Job ID = 6528344 SRX = SRX5360596 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:47:39 prefetch.2.10.7: 1) Downloading 'SRR8559072'... 2020-06-29T14:47:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:48:04 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:48:04 prefetch.2.10.7: 'SRR8559072' is valid 2020-06-29T14:48:04 prefetch.2.10.7: 1) 'SRR8559072' was downloaded successfully Read 1962158 spots for SRR8559072/SRR8559072.sra Written 1962158 spots for SRR8559072/SRR8559072.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:23 1962158 reads; of these: 1962158 (100.00%) were unpaired; of these: 632350 (32.23%) aligned 0 times 1281535 (65.31%) aligned exactly 1 time 48273 (2.46%) aligned >1 times 67.77% overall alignment rate Time searching: 00:00:23 Overall time: 00:00:23 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_rmdupse_core] 1136083 / 1329808 = 0.8543 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 @ Mon, 29 Jun 2020 23:49:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.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 @ Mon, 29 Jun 2020 23:49:40: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:49:40: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:49:41: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:49:41: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:49:41: #1 total tags in treatment: 193725 INFO @ Mon, 29 Jun 2020 23:49:41: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:49:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:49:41: #1 tags after filtering in treatment: 193725 INFO @ Mon, 29 Jun 2020 23:49:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:49:41: #1 finished! INFO @ Mon, 29 Jun 2020 23:49:41: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:49:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:49:41: #2 number of paired peaks: 174 WARNING @ Mon, 29 Jun 2020 23:49:41: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Mon, 29 Jun 2020 23:49:41: start model_add_line... INFO @ Mon, 29 Jun 2020 23:49:41: start X-correlation... INFO @ Mon, 29 Jun 2020 23:49:41: end of X-cor INFO @ Mon, 29 Jun 2020 23:49:41: #2 finished! INFO @ Mon, 29 Jun 2020 23:49:41: #2 predicted fragment length is 50 bps INFO @ Mon, 29 Jun 2020 23:49:41: #2 alternative fragment length(s) may be 50,363,406,446,509 bps INFO @ Mon, 29 Jun 2020 23:49:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.05_model.r WARNING @ Mon, 29 Jun 2020 23:49:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:49:41: #2 You may need to consider one of the other alternative d(s): 50,363,406,446,509 WARNING @ Mon, 29 Jun 2020 23:49:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:49:41: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:49:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:49:41: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:49:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:49:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:49:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.05_summits.bed INFO @ Mon, 29 Jun 2020 23:49:41: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Mon, 29 Jun 2020 23:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.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 @ Mon, 29 Jun 2020 23:50:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:50:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:50:11: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:50:11: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:50:11: #1 total tags in treatment: 193725 INFO @ Mon, 29 Jun 2020 23:50:11: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:50:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:50:11: #1 tags after filtering in treatment: 193725 INFO @ Mon, 29 Jun 2020 23:50:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:50:11: #1 finished! INFO @ Mon, 29 Jun 2020 23:50:11: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:50:11: #2 number of paired peaks: 174 WARNING @ Mon, 29 Jun 2020 23:50:11: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Mon, 29 Jun 2020 23:50:11: start model_add_line... INFO @ Mon, 29 Jun 2020 23:50:11: start X-correlation... INFO @ Mon, 29 Jun 2020 23:50:11: end of X-cor INFO @ Mon, 29 Jun 2020 23:50:11: #2 finished! INFO @ Mon, 29 Jun 2020 23:50:11: #2 predicted fragment length is 50 bps INFO @ Mon, 29 Jun 2020 23:50:11: #2 alternative fragment length(s) may be 50,363,406,446,509 bps INFO @ Mon, 29 Jun 2020 23:50:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.10_model.r WARNING @ Mon, 29 Jun 2020 23:50:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:50:11: #2 You may need to consider one of the other alternative d(s): 50,363,406,446,509 WARNING @ Mon, 29 Jun 2020 23:50:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:50:11: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:50:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:50:11: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.10_summits.bed INFO @ Mon, 29 Jun 2020 23:50:11: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (134 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.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 @ Mon, 29 Jun 2020 23:50:40: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:50:40: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:50:41: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:50:41: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:50:41: #1 total tags in treatment: 193725 INFO @ Mon, 29 Jun 2020 23:50:41: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:50:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:50:41: #1 tags after filtering in treatment: 193725 INFO @ Mon, 29 Jun 2020 23:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:50:41: #1 finished! INFO @ Mon, 29 Jun 2020 23:50:41: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:50:41: #2 number of paired peaks: 174 WARNING @ Mon, 29 Jun 2020 23:50:41: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Mon, 29 Jun 2020 23:50:41: start model_add_line... INFO @ Mon, 29 Jun 2020 23:50:41: start X-correlation... INFO @ Mon, 29 Jun 2020 23:50:41: end of X-cor INFO @ Mon, 29 Jun 2020 23:50:41: #2 finished! INFO @ Mon, 29 Jun 2020 23:50:41: #2 predicted fragment length is 50 bps INFO @ Mon, 29 Jun 2020 23:50:41: #2 alternative fragment length(s) may be 50,363,406,446,509 bps INFO @ Mon, 29 Jun 2020 23:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.20_model.r WARNING @ Mon, 29 Jun 2020 23:50:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:50:41: #2 You may need to consider one of the other alternative d(s): 50,363,406,446,509 WARNING @ Mon, 29 Jun 2020 23:50:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:50:41: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:50:41: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:50:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:50:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:50:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360596/SRX5360596.20_summits.bed INFO @ Mon, 29 Jun 2020 23:50:41: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 1 millis CompletedMACS2peakCalling