Job ID = 5720780 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,063,412 reads read : 50,126,824 reads written : 50,126,824 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 02:18:15 25063412 reads; of these: 25063412 (100.00%) were paired; of these: 6812892 (27.18%) aligned concordantly 0 times 6324633 (25.23%) aligned concordantly exactly 1 time 11925887 (47.58%) aligned concordantly >1 times ---- 6812892 pairs aligned concordantly 0 times; of these: 923454 (13.55%) aligned discordantly 1 time ---- 5889438 pairs aligned 0 times concordantly or discordantly; of these: 11778876 mates make up the pairs; of these: 4342928 (36.87%) aligned 0 times 1082754 (9.19%) aligned exactly 1 time 6353194 (53.94%) aligned >1 times 91.34% overall alignment rate Time searching: 02:18:15 Overall time: 02:18:15 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 20 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] 2521990 / 19058245 = 0.1323 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 04:24:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.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 @ Thu, 16 Apr 2020 04:24:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:24:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:24:16: 1000000 INFO @ Thu, 16 Apr 2020 04:24:22: 2000000 INFO @ Thu, 16 Apr 2020 04:24:27: 3000000 INFO @ Thu, 16 Apr 2020 04:24:33: 4000000 INFO @ Thu, 16 Apr 2020 04:24:38: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 04:24:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.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 @ Thu, 16 Apr 2020 04:24:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:24:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:24:44: 6000000 INFO @ Thu, 16 Apr 2020 04:24:46: 1000000 INFO @ Thu, 16 Apr 2020 04:24:49: 7000000 INFO @ Thu, 16 Apr 2020 04:24:52: 2000000 INFO @ Thu, 16 Apr 2020 04:24:55: 8000000 INFO @ Thu, 16 Apr 2020 04:24:58: 3000000 INFO @ Thu, 16 Apr 2020 04:25:01: 9000000 INFO @ Thu, 16 Apr 2020 04:25:04: 4000000 INFO @ Thu, 16 Apr 2020 04:25:07: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 04:25:09: 5000000 INFO @ Thu, 16 Apr 2020 04:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.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 @ Thu, 16 Apr 2020 04:25:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:25:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:25:12: 11000000 INFO @ Thu, 16 Apr 2020 04:25:15: 6000000 INFO @ Thu, 16 Apr 2020 04:25:17: 1000000 INFO @ Thu, 16 Apr 2020 04:25:18: 12000000 INFO @ Thu, 16 Apr 2020 04:25:21: 7000000 INFO @ Thu, 16 Apr 2020 04:25:24: 13000000 INFO @ Thu, 16 Apr 2020 04:25:24: 2000000 INFO @ Thu, 16 Apr 2020 04:25:28: 8000000 INFO @ Thu, 16 Apr 2020 04:25:30: 14000000 INFO @ Thu, 16 Apr 2020 04:25:31: 3000000 INFO @ Thu, 16 Apr 2020 04:25:34: 9000000 INFO @ Thu, 16 Apr 2020 04:25:36: 15000000 INFO @ Thu, 16 Apr 2020 04:25:38: 4000000 INFO @ Thu, 16 Apr 2020 04:25:40: 10000000 INFO @ Thu, 16 Apr 2020 04:25:42: 16000000 INFO @ Thu, 16 Apr 2020 04:25:44: 5000000 INFO @ Thu, 16 Apr 2020 04:25:46: 11000000 INFO @ Thu, 16 Apr 2020 04:25:48: 17000000 INFO @ Thu, 16 Apr 2020 04:25:50: 6000000 INFO @ Thu, 16 Apr 2020 04:25:52: 12000000 INFO @ Thu, 16 Apr 2020 04:25:54: 18000000 INFO @ Thu, 16 Apr 2020 04:25:56: 7000000 INFO @ Thu, 16 Apr 2020 04:25:58: 13000000 INFO @ Thu, 16 Apr 2020 04:26:00: 19000000 INFO @ Thu, 16 Apr 2020 04:26:02: 8000000 INFO @ Thu, 16 Apr 2020 04:26:05: 14000000 INFO @ Thu, 16 Apr 2020 04:26:06: 20000000 INFO @ Thu, 16 Apr 2020 04:26:08: 9000000 INFO @ Thu, 16 Apr 2020 04:26:11: 15000000 INFO @ Thu, 16 Apr 2020 04:26:13: 21000000 INFO @ Thu, 16 Apr 2020 04:26:14: 10000000 INFO @ Thu, 16 Apr 2020 04:26:17: 16000000 INFO @ Thu, 16 Apr 2020 04:26:19: 22000000 INFO @ Thu, 16 