Job ID = 14168286 SRX = SRX11078119 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T07:51:04 prefetch.2.10.7: 1) Downloading 'SRR14743547'... 2021-12-10T07:51:04 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T07:52:01 prefetch.2.10.7: HTTPS download succeed 2021-12-10T07:52:01 prefetch.2.10.7: 1) 'SRR14743547' was downloaded successfully 2021-12-10T07:52:01 prefetch.2.10.7: 'SRR14743547' has 0 unresolved dependencies Read 27811586 spots for SRR14743547/SRR14743547.sra Written 27811586 spots for SRR14743547/SRR14743547.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169167 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:39 27811586 reads; of these: 27811586 (100.00%) were paired; of these: 25679609 (92.33%) aligned concordantly 0 times 1628706 (5.86%) aligned concordantly exactly 1 time 503271 (1.81%) aligned concordantly >1 times ---- 25679609 pairs aligned concordantly 0 times; of these: 3235 (0.01%) aligned discordantly 1 time ---- 25676374 pairs aligned 0 times concordantly or discordantly; of these: 51352748 mates make up the pairs; of these: 51107518 (99.52%) aligned 0 times 93174 (0.18%) aligned exactly 1 time 152056 (0.30%) aligned >1 times 8.12% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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_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] 95503 / 2133840 = 0.0448 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 17:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.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 17:01:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:01:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:01:21: 1000000 INFO @ Fri, 10 Dec 2021 17:01:26: 2000000 INFO @ Fri, 10 Dec 2021 17:01:31: 3000000 INFO @ Fri, 10 Dec 2021 17:01:36: 4000000 INFO @ Fri, 10 Dec 2021 17:01:37: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 17:01:37: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 17:01:37: #1 total tags in treatment: 2036549 INFO @ Fri, 10 Dec 2021 17:01:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:01:37: #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 17:01:37: #1 tags after filtering in treatment: 1957568 INFO @ Fri, 10 Dec 2021 17:01:37: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 17:01:37: #1 finished! INFO @ Fri, 10 Dec 2021 17:01:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:01:37: #2 number of paired peaks: 918 WARNING @ Fri, 10 Dec 2021 17:01:37: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Fri, 10 Dec 2021 17:01:37: start model_add_line... INFO @ Fri, 10 Dec 2021 17:01:37: start X-correlation... INFO @ Fri, 10 Dec 2021 17:01:37: end of X-cor INFO @ Fri, 10 Dec 2021 17:01:37: #2 finished! INFO @ Fri, 10 Dec 2021 17:01:37: #2 predicted fragment length is 103 bps INFO @ Fri, 10 Dec 2021 17:01:37: #2 alternative fragment length(s) may be 103 bps INFO @ Fri, 10 Dec 2021 17:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.05_model.r INFO @ Fri, 10 Dec 2021 17:01:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:01:42: #3 Call peaks for each chromosome... 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 17:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.05_summits.bed INFO @ Fri, 10 Dec 2021 17:01:44: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (281 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:01:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.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 17:01:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:01:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:01:50: 1000000 INFO @ Fri, 10 Dec 2021 17:01:55: 2000000 INFO @ Fri, 10 Dec 2021 17:01:59: 3000000 INFO @ Fri, 10 Dec 2021 17:02:04: 4000000 INFO @ Fri, 10 Dec 2021 17:02:06: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 17:02:06: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 17:02:06: #1 total tags in treatment: 2036549 INFO @ Fri, 10 Dec 2021 17:02:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:02:06: #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 17:02:06: #1 tags after filtering in treatment: 1957568 INFO @ Fri, 10 Dec 2021 17:02:06: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 17:02:06: #1 finished! INFO @ Fri, 10 Dec 2021 17:02:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:02:06: #2 number of paired peaks: 918 WARNING @ Fri, 10 Dec 2021 17:02:06: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Fri, 10 Dec 2021 17:02:06: start model_add_line... INFO @ Fri, 10 Dec 2021 17:02:06: start X-correlation... INFO @ Fri, 10 Dec 2021 17:02:06: end of X-cor INFO @ Fri, 10 Dec 2021 17:02:06: #2 finished! INFO @ Fri, 10 Dec 2021 17:02:06: #2 predicted fragment length is 103 bps INFO @ Fri, 10 Dec 2021 17:02:06: #2 alternative fragment length(s) may be 103 bps INFO @ Fri, 10 Dec 2021 17:02:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.10_model.r INFO @ Fri, 10 Dec 2021 17:02:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:02:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:02:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:02:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:02:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:02:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.10_summits.bed INFO @ Fri, 10 Dec 2021 17:02:13: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (142 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 17:02:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.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 17:02:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:02:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:02:20: 1000000 INFO @ Fri, 10 Dec 2021 17:02:24: 2000000 INFO @ Fri, 10 Dec 2021 17:02:29: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:02:34: 4000000 INFO @ Fri, 10 Dec 2021 17:02:35: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 17:02:35: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 17:02:35: #1 total tags in treatment: 2036549 INFO @ Fri, 10 Dec 2021 17:02:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:02:35: #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 17:02:35: #1 tags after filtering in treatment: 1957568 INFO @ Fri, 10 Dec 2021 17:02:35: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 17:02:35: #1 finished! INFO @ Fri, 10 Dec 2021 17:02:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:02:35: #2 number of paired peaks: 918 WARNING @ Fri, 10 Dec 2021 17:02:35: Fewer paired peaks (918) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 918 pairs to build model! INFO @ Fri, 10 Dec 2021 17:02:35: start model_add_line... INFO @ Fri, 10 Dec 2021 17:02:35: start X-correlation... INFO @ Fri, 10 Dec 2021 17:02:35: end of X-cor INFO @ Fri, 10 Dec 2021 17:02:35: #2 finished! INFO @ Fri, 10 Dec 2021 17:02:35: #2 predicted fragment length is 103 bps INFO @ Fri, 10 Dec 2021 17:02:35: #2 alternative fragment length(s) may be 103 bps INFO @ Fri, 10 Dec 2021 17:02:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.20_model.r INFO @ Fri, 10 Dec 2021 17:02:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:02:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:02:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:02:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:02:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078119/SRX11078119.20_summits.bed INFO @ Fri, 10 Dec 2021 17:02:42: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 0 millis CompletedMACS2peakCalling