Job ID = 14168358 SRX = SRX11078125 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T09:07:06 prefetch.2.10.7: 1) Downloading 'SRR14743553'... 2021-12-10T09:07:06 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T09:07:24 prefetch.2.10.7: HTTPS download succeed 2021-12-10T09:07:25 prefetch.2.10.7: 'SRR14743553' is valid 2021-12-10T09:07:25 prefetch.2.10.7: 1) 'SRR14743553' was downloaded successfully 2021-12-10T09:07:25 prefetch.2.10.7: 'SRR14743553' has 0 unresolved dependencies Read 9434333 spots for SRR14743553/SRR14743553.sra Written 9434333 spots for SRR14743553/SRR14743553.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169530 ("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: 00:02:00 9434333 reads; of these: 9434333 (100.00%) were paired; of these: 9037360 (95.79%) aligned concordantly 0 times 292307 (3.10%) aligned concordantly exactly 1 time 104666 (1.11%) aligned concordantly >1 times ---- 9037360 pairs aligned concordantly 0 times; of these: 429 (0.00%) aligned discordantly 1 time ---- 9036931 pairs aligned 0 times concordantly or discordantly; of these: 18073862 mates make up the pairs; of these: 17984176 (99.50%) aligned 0 times 22233 (0.12%) aligned exactly 1 time 67453 (0.37%) aligned >1 times 4.69% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 9445 / 397140 = 0.0238 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 18:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.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 18:11:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:11:06: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:11:06: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:11:06: #1 total tags in treatment: 387534 INFO @ Fri, 10 Dec 2021 18:11:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:11:06: #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 18:11:06: #1 tags after filtering in treatment: 383005 INFO @ Fri, 10 Dec 2021 18:11:06: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:11:06: #1 finished! INFO @ Fri, 10 Dec 2021 18:11:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:11:06: #2 number of paired peaks: 723 WARNING @ Fri, 10 Dec 2021 18:11:06: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Fri, 10 Dec 2021 18:11:06: start model_add_line... INFO @ Fri, 10 Dec 2021 18:11:06: start X-correlation... INFO @ Fri, 10 Dec 2021 18:11:06: end of X-cor INFO @ Fri, 10 Dec 2021 18:11:06: #2 finished! INFO @ Fri, 10 Dec 2021 18:11:06: #2 predicted fragment length is 91 bps INFO @ Fri, 10 Dec 2021 18:11:06: #2 alternative fragment length(s) may be 91 bps INFO @ Fri, 10 Dec 2021 18:11:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.05_model.r INFO @ Fri, 10 Dec 2021 18:11:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:11:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:11:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.05_summits.bed INFO @ Fri, 10 Dec 2021 18:11:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (75 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 18:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.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 18:11:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:11:35: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:11:35: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:11:35: #1 total tags in treatment: 387534 INFO @ Fri, 10 Dec 2021 18:11:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:11:35: #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 18:11:35: #1 tags after filtering in treatment: 383005 INFO @ Fri, 10 Dec 2021 18:11:35: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:11:35: #1 finished! INFO @ Fri, 10 Dec 2021 18:11:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:11:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:11:35: #2 number of paired peaks: 723 WARNING @ Fri, 10 Dec 2021 18:11:35: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Fri, 10 Dec 2021 18:11:35: start model_add_line... INFO @ Fri, 10 Dec 2021 18:11:35: start X-correlation... INFO @ Fri, 10 Dec 2021 18:11:35: end of X-cor INFO @ Fri, 10 Dec 2021 18:11:35: #2 finished! INFO @ Fri, 10 Dec 2021 18:11:35: #2 predicted fragment length is 91 bps INFO @ Fri, 10 Dec 2021 18:11:35: #2 alternative fragment length(s) may be 91 bps INFO @ Fri, 10 Dec 2021 18:11:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.10_model.r INFO @ Fri, 10 Dec 2021 18:11:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:11:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:11:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.10_summits.bed INFO @ Fri, 10 Dec 2021 18:11:36: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 1 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 18:12:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.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 18:12:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:12:00: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:12:05: #1 tag size is determined as 40 bps INFO @ Fri, 10 Dec 2021 18:12:05: #1 tag size = 40 INFO @ Fri, 10 Dec 2021 18:12:05: #1 total tags in treatment: 387534 INFO @ Fri, 10 Dec 2021 18:12:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:12:05: #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 18:12:05: #1 tags after filtering in treatment: 383005 INFO @ Fri, 10 Dec 2021 18:12:05: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 10 Dec 2021 18:12:05: #1 finished! INFO @ Fri, 10 Dec 2021 18:12:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:12:05: #2 number of paired peaks: 723 WARNING @ Fri, 10 Dec 2021 18:12:05: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Fri, 10 Dec 2021 18:12:05: start model_add_line... INFO @ Fri, 10 Dec 2021 18:12:05: start X-correlation... INFO @ Fri, 10 Dec 2021 18:12:05: end of X-cor INFO @ Fri, 10 Dec 2021 18:12:05: #2 finished! INFO @ Fri, 10 Dec 2021 18:12:05: #2 predicted fragment length is 91 bps INFO @ Fri, 10 Dec 2021 18:12:05: #2 alternative fragment length(s) may be 91 bps INFO @ Fri, 10 Dec 2021 18:12:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.20_model.r INFO @ Fri, 10 Dec 2021 18:12:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:12:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:12:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11078125/SRX11078125.20_summits.bed INFO @ Fri, 10 Dec 2021 18:12:07: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 8 millis CompletedMACS2peakCalling