Job ID = 16439400 SRX = SRX13453897 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8963296 spots for SRR17276241/SRR17276241.sra Written 8963296 spots for SRR17276241/SRR17276241.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439576 ("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: 00:25:25 8963296 reads; of these: 8963296 (100.00%) were paired; of these: 452526 (5.05%) aligned concordantly 0 times 6838245 (76.29%) aligned concordantly exactly 1 time 1672525 (18.66%) aligned concordantly >1 times ---- 452526 pairs aligned concordantly 0 times; of these: 124132 (27.43%) aligned discordantly 1 time ---- 328394 pairs aligned 0 times concordantly or discordantly; of these: 656788 mates make up the pairs; of these: 361801 (55.09%) aligned 0 times 176599 (26.89%) aligned exactly 1 time 118388 (18.03%) aligned >1 times 97.98% overall alignment rate Time searching: 00:25:25 Overall time: 00:25:25 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 8 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] 213128 / 8581810 = 0.0248 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 15:40:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.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 15:40:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:40:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:40:29: 1000000 INFO @ Tue, 02 Aug 2022 15:40:38: 2000000 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 15:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.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 15:40:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:40:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:40:48: 3000000 INFO @ Tue, 02 Aug 2022 15:40:57: 1000000 INFO @ Tue, 02 Aug 2022 15:40:58: 4000000 INFO @ Tue, 02 Aug 2022 15:41:07: 2000000 INFO @ Tue, 02 Aug 2022 15:41:07: 5000000 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 15:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.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 15:41:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:41:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:41:17: 6000000 INFO @ Tue, 02 Aug 2022 15:41:17: 3000000 INFO @ Tue, 02 Aug 2022 15:41:26: 1000000 INFO @ Tue, 02 Aug 2022 15:41:27: 7000000 INFO @ Tue, 02 Aug 2022 15:41:28: 4000000 INFO @ Tue, 02 Aug 2022 15:41:36: 2000000 INFO @ Tue, 02 Aug 2022 15:41:36: 8000000 INFO @ Tue, 02 Aug 2022 15:41:38: 5000000 INFO @ Tue, 02 Aug 2022 15:41:45: 3000000 INFO @ Tue, 02 Aug 2022 15:41:46: 9000000 INFO @ Tue, 02 Aug 2022 15:41:48: 6000000 INFO @ Tue, 02 Aug 2022 15:41:55: 4000000 INFO @ Tue, 02 Aug 2022 15:41:55: 10000000 INFO @ Tue, 02 Aug 2022 15:41:58: 7000000 INFO @ Tue, 02 Aug 2022 15:42:04: 5000000 INFO @ Tue, 02 Aug 2022 15:42:05: 11000000 INFO @ Tue, 02 Aug 2022 15:42:07: 8000000 INFO @ Tue, 02 Aug 2022 15:42:13: 6000000 INFO @ Tue, 02 Aug 2022 15:42:14: 12000000 INFO @ Tue, 02 Aug 2022 15:42:17: 9000000 INFO @ Tue, 02 Aug 2022 15:42:22: 7000000 INFO @ Tue, 02 Aug 2022 15:42:24: 13000000 INFO @ Tue, 02 Aug 2022 15:42:27: 10000000 INFO @ Tue, 02 Aug 2022 15:42:31: 8000000 INFO @ Tue, 02 Aug 2022 15:42:33: 14000000 INFO @ Tue, 02 Aug 2022 15:42:38: 11000000 INFO @ Tue, 02 Aug 2022 15:42:41: 9000000 INFO @ Tue, 02 Aug 2022 15:42:43: 15000000 INFO @ Tue, 02 Aug 2022 15:42:48: 12000000 INFO @ Tue, 02 Aug 2022 15:42:50: 10000000 INFO @ Tue, 02 Aug 2022 15:42:52: 16000000 INFO @ Tue, 02 Aug 2022 15:42:58: 13000000 INFO @ Tue, 02 Aug 2022 15:42:59: 11000000 INFO @ Tue, 02 Aug 2022 15:43:02: 17000000 INFO @ Tue, 02 Aug 2022 15:43:04: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:43:04: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:43:04: #1 total tags in treatment: 8298172 INFO @ Tue, 02 Aug 2022 15:43:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:43:04: #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 15:43:04: #1 tags after filtering in treatment: 8037699 INFO @ Tue, 02 Aug 2022 15:43:04: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:43:04: #1 finished! INFO @ Tue, 02 Aug 2022 15:43:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:43:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:43:05: #2 number of paired peaks: 171 WARNING @ Tue, 02 Aug 2022 15:43:05: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Tue, 02 Aug 2022 15:43:05: start model_add_line... INFO @ Tue, 02 Aug 2022 15:43:05: start X-correlation... INFO @ Tue, 02 Aug 2022 15:43:05: end of X-cor INFO @ Tue, 02 Aug 2022 15:43:05: #2 finished! INFO @ Tue, 02 Aug 2022 