Job ID = 14167263 SRX = SRX8076968 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15856343 spots for SRR11504840/SRR11504840.sra Written 15856343 spots for SRR11504840/SRR11504840.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167893 ("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: 00:10:18 15856343 reads; of these: 15856343 (100.00%) were paired; of these: 8557300 (53.97%) aligned concordantly 0 times 6355311 (40.08%) aligned concordantly exactly 1 time 943732 (5.95%) aligned concordantly >1 times ---- 8557300 pairs aligned concordantly 0 times; of these: 949861 (11.10%) aligned discordantly 1 time ---- 7607439 pairs aligned 0 times concordantly or discordantly; of these: 15214878 mates make up the pairs; of these: 14439589 (94.90%) aligned 0 times 421040 (2.77%) aligned exactly 1 time 354249 (2.33%) aligned >1 times 54.47% overall alignment rate Time searching: 00:10:18 Overall time: 00:10:18 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] 1175503 / 8246575 = 0.1425 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 @ Fri, 10 Dec 2021 11:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.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 @ Fri, 10 Dec 2021 11:38:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:38:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:38:29: 1000000 INFO @ Fri, 10 Dec 2021 11:38:34: 2000000 INFO @ Fri, 10 Dec 2021 11:38:38: 3000000 INFO @ Fri, 10 Dec 2021 11:38:43: 4000000 INFO @ Fri, 10 Dec 2021 11:38:48: 5000000 INFO @ Fri, 10 Dec 2021 11:38:52: 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 @ Fri, 10 Dec 2021 11:38:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.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 @ Fri, 10 Dec 2021 11:38:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:38:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:38:58: 7000000 INFO @ Fri, 10 Dec 2021 11:39:01: 1000000 INFO @ Fri, 10 Dec 2021 11:39:03: 8000000 INFO @ Fri, 10 Dec 2021 11:39:07: 2000000 INFO @ Fri, 10 Dec 2021 11:39:09: 9000000 INFO @ Fri, 10 Dec 2021 11:39:13: 3000000 INFO @ Fri, 10 Dec 2021 11:39:15: 10000000 INFO @ Fri, 10 Dec 2021 11:39:19: 4000000 INFO @ Fri, 10 Dec 2021 11:39:20: 11000000 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 @ Fri, 10 Dec 2021 11:39:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.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 @ Fri, 10 Dec 2021 11:39:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:39:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:39:25: 5000000 INFO @ Fri, 10 Dec 2021 11:39:26: 12000000 INFO @ Fri, 10 Dec 2021 11:39:30: 1000000 INFO @ Fri, 10 Dec 2021 11:39:31: 6000000 INFO @ Fri, 10 Dec 2021 11:39:32: 13000000 INFO @ Fri, 10 Dec 2021 11:39:36: 2000000 INFO @ Fri, 10 Dec 2021 11:39:38: 7000000 INFO @ Fri, 10 Dec 2021 11:39:38: 14000000 INFO @ Fri, 10 Dec 2021 11:39:42: 3000000 INFO @ Fri, 10 Dec 2021 11:39:43: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:39:43: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:39:43: #1 total tags in treatment: 6225043 INFO @ Fri, 10 Dec 2021 11:39:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:39:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:39:43: #1 tags after filtering in treatment: 6039104 INFO @ Fri, 10 Dec 2021 11:39:43: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 11:39:43: #1 finished! INFO @ Fri, 10 Dec 2021 11:39:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:39:44: #2 number of paired peaks: 672 WARNING @ Fri, 10 Dec 2021 11:39:44: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Fri, 10 Dec 2021 11:39:44: start model_add_line... INFO @ Fri, 10 Dec 2021 11:39:44: start X-correlation... INFO @ Fri, 10 Dec 2021 11:39:44: end of X-cor INFO @ Fri, 10 Dec 2021 11:39:44: #2 finished! INFO @ Fri, 10 Dec 2021 11:39:44: #2 predicted fragment length is 278 bps INFO @ Fri, 10 Dec 2021 11:39:44: #2 alternative fragment length(s) may be 278,304 bps INFO @ Fri, 10 Dec 2021 11:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.05_model.r INFO @ Fri, 10 Dec 2021 11:39:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:39:44: 8000000 INFO @ Fri, 10 Dec 2021 11:39:48: 4000000 INFO @ Fri, 10 Dec 2021 11:39:50: 9000000 INFO @ Fri, 10 Dec 2021 11:39:53: 5000000 INFO @ Fri, 10 Dec 2021 11:39:56: 10000000 INFO @ Fri, 10 Dec 2021 11:39:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:39:59: 