Job ID = 6457587 SRX = SRX4669066 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:40:40 prefetch.2.10.7: 1) Downloading 'SRR7817591'... 2020-06-21T11:40:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:40:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:40:59 prefetch.2.10.7: 'SRR7817591' is valid 2020-06-21T11:40:59 prefetch.2.10.7: 1) 'SRR7817591' was downloaded successfully 2020-06-21T11:40:59 prefetch.2.10.7: 'SRR7817591' has 0 unresolved dependencies Read 816505 spots for SRR7817591/SRR7817591.sra Written 816505 spots for SRR7817591/SRR7817591.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:12 816505 reads; of these: 816505 (100.00%) were unpaired; of these: 66681 (8.17%) aligned 0 times 655639 (80.30%) aligned exactly 1 time 94185 (11.54%) aligned >1 times 91.83% overall alignment rate Time searching: 00:00:13 Overall time: 00:00:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 75252 / 749824 = 0.1004 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 @ Sun, 21 Jun 2020 20:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.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 @ Sun, 21 Jun 2020 20:41:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:41:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:42:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:42:05: #1 total tags in treatment: 674572 INFO @ Sun, 21 Jun 2020 20:42:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:42:05: #1 tags after filtering in treatment: 673818 INFO @ Sun, 21 Jun 2020 20:42:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:05: #2 number of paired peaks: 647 WARNING @ Sun, 21 Jun 2020 20:42:05: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sun, 21 Jun 2020 20:42:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:05: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 20:42:05: #2 alternative fragment length(s) may be 80,141,166,191 bps INFO @ Sun, 21 Jun 2020 20:42:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.05_model.r INFO @ Sun, 21 Jun 2020 20:42:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:42:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.05_summits.bed INFO @ Sun, 21 Jun 2020 20:42:08: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 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 @ Sun, 21 Jun 2020 20:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.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 @ Sun, 21 Jun 2020 20:42:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:42:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:42:35: #1 total tags in treatment: 674572 INFO @ Sun, 21 Jun 2020 20:42:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:42:35: #1 tags after filtering in treatment: 673818 INFO @ Sun, 21 Jun 2020 20:42:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:35: #2 number of paired peaks: 647 WARNING @ Sun, 21 Jun 2020 20:42:35: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sun, 21 Jun 2020 20:42:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:35: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 20:42:35: #2 alternative fragment length(s) may be 80,141,166,191 bps INFO @ Sun, 21 Jun 2020 20:42:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.10_model.r INFO @ Sun, 21 Jun 2020 20:42:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:42:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.10_summits.bed INFO @ Sun, 21 Jun 2020 20:42:38: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 2 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 INFO @ Sun, 21 Jun 2020 20:42:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.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 @ Sun, 21 Jun 2020 20:42:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:59: #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 @ Sun, 21 Jun 2020 20:43:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:43:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:43:05: #1 total tags in treatment: 674572 INFO @ Sun, 21 Jun 2020 20:43:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:43:06: #1 tags after filtering in treatment: 673818 INFO @ Sun, 21 Jun 2020 20:43:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:06: #2 number of paired peaks: 647 WARNING @ Sun, 21 Jun 2020 20:43:06: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sun, 21 Jun 2020 20:43:06: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:06: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:06: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:06: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:06: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 20:43:06: #2 alternative fragment length(s) may be 80,141,166,191 bps INFO @ Sun, 21 Jun 2020 20:43:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.20_model.r INFO @ Sun, 21 Jun 2020 20:43:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669066/SRX4669066.20_summits.bed INFO @ Sun, 21 Jun 2020 20:43:09: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 6 millis CompletedMACS2peakCalling