Apr 2020 04:26:20: 11000000 INFO @ Thu, 16 Apr 2020 04:26:23: 17000000 INFO @ Thu, 16 Apr 2020 04:26:25: 23000000 INFO @ Thu, 16 Apr 2020 04:26:26: 12000000 INFO @ Thu, 16 Apr 2020 04:26:29: 18000000 INFO @ Thu, 16 Apr 2020 04:26:31: 24000000 INFO @ Thu, 16 Apr 2020 04:26:32: 13000000 INFO @ Thu, 16 Apr 2020 04:26:35: 19000000 INFO @ Thu, 16 Apr 2020 04:26:37: 25000000 INFO @ Thu, 16 Apr 2020 04:26:38: 14000000 INFO @ Thu, 16 Apr 2020 04:26:41: 20000000 INFO @ Thu, 16 Apr 2020 04:26:43: 26000000 INFO @ Thu, 16 Apr 2020 04:26:45: 15000000 INFO @ Thu, 16 Apr 2020 04:26:47: 21000000 INFO @ Thu, 16 Apr 2020 04:26:49: 27000000 INFO @ Thu, 16 Apr 2020 04:26:51: 16000000 INFO @ Thu, 16 Apr 2020 04:26:53: 22000000 INFO @ Thu, 16 Apr 2020 04:26:55: 28000000 INFO @ Thu, 16 Apr 2020 04:26:56: 17000000 INFO @ Thu, 16 Apr 2020 04:27:00: 23000000 INFO @ Thu, 16 Apr 2020 04:27:01: 29000000 INFO @ Thu, 16 Apr 2020 04:27:03: 18000000 INFO @ Thu, 16 Apr 2020 04:27:06: 24000000 INFO @ Thu, 16 Apr 2020 04:27:07: 30000000 INFO @ Thu, 16 Apr 2020 04:27:09: 19000000 INFO @ Thu, 16 Apr 2020 04:27:12: 25000000 INFO @ Thu, 16 Apr 2020 04:27:13: 31000000 INFO @ Thu, 16 Apr 2020 04:27:16: 20000000 INFO @ Thu, 16 Apr 2020 04:27:18: 26000000 INFO @ Thu, 16 Apr 2020 04:27:19: 32000000 INFO @ Thu, 16 Apr 2020 04:27:22: 21000000 INFO @ Thu, 16 Apr 2020 04:27:25: 27000000 INFO @ Thu, 16 Apr 2020 04:27:25: 33000000 INFO @ Thu, 16 Apr 2020 04:27:28: 22000000 INFO @ Thu, 16 Apr 2020 04:27:31: 28000000 INFO @ Thu, 16 Apr 2020 04:27:31: 34000000 INFO @ Thu, 16 Apr 2020 04:27:34: 23000000 INFO @ Thu, 16 Apr 2020 04:27:37: 29000000 INFO @ Thu, 16 Apr 2020 04:27:38: 35000000 INFO @ Thu, 16 Apr 2020 04:27:40: 24000000 INFO @ Thu, 16 Apr 2020 04:27:43: 30000000 INFO @ Thu, 16 Apr 2020 04:27:44: 36000000 INFO @ Thu, 16 Apr 2020 04:27:46: 25000000 INFO @ Thu, 16 Apr 2020 04:27:49: 31000000 INFO @ Thu, 16 Apr 2020 04:27:50: 37000000 INFO @ Thu, 16 Apr 2020 04:27:52: 26000000 INFO @ Thu, 16 Apr 2020 04:27:55: 32000000 INFO @ Thu, 16 Apr 2020 04:27:56: 38000000 INFO @ Thu, 16 Apr 2020 04:27:58: 27000000 INFO @ Thu, 16 Apr 2020 04:28:02: 33000000 INFO @ Thu, 16 Apr 2020 04:28:02: 39000000 INFO @ Thu, 16 Apr 2020 04:28:04: 28000000 INFO @ Thu, 16 Apr 2020 04:28:08: 34000000 INFO @ Thu, 16 Apr 2020 04:28:08: 40000000 INFO @ Thu, 16 Apr 2020 04:28:10: 29000000 INFO @ Thu, 16 Apr 2020 04:28:13: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:28:13: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:28:13: #1 total tags in treatment: 15833592 INFO @ Thu, 16 Apr 2020 04:28:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:28:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:28:13: #1 tags after filtering in treatment: 13318938 INFO @ Thu, 16 Apr 2020 04:28:13: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 04:28:13: #1 finished! INFO @ Thu, 16 Apr 2020 04:28:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:28:14: 35000000 INFO @ Thu, 16 Apr 2020 04:28:14: #2 number of paired peaks: 3232 INFO @ Thu, 16 Apr 2020 04:28:14: start model_add_line... INFO @ Thu, 16 Apr 2020 04:28:14: start X-correlation... INFO @ Thu, 16 Apr 2020 04:28:14: end of X-cor INFO @ Thu, 16 Apr 2020 04:28:14: #2 finished! INFO @ Thu, 16 Apr 2020 04:28:14: #2 predicted fragment length is 219 bps INFO @ Thu, 16 Apr 2020 04:28:14: #2 alternative fragment length(s) may be 219 bps INFO @ Thu, 16 Apr 2020 04:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.05_model.r INFO @ Thu, 16 Apr 2020 04:28:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:28:16: 30000000 INFO @ Thu, 16 Apr 2020 04:28:20: 36000000 INFO @ Thu, 16 Apr 2020 04:28:22: 31000000 INFO @ Thu, 16 Apr 2020 04:28:26: 37000000 INFO @ Thu, 16 Apr 2020 04:28:28: 32000000 INFO @ Thu, 16 Apr 2020 04:28:33: 38000000 INFO @ Thu, 16 Apr 2020 04:28:33: 