Job ID = 6626513 SRX = SRX5736488 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10280612 spots for SRR8956899/SRR8956899.sra Written 10280612 spots for SRR8956899/SRR8956899.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626702 ("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: 00:24:49 10280612 reads; of these: 10280612 (100.00%) were paired; of these: 2236083 (21.75%) aligned concordantly 0 times 5728583 (55.72%) aligned concordantly exactly 1 time 2315946 (22.53%) aligned concordantly >1 times ---- 2236083 pairs aligned concordantly 0 times; of these: 1061529 (47.47%) aligned discordantly 1 time ---- 1174554 pairs aligned 0 times concordantly or discordantly; of these: 2349108 mates make up the pairs; of these: 1083594 (46.13%) aligned 0 times 499613 (21.27%) aligned exactly 1 time 765901 (32.60%) aligned >1 times 94.73% overall alignment rate Time searching: 00:24:49 Overall time: 00:24:49 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] 567793 / 9079375 = 0.0625 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 @ Tue, 14 Jul 2020 07:47:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.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, 14 Jul 2020 07:47:41: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:47:41: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:47:46: 1000000 INFO @ Tue, 14 Jul 2020 07:47:51: 2000000 INFO @ Tue, 14 Jul 2020 07:47:57: 3000000 INFO @ Tue, 14 Jul 2020 07:48:03: 4000000 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 @ Tue, 14 Jul 2020 07:48:09: 5000000 INFO @ Tue, 14 Jul 2020 07:48:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.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, 14 Jul 2020 07:48:11: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:48:11: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:48:15: 6000000 INFO @ Tue, 14 Jul 2020 07:48:17: 1000000 INFO @ Tue, 14 Jul 2020 07:48:21: 7000000 INFO @ Tue, 14 Jul 2020 07:48:23: 2000000 INFO @ Tue, 14 Jul 2020 07:48:27: 8000000 INFO @ Tue, 14 Jul 2020 07:48:29: 3000000 INFO @ Tue, 14 Jul 2020 07:48:33: 9000000 INFO @ Tue, 14 Jul 2020 07:48:35: 4000000 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 @ Tue, 14 Jul 2020 07:48:40: 10000000 INFO @ Tue, 14 Jul 2020 07:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.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, 14 Jul 2020 07:48:41: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:48:41: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:48:41: 5000000 INFO @ Tue, 14 Jul 2020 07:48:47: 11000000 INFO @ Tue, 14 Jul 2020 07:48:47: 1000000 INFO @ Tue, 14 Jul 2020 07:48:48: 6000000 INFO @ Tue, 14 Jul 2020 07:48:53: 12000000 INFO @ Tue, 14 Jul 2020 07:48:53: 2000000 INFO @ Tue, 14 Jul 2020 07:48:54: 7000000 INFO @ Tue, 14 Jul 2020 07:48:59: 13000000 INFO @ Tue, 14 Jul 2020 07:49:00: 3000000 INFO @ Tue, 14 Jul 2020 07:49:00: 8000000 INFO @ Tue, 14 Jul 2020 07:49:06: 14000000 INFO @ Tue, 14 Jul 2020 07:49:06: 4000000 INFO @ Tue, 14 Jul 2020 07:49:06: 9000000 INFO @ Tue, 14 Jul 2020 07:49:12: 15000000 INFO @ Tue, 14 Jul 2020 07:49:12: 5000000 INFO @ Tue, 14 Jul 2020 07:49:12: 10000000 INFO @ Tue, 14 Jul 2020 07:49:18: 16000000 INFO @ Tue, 14 Jul 2020 07:49:18: 6000000 INFO @ Tue, 14 Jul 2020 07:49:18: 11000000 INFO @ Tue, 14 Jul 2020 07:49:24: 7000000 INFO @ Tue, 14 Jul 2020 07:49:25: 12000000 INFO @ Tue, 14 Jul 2020 07:49:25: 17000000 INFO @ Tue, 14 Jul 2020 07:49:31: 8000000 INFO @ Tue, 14 Jul 2020 07:49:31: 13000000 INFO @ Tue, 14 Jul 2020 07:49:32: 18000000 INFO @ Tue, 14 Jul 2020 07:49:35: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:49:35: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:49:35: #1 total tags in treatment: 7558038 INFO @ Tue, 14 Jul 2020 07:49:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:49:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:49:35: #1 tags after filtering in treatment: 6799839 INFO @ Tue, 14 Jul 2020 07:49:35: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:49:35: #1 finished! INFO @ Tue, 14 Jul 2020 07:49:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:49:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:49:35: #2 number of paired peaks: 430 WARNING @ Tue, 14 Jul 2020 07:49:35: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Tue, 14 Jul 2020 07:49:35: start model_add_line... INFO @ Tue, 14 Jul 2020 07:49:35: start X-correlation... INFO @ Tue, 14 Jul 2020 07:49:35: end of X-cor INFO @ Tue, 14 Jul 2020 07:49:35: #2 finished! INFO @ Tue, 14 Jul 2020 07:49:35: #2 predicted fragment length is 179 bps INFO @ Tue, 14 Jul 2020 07:49:35: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 14 Jul 2020 07:49:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.05_model.r INFO @ Tue, 14 Jul 2020 07:49:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:49:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:49:37: 9000000 INFO @ Tue, 14 Jul 2020 07:49:37: 14000000 INFO @ Tue, 14 Jul 2020 07:49:43: 10000000 INFO @ Tue, 14 Jul 2020 07:49:44: 15000000 INFO @ Tue, 14 Jul 2020 07:49:49: 11000000 INFO @ Tue, 14 Jul 2020 07:49:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:49:50: 16000000 INFO @ Tue, 14 Jul 2020 07:49:55: 12000000 INFO @ Tue, 14 Jul 2020 07:49:56: 17000000 INFO @ Tue, 14 Jul 2020 07:49:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:49:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:49:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.05_summits.bed INFO @ Tue, 14 Jul 2020 07:49:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5930 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:50:02: 13000000 INFO @ Tue, 14 Jul 2020 07:50:03: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:50:05: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:50:05: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:50:05: #1 total tags in treatment: 7558038 INFO @ Tue, 14 Jul 2020 07:50:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:50:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:50:05: #1 tags after filtering in treatment: 6799839 INFO @ Tue, 14 Jul 2020 07:50:05: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:50:05: #1 finished! INFO @ Tue, 14 Jul 2020 07:50:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:50:05: #2 number of paired peaks: 430 WARNING @ Tue, 14 Jul 2020 07:50:05: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Tue, 14 Jul 2020 07:50:05: start model_add_line... INFO @ Tue, 14 Jul 2020 07:50:05: start X-correlation... INFO @ Tue, 14 Jul 2020 07:50:05: end of X-cor INFO @ Tue, 14 Jul 2020 07:50:05: #2 finished! INFO @ Tue, 14 Jul 2020 07:50:05: #2 predicted fragment length is 179 bps INFO @ Tue, 14 Jul 2020 07:50:05: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 14 Jul 2020 07:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.10_model.r INFO @ Tue, 14 Jul 2020 07:50:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:50:08: 14000000 INFO @ Tue, 14 Jul 2020 07:50:14: 15000000 INFO @ Tue, 14 Jul 2020 07:50:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:50:19: 16000000 INFO @ Tue, 14 Jul 2020 07:50:25: 17000000 INFO @ Tue, 14 Jul 2020 07:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.10_summits.bed INFO @ Tue, 14 Jul 2020 07:50:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2364 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:50:31: 18000000 INFO @ Tue, 14 Jul 2020 07:50:33: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:50:33: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:50:33: #1 total tags in treatment: 7558038 INFO @ Tue, 14 Jul 2020 07:50:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:50:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:50:33: #1 tags after filtering in treatment: 6799839 INFO @ Tue, 14 Jul 2020 07:50:33: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 14 Jul 2020 07:50:33: #1 finished! INFO @ Tue, 14 Jul 2020 07:50:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:50:34: #2 number of paired peaks: 430 WARNING @ Tue, 14 Jul 2020 07:50:34: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Tue, 14 Jul 2020 07:50:34: start model_add_line... INFO @ Tue, 14 Jul 2020 07:50:34: start X-correlation... INFO @ Tue, 14 Jul 2020 07:50:34: end of X-cor INFO @ Tue, 14 Jul 2020 07:50:34: #2 finished! INFO @ Tue, 14 Jul 2020 07:50:34: #2 predicted fragment length is 179 bps INFO @ Tue, 14 Jul 2020 07:50:34: #2 alternative fragment length(s) may be 179 bps INFO @ Tue, 14 Jul 2020 07:50:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.20_model.r INFO @ Tue, 14 Jul 2020 07:50:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:50:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:50:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736488/SRX5736488.20_summits.bed INFO @ Tue, 14 Jul 2020 07:50:55: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (742 records, 4 fields): 2 millis CompletedMACS2peakCalling