Job ID = 14170669 SRX = SRX9434476 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24549887 spots for SRR12982874/SRR12982874.sra Written 24549887 spots for SRR12982874/SRR12982874.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171257 ("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: 00:47:14 24549887 reads; of these: 24549887 (100.00%) were paired; of these: 1784854 (7.27%) aligned concordantly 0 times 16555519 (67.44%) aligned concordantly exactly 1 time 6209514 (25.29%) aligned concordantly >1 times ---- 1784854 pairs aligned concordantly 0 times; of these: 210474 (11.79%) aligned discordantly 1 time ---- 1574380 pairs aligned 0 times concordantly or discordantly; of these: 3148760 mates make up the pairs; of these: 1774328 (56.35%) aligned 0 times 565237 (17.95%) aligned exactly 1 time 809195 (25.70%) aligned >1 times 96.39% overall alignment rate Time searching: 00:47:14 Overall time: 00:47:14 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] 1975658 / 22943448 = 0.0861 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 08:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.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 08:53:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:53:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:53:44: 1000000 INFO @ Sat, 11 Dec 2021 08:53:48: 2000000 INFO @ Sat, 11 Dec 2021 08:53:52: 3000000 INFO @ Sat, 11 Dec 2021 08:53:56: 4000000 INFO @ Sat, 11 Dec 2021 08:54:00: 5000000 INFO @ Sat, 11 Dec 2021 08:54:04: 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 08:54:08: 7000000 INFO @ Sat, 11 Dec 2021 08:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.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 08:54:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:54:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:54:12: 8000000 INFO @ Sat, 11 Dec 2021 08:54:14: 1000000 INFO @ Sat, 11 Dec 2021 08:54:17: 9000000 INFO @ Sat, 11 Dec 2021 08:54:18: 2000000 INFO @ Sat, 11 Dec 2021 08:54:21: 10000000 INFO @ Sat, 11 Dec 2021 08:54:22: 3000000 INFO @ Sat, 11 Dec 2021 08:54:25: 11000000 INFO @ Sat, 11 Dec 2021 08:54:27: 4000000 INFO @ Sat, 11 Dec 2021 08:54:29: 12000000 INFO @ Sat, 11 Dec 2021 08:54:31: 5000000 INFO @ Sat, 11 Dec 2021 08:54:33: 13000000 INFO @ Sat, 11 Dec 2021 08:54:35: 6000000 INFO @ Sat, 11 Dec 2021 08:54:37: 14000000 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 08:54:39: 7000000 INFO @ Sat, 11 Dec 2021 08:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.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 08:54:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:54:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:54:41: 15000000 INFO @ Sat, 11 Dec 2021 08:54:43: 8000000 INFO @ Sat, 11 Dec 2021 08:54:44: 1000000 INFO @ Sat, 11 Dec 2021 08:54:46: 16000000 INFO @ Sat, 11 Dec 2021 08:54:47: 9000000 INFO @ Sat, 11 Dec 2021 08:54:48: 2000000 INFO @ Sat, 11 Dec 2021 08:54:50: 17000000 INFO @ Sat, 11 Dec 2021 08:54:51: 10000000 INFO @ Sat, 11 Dec 2021 08:54:52: 3000000 INFO @ Sat, 11 Dec 2021 08:54:54: 18000000 INFO @ Sat, 11 Dec 2021 08:54:56: 11000000 INFO @ Sat, 11 Dec 2021 08:54:57: 4000000 INFO @ Sat, 11 Dec 2021 08:54:58: 19000000 INFO @ Sat, 11 Dec 2021 08:55:00: 12000000 INFO @ Sat, 11 Dec 2021 08:55:01: 5000000 INFO @ Sat, 11 Dec 2021 08:55:02: 20000000 INFO @ Sat, 11 Dec 2021 08:55:04: 13000000 INFO @ Sat, 11 Dec 2021 08:55:05: 6000000 INFO @ Sat, 11 Dec 2021 08:55:07: 21000000 INFO @ Sat, 11 Dec 2021 08:55:08: 14000000 INFO @ Sat, 11 Dec 2021 08:55:09: 7000000 INFO @ Sat, 11 Dec 2021 08:55:11: 22000000 INFO @ Sat, 11 Dec 2021 08:55:12: 15000000 INFO @ Sat, 11 Dec 2021 08:55:13: 8000000 INFO @ Sat, 11 Dec 2021 08:55:15: 23000000 INFO @ Sat, 11 Dec 2021 08:55:17: 16000000 INFO @ Sat, 11 Dec 2021 08:55:18: 9000000 INFO @ Sat, 11 Dec 2021 08:55:19: 24000000 INFO @ Sat, 11 Dec 2021 08:55:21: 17000000 INFO @ Sat, 11 Dec 2021 08:55:22: 10000000 INFO @ Sat, 11 Dec 2021 08:55:23: 25000000 INFO @ Sat, 11 Dec 2021 08:55:25: 18000000 INFO @ Sat, 11 Dec 2021 08:55:26: 11000000 INFO @ Sat, 11 Dec 2021 08:55:27: 26000000 INFO @ Sat, 11 Dec 2021 