Job ID = 16439377 SRX = SRX15312087 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:00:52 prefetch.2.10.7: 1) Downloading 'SRR19251496'... 2022-08-02T06:00:52 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:01:42 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:01:42 prefetch.2.10.7: 1) 'SRR19251496' was downloaded successfully 2022-08-02T06:01:42 prefetch.2.10.7: 'SRR19251496' has 0 unresolved dependencies Read 24098090 spots for SRR19251496/SRR19251496.sra Written 24098090 spots for SRR19251496/SRR19251496.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439535 ("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: 00:22:24 24098090 reads; of these: 24098090 (100.00%) were paired; of these: 1130655 (4.69%) aligned concordantly 0 times 20853707 (86.54%) aligned concordantly exactly 1 time 2113728 (8.77%) aligned concordantly >1 times ---- 1130655 pairs aligned concordantly 0 times; of these: 199490 (17.64%) aligned discordantly 1 time ---- 931165 pairs aligned 0 times concordantly or discordantly; of these: 1862330 mates make up the pairs; of these: 1221020 (65.56%) aligned 0 times 501608 (26.93%) aligned exactly 1 time 139702 (7.50%) aligned >1 times 97.47% overall alignment rate Time searching: 00:22:24 Overall time: 00:22:24 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 16 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] 2725089 / 23055175 = 0.1182 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 15:39:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.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 15:39:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:39:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:40:05: 1000000 INFO @ Tue, 02 Aug 2022 15:40:10: 2000000 INFO @ Tue, 02 Aug 2022 15:40:15: 3000000 INFO @ Tue, 02 Aug 2022 15:40:20: 4000000 INFO @ Tue, 02 Aug 2022 15:40:25: 5000000 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 15:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.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 15:40:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:40:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:40:30: 6000000 INFO @ Tue, 02 Aug 2022 15:40:34: 1000000 INFO @ Tue, 02 Aug 2022 15:40:35: 7000000 INFO @ Tue, 02 Aug 2022 15:40:40: 2000000 INFO @ Tue, 02 Aug 2022 15:40:40: 8000000 INFO @ Tue, 02 Aug 2022 15:40:45: 3000000 INFO @ Tue, 02 Aug 2022 15:40:46: 9000000 INFO @ Tue, 02 Aug 2022 15:40:51: 4000000 INFO @ Tue, 02 Aug 2022 15:40:51: 10000000 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 15:40:56: 11000000 INFO @ Tue, 02 Aug 2022 15:40:57: 5000000 INFO @ Tue, 02 Aug 2022 15:40:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.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 15:40:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:40:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:41:02: 12000000 INFO @ Tue, 02 Aug 2022 15:41:02: 6000000 INFO @ Tue, 02 Aug 2022 15:41:04: 1000000 INFO @ Tue, 02 Aug 2022 15:41:07: 13000000 INFO @ Tue, 02 Aug 2022 15:41:08: 7000000 INFO @ Tue, 02 Aug 2022 15:41:10: 2000000 INFO @ Tue, 02 Aug 2022 15:41:12: 14000000 INFO @ Tue, 02 Aug 2022 15:41:14: 8000000 INFO @ Tue, 02 Aug 2022 15:41:15: 3000000 INFO @ Tue, 02 Aug 2022 15:41:18: 15000000 INFO @ Tue, 02 Aug 2022 15:41:19: 9000000 INFO @ Tue, 02 Aug 2022 15:41:20: 4000000 INFO @ Tue, 02 Aug 2022 15:41:24: 16000000 INFO @ Tue, 02 Aug 2022 15:41:25: 10000000 INFO @ Tue, 02 Aug 2022 15:41:25: 5000000 INFO @ Tue, 02 Aug 2022 15:41:29: 17000000 INFO @ Tue, 02 Aug 2022 15:41:30: 11000000 INFO @ Tue, 02 Aug 2022 15:41:31: 6000000 INFO @ Tue, 02 Aug 2022 15:41:35: 18000000 INFO @ Tue, 02 Aug 2022 15:41:36: 12000000 INFO @ Tue, 02 Aug 2022 15:41:37: 7000000 INFO @ Tue, 02 Aug 2022 15:41:40: 19000000 INFO @ Tue, 02 Aug 2022 15:41:42: 13000000 INFO @ Tue, 02 Aug 2022 15:41:42: 8000000 INFO @ Tue, 02 Aug 2022 15:41:46: 20000000 INFO @ Tue, 02 Aug 2022 15:41:47: 14000000 INFO @ Tue, 02 Aug 2022 15:41:48: 9000000 INFO @ Tue, 02 Aug 2022 15:41:51: 21000000 INFO @ Tue, 02 Aug 2022 15:41:53: 15000000 INFO @ Tue, 02 Aug 2022 15:41:53: 10000000 INFO @ Tue, 02 Aug 2022 15:41:56: 22000000 INFO @ Tue, 02 Aug 2022 15:41:59: 16000000 INFO @ Tue, 02 Aug 2022 15:41:59: 11000000 INFO @ Tue, 02 Aug 2022 15:42:02: 23000000 INFO @ Tue, 02 Aug 2022 15:42:04: 12000000 INFO @ Tue, 02 Aug 2022 15:42:04: 17000000 INFO @ Tue, 02 Aug 2022 15:42:07: 24000000 INFO @ Tue, 02 Aug 2022 15:42:10: 13000000 INFO @ Tue, 02 Aug 2022 15:42:10: 18000000 INFO @ Tue, 02 Aug 2022 15:42:13: 25000000 INFO @ Tue, 02 Aug 2022 15:42:15: 14000000 INFO @ Tue, 02 Aug 2022 15:42:16: 19000000 INFO @ Tue, 02 Aug 2022 15:42:18: 26000000 INFO @ Tue, 02 Aug 2022 15:42:21: 15000000 INFO @ Tue, 02 Aug 2022 15:42:21: 20000000 INFO @ Tue, 02 Aug 2022 15:42:24: 27000000 INFO @ Tue, 02 Aug 2022 15:42:27: 16000000 INFO @ Tue, 02 Aug 2022 15:42:27: 21000000 INFO @ Tue, 02 Aug 2022 15:42:30: 28000000 INFO @ Tue, 02 Aug 2022 15:42:33: 17000000 INFO @ Tue, 02 Aug 2022 15:42:33: 22000000 INFO @ Tue, 02 Aug 2022 15:42:35: 29000000 INFO @ Tue, 02 Aug 2022 15:42:38: 18000000 INFO @ Tue, 02 Aug 2022 15:42:39: 23000000 INFO @ Tue, 02 Aug 2022 15:42:41: 30000000 INFO @ Tue, 02 Aug 2022 15:42:44: 19000000 INFO @ Tue, 02 Aug 2022 15:42:45: 24000000 INFO @ Tue, 02 Aug 2022 15:42:47: 31000000 INFO @ Tue, 02 Aug 2022 15:42:50: 20000000 INFO @ Tue, 02 Aug 2022 15:42:51: 25000000 INFO @ Tue, 02 Aug 2022 15:42:53: 32000000 INFO @ Tue, 02 Aug 2022 15:42:56: 21000000 INFO @ Tue, 02 Aug 2022 15:42:56: 26000000 INFO @ Tue, 02 Aug 2022 15:42:58: 33000000 INFO @ Tue, 02 Aug 2022 15:43:01: 22000000 INFO @ Tue, 02 Aug 2022 15:43:02: 27000000 INFO @ Tue, 02 Aug 2022 15:43:04: 34000000 INFO @ Tue, 02 Aug 2022 15:43:07: 23000000 INFO @ Tue, 02 Aug 2022 15:43:08: 28000000 INFO @ Tue, 02 Aug 2022 15:43:10: 35000000 INFO @ Tue, 02 Aug 2022 15:43:13: 24000000 INFO @ Tue, 02 Aug 2022 15:43:13: 29000000 INFO @ Tue, 02 Aug 2022 15:43:16: 36000000 INFO @ Tue, 02 Aug 2022 15:43:19: 25000000 INFO @ Tue, 02 Aug 2022 15:43:19: 30000000 INFO @ Tue, 02 Aug 2022 15:43:21: 37000000 INFO @ Tue, 02 Aug 2022 15:43:25: 26000000 INFO @ Tue, 02 Aug 2022 15:43:25: 31000000 INFO @ Tue, 02 Aug 2022 15:43:27: 38000000 INFO @ Tue, 02 Aug 2022 15:43:31: 27000000 INFO @ Tue, 02 Aug 2022 15:43:31: 32000000 INFO @ Tue, 02 Aug 2022 15:43:33: 39000000 INFO @ Tue, 02 Aug 2022 15:43:37: 28000000 INFO @ Tue, 02 Aug 2022 15:43:37: 33000000 INFO @ Tue, 02 Aug 2022 15:43:39: 40000000 INFO @ Tue, 02 Aug 2022 15:43:43: 29000000 INFO @ Tue, 02 Aug 2022 15:43:43: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:43:45: 41000000 INFO @ Tue, 02 Aug 2022 15:43:48: 30000000 INFO @ Tue, 02 Aug 2022 15:43:48: #1 tag size is determined as 40 bps INFO @ Tue, 02 Aug 2022 15:43:48: #1 tag size = 40 INFO @ Tue, 02 Aug 2022 15:43:48: #1 total tags in treatment: 20245348 INFO @ Tue, 02 Aug 2022 15:43:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:43:48: #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 15:43:49: 35000000 INFO @ Tue, 02 Aug 2022 15:43:49: #1 tags after filtering in treatment: 11489879 INFO @ Tue, 02 Aug 2022 15:43:49: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 02 Aug 2022 15:43:49: #1 finished! INFO @ Tue, 02 Aug 2022 15:43:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:43:50: #2 number of paired peaks: 4789 INFO @ Tue, 02 Aug 2022 15:43:50: start model_add_line... INFO @ Tue, 02 Aug 2022 15:43:50: start X-correlation... INFO @ Tue, 02 Aug 2022 15:43:50: end of X-cor INFO @ Tue, 02 Aug 2022 15:43:50: #2 finished! INFO @ Tue, 02 Aug 2022 15:43:50: #2 predicted fragment length is 103 bps INFO @ Tue, 02 Aug 2022 15:43:50: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 02 Aug 2022 15:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.05_model.r INFO @ Tue, 02 Aug 2022 15:43:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:43:54: 31000000 INFO @ Tue, 02 Aug 2022 15:43:54: 36000000 INFO @ Tue, 02 Aug 2022 15:44:00: 37000000 INFO @ Tue, 