15:43:05: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 15:43:05: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 15:43:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.05_model.r INFO @ Tue, 02 Aug 2022 15:43:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:43:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:43:09: 14000000 INFO @ Tue, 02 Aug 2022 15:43:09: 12000000 INFO @ Tue, 02 Aug 2022 15:43:19: 13000000 INFO @ Tue, 02 Aug 2022 15:43:20: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:43:30: 14000000 INFO @ Tue, 02 Aug 2022 15:43:31: 16000000 INFO @ Tue, 02 Aug 2022 15:43:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:43:40: 15000000 INFO @ Tue, 02 Aug 2022 15:43:41: 17000000 INFO @ Tue, 02 Aug 2022 15:43:43: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:43:43: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:43:43: #1 total tags in treatment: 8298172 INFO @ Tue, 02 Aug 2022 15:43:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:43:43: #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 15:43:43: #1 tags after filtering in treatment: 8037699 INFO @ Tue, 02 Aug 2022 15:43:43: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:43:43: #1 finished! INFO @ Tue, 02 Aug 2022 15:43:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:43:44: #2 number of paired peaks: 171 WARNING @ Tue, 02 Aug 2022 15:43:44: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Tue, 02 Aug 2022 15:43:44: start model_add_line... INFO @ Tue, 02 Aug 2022 15:43:44: start X-correlation... INFO @ Tue, 02 Aug 2022 15:43:44: end of X-cor INFO @ Tue, 02 Aug 2022 15:43:44: #2 finished! INFO @ Tue, 02 Aug 2022 15:43:44: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 15:43:44: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 15:43:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.10_model.r INFO @ Tue, 02 Aug 2022 15:43:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:43:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:43:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:43:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:43:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.05_summits.bed INFO @ Tue, 02 Aug 2022 15:43:48: Done! pass1 - making usageList (12 chroms): 5 millis pass2 - checking and writing primary data (2244 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:43:49: 16000000 INFO @ Tue, 02 Aug 2022 15:43:58: 17000000 INFO @ Tue, 02 Aug 2022 15:43:59: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:43:59: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:43:59: #1 total tags in treatment: 8298172 INFO @ Tue, 02 Aug 2022 15:43:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:43:59: #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 15:43:59: #1 tags after filtering in treatment: 8037699 INFO @ Tue, 02 Aug 2022 15:43:59: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:43:59: #1 finished! INFO @ Tue, 02 Aug 2022 15:43:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:43:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:44:00: #2 number of paired peaks: 171 WARNING @ Tue, 02 Aug 2022 15:44:00: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Tue, 02 Aug 2022 15:44:00: start model_add_line... INFO @ Tue, 02 Aug 2022 15:44:00: start X-correlation... INFO @ Tue, 02 Aug 2022 15:44:00: end of X-cor INFO @ Tue, 02 Aug 2022 15:44:00: #2 finished! INFO @ Tue, 02 Aug 2022 15:44:00: #2 predicted fragment length is 185 bps INFO @ Tue, 02 Aug 2022 15:44:00: #2 alternative fragment length(s) may be 185 bps INFO @ Tue, 02 Aug 2022 15:44:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.20_model.r INFO @ Tue, 02 Aug 2022 15:44:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:44:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:44:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:44:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:44:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:44:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.10_summits.bed INFO @ Tue, 02 Aug 2022 15:44:25: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (821 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:44:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:44:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:44:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:44:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453897/SRX13453897.20_summits.bed INFO @ Tue, 02 Aug 2022 15:44:42: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (334 records, 4 fields): 19 millis CompletedMACS2peakCalling