... INFO @ Tue, 02 Aug 2022 16:57:20: start X-correlation... INFO @ Tue, 02 Aug 2022 16:57:20: end of X-cor INFO @ Tue, 02 Aug 2022 16:57:20: #2 finished! INFO @ Tue, 02 Aug 2022 16:57:20: #2 predicted fragment length is 284 bps INFO @ Tue, 02 Aug 2022 16:57:20: #2 alternative fragment length(s) may be 284 bps INFO @ Tue, 02 Aug 2022 16:57:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.10_model.r INFO @ Tue, 02 Aug 2022 16:57:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:57:23: 31000000 INFO @ Tue, 02 Aug 2022 16:57:30: 32000000 INFO @ Tue, 02 Aug 2022 16:57:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:57:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:57:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.05_summits.bed INFO @ Tue, 02 Aug 2022 16:57:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7388 records, 4 fields): 201 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:57:36: 33000000 INFO @ Tue, 02 Aug 2022 16:57:43: 34000000 INFO @ Tue, 02 Aug 2022 16:57:45: #1 tag size is determined as 128 bps INFO @ Tue, 02 Aug 2022 16:57:45: #1 tag size = 128 INFO @ Tue, 02 Aug 2022 16:57:45: #1 total tags in treatment: 15048523 INFO @ Tue, 02 Aug 2022 16:57:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:57:45: #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 16:57:45: #1 tags after filtering in treatment: 9834522 INFO @ Tue, 02 Aug 2022 16:57:45: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 16:57:45: #1 finished! INFO @ Tue, 02 Aug 2022 16:57:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:57:46: #2 number of paired peaks: 6710 INFO @ Tue, 02 Aug 2022 16:57:46: start model_add_line... INFO @ Tue, 02 Aug 2022 16:57:46: start X-correlation... INFO @ Tue, 02 Aug 2022 16:57:46: end of X-cor INFO @ Tue, 02 Aug 2022 16:57:46: #2 finished! INFO @ Tue, 02 Aug 2022 16:57:46: #2 predicted fragment length is 284 bps INFO @ Tue, 02 Aug 2022 16:57:46: #2 alternative fragment length(s) may be 284 bps INFO @ Tue, 02 Aug 2022 16:57:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.20_model.r INFO @ Tue, 02 Aug 2022 16:57:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:57:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:57:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:58:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:58:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:58:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.10_summits.bed INFO @ Tue, 02 Aug 2022 16:58:01: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6523 records, 4 fields): 102 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:58:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:58:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:58:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:58:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499372/SRX11499372.20_summits.bed INFO @ Tue, 02 Aug 2022 16:58:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5628 records, 4 fields): 26 millis CompletedMACS2peakCalling