08:55:29: 19000000 INFO @ Sat, 11 Dec 2021 08:55:30: 12000000 INFO @ Sat, 11 Dec 2021 08:55:32: 27000000 INFO @ Sat, 11 Dec 2021 08:55:33: 20000000 INFO @ Sat, 11 Dec 2021 08:55:34: 13000000 INFO @ Sat, 11 Dec 2021 08:55:36: 28000000 INFO @ Sat, 11 Dec 2021 08:55:38: 21000000 INFO @ Sat, 11 Dec 2021 08:55:39: 14000000 INFO @ Sat, 11 Dec 2021 08:55:40: 29000000 INFO @ Sat, 11 Dec 2021 08:55:42: 22000000 INFO @ Sat, 11 Dec 2021 08:55:43: 15000000 INFO @ Sat, 11 Dec 2021 08:55:44: 30000000 INFO @ Sat, 11 Dec 2021 08:55:46: 23000000 INFO @ Sat, 11 Dec 2021 08:55:47: 16000000 INFO @ Sat, 11 Dec 2021 08:55:48: 31000000 INFO @ Sat, 11 Dec 2021 08:55:50: 24000000 INFO @ Sat, 11 Dec 2021 08:55:51: 17000000 INFO @ Sat, 11 Dec 2021 08:55:52: 32000000 INFO @ Sat, 11 Dec 2021 08:55:54: 25000000 INFO @ Sat, 11 Dec 2021 08:55:55: 18000000 INFO @ Sat, 11 Dec 2021 08:55:56: 33000000 INFO @ Sat, 11 Dec 2021 08:55:58: 26000000 INFO @ Sat, 11 Dec 2021 08:55:59: 19000000 INFO @ Sat, 11 Dec 2021 08:56:00: 34000000 INFO @ Sat, 11 Dec 2021 08:56:02: 27000000 INFO @ Sat, 11 Dec 2021 08:56:04: 20000000 INFO @ Sat, 11 Dec 2021 08:56:04: 35000000 INFO @ Sat, 11 Dec 2021 08:56:06: 28000000 INFO @ Sat, 11 Dec 2021 08:56:08: 21000000 INFO @ Sat, 11 Dec 2021 08:56:09: 36000000 INFO @ Sat, 11 Dec 2021 08:56:10: 29000000 INFO @ Sat, 11 Dec 2021 08:56:12: 22000000 INFO @ Sat, 11 Dec 2021 08:56:13: 37000000 INFO @ Sat, 11 Dec 2021 08:56:15: 30000000 INFO @ Sat, 11 Dec 2021 08:56:16: 23000000 INFO @ Sat, 11 Dec 2021 08:56:17: 38000000 INFO @ Sat, 11 Dec 2021 08:56:19: 31000000 INFO @ Sat, 11 Dec 2021 08:56:20: 24000000 INFO @ Sat, 11 Dec 2021 08:56:21: 39000000 INFO @ Sat, 11 Dec 2021 08:56:23: 32000000 INFO @ Sat, 11 Dec 2021 08:56:24: 25000000 INFO @ Sat, 11 Dec 2021 08:56:25: 40000000 INFO @ Sat, 11 Dec 2021 08:56:27: 33000000 INFO @ Sat, 11 Dec 2021 08:56:28: 26000000 INFO @ Sat, 11 Dec 2021 08:56:29: 41000000 INFO @ Sat, 11 Dec 2021 08:56:31: 34000000 INFO @ Sat, 11 Dec 2021 08:56:33: 27000000 INFO @ Sat, 11 Dec 2021 08:56:33: 42000000 INFO @ Sat, 11 Dec 2021 08:56:35: 35000000 INFO @ Sat, 11 Dec 2021 08:56:37: 28000000 INFO @ Sat, 11 Dec 2021 08:56:38: 43000000 INFO @ Sat, 11 Dec 2021 08:56:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:56:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:56:39: #1 total tags in treatment: 20805527 INFO @ Sat, 11 Dec 2021 08:56:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:56:39: #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 08:56:39: 36000000 INFO @ Sat, 11 Dec 2021 08:56:40: #1 tags after filtering in treatment: 19470642 INFO @ Sat, 11 Dec 2021 08:56:40: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 08:56:40: #1 finished! INFO @ Sat, 11 Dec 2021 08:56:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:56:41: 29000000 INFO @ Sat, 11 Dec 2021 08:56:41: #2 number of paired peaks: 376 WARNING @ Sat, 11 Dec 2021 08:56:41: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Sat, 11 Dec 2021 08:56:41: start model_add_line... INFO @ Sat, 11 Dec 2021 08:56:41: start X-correlation... INFO @ Sat, 11 Dec 2021 08:56:41: end of X-cor INFO @ Sat, 11 Dec 2021 08:56:41: #2 finished! INFO @ Sat, 11 Dec 2021 08:56:41: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 08:56:41: #2 alternative fragment length(s) may be 4,168 bps INFO @ Sat, 11 Dec 2021 08:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.05_model.r INFO @ Sat, 11 Dec 2021 08:56:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:56:43: 37000000 INFO @ Sat, 11 Dec 2021 08:56:45: 30000000 INFO @ Sat, 11 Dec 2021 08:56:48: 38000000 INFO @ Sat, 11 Dec 2021 08:56:49: 31000000 INFO @ Sat, 11 Dec 2021 08:56:52: 39000000 INFO @ Sat, 11 Dec 2021 08:56:53: 32000000 INFO @ Sat, 11 Dec 2021 08:56:56: 40000000 INFO @ Sat, 11 Dec 2021 08:56:57: 33000000 INFO @ Sat, 11 Dec 2021 08:57:00: 41000000 INFO @ Sat, 11 Dec 2021 08:57:01: 34000000 INFO @ Sat, 11 Dec 2021 08:57:04: 42000000 INFO @ Sat, 11 Dec 2021 08:57:05: 35000000 INFO @ Sat, 11 Dec 2021 08:57:08: 43000000 INFO @ Sat, 11 Dec 2021 08:57:10: 36000000 INFO @ Sat, 11 Dec 2021 