02 Aug 2022 15:44:00: 32000000 INFO @ Tue, 02 Aug 2022 15:44:06: 38000000 INFO @ Tue, 02 Aug 2022 15:44:06: 33000000 INFO @ Tue, 02 Aug 2022 15:44:12: 39000000 INFO @ Tue, 02 Aug 2022 15:44:12: 34000000 INFO @ Tue, 02 Aug 2022 15:44:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:44:17: 35000000 INFO @ Tue, 02 Aug 2022 15:44:17: 40000000 INFO @ Tue, 02 Aug 2022 15:44:22: 36000000 INFO @ Tue, 02 Aug 2022 15:44:23: 41000000 INFO @ Tue, 02 Aug 2022 15:44:27: #1 tag size is determined as 40 bps INFO @ Tue, 02 Aug 2022 15:44:27: #1 tag size = 40 INFO @ Tue, 02 Aug 2022 15:44:27: #1 total tags in treatment: 20245348 INFO @ Tue, 02 Aug 2022 15:44:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:44:27: #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 15:44:27: 37000000 INFO @ Tue, 02 Aug 2022 15:44:27: #1 tags after filtering in treatment: 11489879 INFO @ Tue, 02 Aug 2022 15:44:27: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 02 Aug 2022 15:44:27: #1 finished! INFO @ Tue, 02 Aug 2022 15:44:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:44:28: #2 number of paired peaks: 4789 INFO @ Tue, 02 Aug 2022 15:44:28: start model_add_line... INFO @ Tue, 02 Aug 2022 15:44:29: start X-correlation... INFO @ Tue, 02 Aug 2022 15:44:29: end of X-cor INFO @ Tue, 02 Aug 2022 15:44:29: #2 finished! INFO @ Tue, 02 Aug 2022 15:44:29: #2 predicted fragment length is 103 bps INFO @ Tue, 02 Aug 2022 15:44:29: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 02 Aug 2022 15:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.10_model.r INFO @ Tue, 02 Aug 2022 15:44:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:44:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:44:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:44:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.05_summits.bed INFO @ Tue, 02 Aug 2022 15:44:31: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (19404 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:44:32: 38000000 INFO @ Tue, 02 Aug 2022 15:44:37: 39000000 INFO @ Tue, 02 Aug 2022 15:44:41: 40000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:44:46: 41000000 INFO @ Tue, 02 Aug 2022 15:44:49: #1 tag size is determined as 40 bps INFO @ Tue, 02 Aug 2022 15:44:49: #1 tag size = 40 INFO @ Tue, 02 Aug 2022 15:44:49: #1 total tags in treatment: 20245348 INFO @ Tue, 02 Aug 2022 15:44:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:44:49: #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 15:44:49: #1 tags after filtering in treatment: 11489879 INFO @ Tue, 02 Aug 2022 15:44:49: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 02 Aug 2022 15:44:49: #1 finished! INFO @ Tue, 02 Aug 2022 15:44:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:44:51: #2 number of paired peaks: 4789 INFO @ Tue, 02 Aug 2022 15:44:51: start model_add_line... INFO @ Tue, 02 Aug 2022 15:44:51: start X-correlation... INFO @ Tue, 02 Aug 2022 15:44:51: end of X-cor INFO @ Tue, 02 Aug 2022 15:44:51: #2 finished! INFO @ Tue, 02 Aug 2022 15:44:51: #2 predicted fragment length is 103 bps INFO @ Tue, 02 Aug 2022 15:44:51: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 02 Aug 2022 15:44:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.20_model.r INFO @ Tue, 02 Aug 2022 15:44:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:44:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:44:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:45:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:45:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:45:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.10_summits.bed INFO @ Tue, 02 Aug 2022 15:45:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (13847 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:45:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15312087/SRX15312087.20_summits.bed INFO @ Tue, 02 Aug 2022 15:45:26: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6588 records, 4 fields): 42 millis CompletedMACS2peakCalling