33000000 INFO @ Thu, 16 Apr 2020 04:28:39: 39000000 INFO @ Thu, 16 Apr 2020 04:28:39: 34000000 INFO @ Thu, 16 Apr 2020 04:28:45: 40000000 INFO @ Thu, 16 Apr 2020 04:28:45: 35000000 INFO @ Thu, 16 Apr 2020 04:28:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:28:50: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:28:50: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:28:50: #1 total tags in treatment: 15833592 INFO @ Thu, 16 Apr 2020 04:28:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:28:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:28:50: #1 tags after filtering in treatment: 13318938 INFO @ Thu, 16 Apr 2020 04:28:50: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 04:28:50: #1 finished! INFO @ Thu, 16 Apr 2020 04:28:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:28:51: 36000000 INFO @ Thu, 16 Apr 2020 04:28:51: #2 number of paired peaks: 3232 INFO @ Thu, 16 Apr 2020 04:28:51: start model_add_line... INFO @ Thu, 16 Apr 2020 04:28:51: start X-correlation... INFO @ Thu, 16 Apr 2020 04:28:51: end of X-cor INFO @ Thu, 16 Apr 2020 04:28:51: #2 finished! INFO @ Thu, 16 Apr 2020 04:28:51: #2 predicted fragment length is 219 bps INFO @ Thu, 16 Apr 2020 04:28:51: #2 alternative fragment length(s) may be 219 bps INFO @ Thu, 16 Apr 2020 04:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.10_model.r INFO @ Thu, 16 Apr 2020 04:28:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:28:56: 37000000 INFO @ Thu, 16 Apr 2020 04:29:02: 38000000 INFO @ Thu, 16 Apr 2020 04:29:08: 39000000 INFO @ Thu, 16 Apr 2020 04:29:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:29:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:29:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.05_summits.bed INFO @ Thu, 16 Apr 2020 04:29:08: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14984 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:29:13: 40000000 INFO @ Thu, 16 Apr 2020 04:29:18: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:29:18: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:29:18: #1 total tags in treatment: 15833592 INFO @ Thu, 16 Apr 2020 04:29:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:29:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:29:18: #1 tags after filtering in treatment: 13318938 INFO @ Thu, 16 Apr 2020 04:29:18: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 04:29:18: #1 finished! INFO @ Thu, 16 Apr 2020 04:29:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:29:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:29:19: #2 number of paired peaks: 3232 INFO @ Thu, 16 Apr 2020 04:29:19: start model_add_line... INFO @ Thu, 16 Apr 2020 04:29:19: start X-correlation... INFO @ Thu, 16 Apr 2020 04:29:19: end of X-cor INFO @ Thu, 16 Apr 2020 04:29:19: #2 finished! INFO @ Thu, 16 Apr 2020 04:29:19: #2 predicted fragment length is 219 bps INFO @ Thu, 16 Apr 2020 04:29:19: #2 alternative fragment length(s) may be 219 bps INFO @ Thu, 16 Apr 2020 04:29:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.20_model.r INFO @ Thu, 16 Apr 2020 04:29:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:29:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:29:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.10_summits.bed INFO @ Thu, 16 Apr 2020 04:29:43: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10293 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:29:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:30:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:30:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:30:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246873/SRX5246873.20_summits.bed INFO @ Thu, 16 Apr 2020 04:30:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5905 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。