08:57:10: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:57:10: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:57:10: #1 total tags in treatment: 20805527 INFO @ Sat, 11 Dec 2021 08:57:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:57:10: #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 08:57:10: #1 tags after filtering in treatment: 19470642 INFO @ Sat, 11 Dec 2021 08:57:10: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 08:57:10: #1 finished! INFO @ Sat, 11 Dec 2021 08:57:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:57:11: #2 number of paired peaks: 376 WARNING @ Sat, 11 Dec 2021 08:57:11: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Sat, 11 Dec 2021 08:57:11: start model_add_line... INFO @ Sat, 11 Dec 2021 08:57:11: start X-correlation... INFO @ Sat, 11 Dec 2021 08:57:11: end of X-cor INFO @ Sat, 11 Dec 2021 08:57:11: #2 finished! INFO @ Sat, 11 Dec 2021 08:57:11: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 08:57:11: #2 alternative fragment length(s) may be 4,168 bps INFO @ Sat, 11 Dec 2021 08:57:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.10_model.r INFO @ Sat, 11 Dec 2021 08:57:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:57:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:57:14: 37000000 INFO @ Sat, 11 Dec 2021 08:57:18: 38000000 INFO @ Sat, 11 Dec 2021 08:57:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:57:22: 39000000 INFO @ Sat, 11 Dec 2021 08:57:26: 40000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:57:30: 41000000 INFO @ Sat, 11 Dec 2021 08:57:34: 42000000 INFO @ Sat, 11 Dec 2021 08:57:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:57:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:57:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.05_summits.bed INFO @ Sat, 11 Dec 2021 08:57:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2652 records, 4 fields): 72 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:57:38: 43000000 INFO @ Sat, 11 Dec 2021 08:57:40: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:57:40: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:57:40: #1 total tags in treatment: 20805527 INFO @ Sat, 11 Dec 2021 08:57:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:57:40: #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 08:57:40: #1 tags after filtering in treatment: 19470642 INFO @ Sat, 11 Dec 2021 08:57:40: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 08:57:40: #1 finished! INFO @ Sat, 11 Dec 2021 08:57:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:57:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:57:41: #2 number of paired peaks: 376 WARNING @ Sat, 11 Dec 2021 08:57:41: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Sat, 11 Dec 2021 08:57:41: start model_add_line... INFO @ Sat, 11 Dec 2021 08:57:41: start X-correlation... INFO @ Sat, 11 Dec 2021 08:57:41: end of X-cor INFO @ Sat, 11 Dec 2021 08:57:41: #2 finished! INFO @ Sat, 11 Dec 2021 08:57:41: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 08:57:41: #2 alternative fragment length(s) may be 4,168 bps INFO @ Sat, 11 Dec 2021 08:57:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.20_model.r INFO @ Sat, 11 Dec 2021 08:57:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:57:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:57:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:58:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:58:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:58:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.10_summits.bed INFO @ Sat, 11 Dec 2021 08:58:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1562 records, 4 fields): 78 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:58:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:58:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:58:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:58:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434476/SRX9434476.20_summits.bed INFO @ Sat, 11 Dec 2021 08:58:35: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (796 records, 4 fields): 183 millis CompletedMACS2peakCalling BigWig に変換しました。