6000000 INFO @ Fri, 10 Dec 2021 11:40:02: 11000000 INFO @ Fri, 10 Dec 2021 11:40:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:40:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:40:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.05_summits.bed INFO @ Fri, 10 Dec 2021 11:40:02: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (2354 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:40:05: 7000000 INFO @ Fri, 10 Dec 2021 11:40:08: 12000000 INFO @ Fri, 10 Dec 2021 11:40:11: 8000000 INFO @ Fri, 10 Dec 2021 11:40:15: 13000000 INFO @ Fri, 10 Dec 2021 11:40:16: 9000000 INFO @ Fri, 10 Dec 2021 11:40:21: 14000000 INFO @ Fri, 10 Dec 2021 11:40:22: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:40:26: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:40:26: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:40:26: #1 total tags in treatment: 6225043 INFO @ Fri, 10 Dec 2021 11:40:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:40:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:40:27: #1 tags after filtering in treatment: 6039104 INFO @ Fri, 10 Dec 2021 11:40:27: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 11:40:27: #1 finished! INFO @ Fri, 10 Dec 2021 11:40:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:40:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:40:27: #2 number of paired peaks: 672 WARNING @ Fri, 10 Dec 2021 11:40:27: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Fri, 10 Dec 2021 11:40:27: start model_add_line... INFO @ Fri, 10 Dec 2021 11:40:27: start X-correlation... INFO @ Fri, 10 Dec 2021 11:40:27: end of X-cor INFO @ Fri, 10 Dec 2021 11:40:27: #2 finished! INFO @ Fri, 10 Dec 2021 11:40:27: #2 predicted fragment length is 278 bps INFO @ Fri, 10 Dec 2021 11:40:27: #2 alternative fragment length(s) may be 278,304 bps INFO @ Fri, 10 Dec 2021 11:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.10_model.r INFO @ Fri, 10 Dec 2021 11:40:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:40:28: 11000000 INFO @ Fri, 10 Dec 2021 11:40:33: 12000000 INFO @ Fri, 10 Dec 2021 11:40:38: 13000000 INFO @ Fri, 10 Dec 2021 11:40:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:40:44: 14000000 INFO @ Fri, 10 Dec 2021 11:40:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:40:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:40:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.10_summits.bed INFO @ Fri, 10 Dec 2021 11:40:45: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (488 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:40:48: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:40:48: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:40:48: #1 total tags in treatment: 6225043 INFO @ Fri, 10 Dec 2021 11:40:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:40:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:40:48: #1 tags after filtering in treatment: 6039104 INFO @ Fri, 10 Dec 2021 11:40:48: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 11:40:48: #1 finished! INFO @ Fri, 10 Dec 2021 11:40:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:40:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:40:49: #2 number of paired peaks: 672 WARNING @ Fri, 10 Dec 2021 11:40:49: Fewer paired peaks (672) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 672 pairs to build model! INFO @ Fri, 10 Dec 2021 11:40:49: start model_add_line... INFO @ Fri, 10 Dec 2021 11:40:49: start X-correlation... INFO @ Fri, 10 Dec 2021 11:40:49: end of X-cor INFO @ Fri, 10 Dec 2021 11:40:49: #2 finished! INFO @ Fri, 10 Dec 2021 11:40:49: #2 predicted fragment length is 278 bps INFO @ Fri, 10 Dec 2021 11:40:49: #2 alternative fragment length(s) may be 278,304 bps INFO @ Fri, 10 Dec 2021 11:40:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.20_model.r INFO @ Fri, 10 Dec 2021 11:40:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:40:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:41:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:41:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:41:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:41:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076968/SRX8076968.20_summits.bed INFO @ Fri, 10 Dec 2021 11:41:08: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (74 records, 4 fields): 1 millis CompletedMACS2peakCalling