Job ID = 6452688 SRX = SRX025488 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:58:14 prefetch.2.10.7: 1) Downloading 'SRR063892'... 2020-06-21T07:58:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:58:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:58:35 prefetch.2.10.7: 'SRR063892' is valid 2020-06-21T07:58:35 prefetch.2.10.7: 1) 'SRR063892' was downloaded successfully Read 1826540 spots for SRR063892/SRR063892.sra Written 1826540 spots for SRR063892/SRR063892.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 1826540 reads; of these: 1826540 (100.00%) were unpaired; of these: 133013 (7.28%) aligned 0 times 1224996 (67.07%) aligned exactly 1 time 468531 (25.65%) aligned >1 times 92.72% 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: 1870 sequences. [bam_rmdupse_core] 127097 / 1693527 = 0.0750 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 16:59:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.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 16:59:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:59:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:00:04: 1000000 INFO @ Sun, 21 Jun 2020 17:00:07: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:00:07: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:00:07: #1 total tags in treatment: 1566430 INFO @ Sun, 21 Jun 2020 17:00:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:07: #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 17:00:07: #1 tags after filtering in treatment: 1566103 INFO @ Sun, 21 Jun 2020 17:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:07: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:07: #2 number of paired peaks: 624 WARNING @ Sun, 21 Jun 2020 17:00:07: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Sun, 21 Jun 2020 17:00:07: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:07: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:07: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:07: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:07: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 17:00:07: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 17:00:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.05_model.r INFO @ Sun, 21 Jun 2020 17:00:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:00:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.05_summits.bed INFO @ Sun, 21 Jun 2020 17:00:13: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (295 records, 4 fields): 4 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 17:00:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.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 17:00:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:00:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:00:34: 1000000 INFO @ Sun, 21 Jun 2020 17:00:37: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:00:37: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:00:37: #1 total tags in treatment: 1566430 INFO @ Sun, 21 Jun 2020 17:00:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:37: #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 17:00:37: #1 tags after filtering in treatment: 1566103 INFO @ Sun, 21 Jun 2020 17:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:37: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:37: #2 number of paired peaks: 624 WARNING @ Sun, 21 Jun 2020 17:00:37: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Sun, 21 Jun 2020 17:00:37: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:37: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:37: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:37: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:37: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 17:00:37: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 17:00:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.10_model.r INFO @ Sun, 21 Jun 2020 17:00:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:00:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.10_summits.bed INFO @ Sun, 21 Jun 2020 17:00:43: Done! pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 3 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 17:00:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.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 17:00:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:00:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:01:04: 1000000 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 17:01:07: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:01:07: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:01:07: #1 total tags in treatment: 1566430 INFO @ Sun, 21 Jun 2020 17:01:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:01:07: #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 17:01:07: #1 tags after filtering in treatment: 1566103 INFO @ Sun, 21 Jun 2020 17:01:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:01:07: #1 finished! INFO @ Sun, 21 Jun 2020 17:01:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:01:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:01:07: #2 number of paired peaks: 624 WARNING @ Sun, 21 Jun 2020 17:01:07: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Sun, 21 Jun 2020 17:01:07: start model_add_line... INFO @ Sun, 21 Jun 2020 17:01:08: start X-correlation... INFO @ Sun, 21 Jun 2020 17:01:08: end of X-cor INFO @ Sun, 21 Jun 2020 17:01:08: #2 finished! INFO @ Sun, 21 Jun 2020 17:01:08: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 17:01:08: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 17:01:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.20_model.r INFO @ Sun, 21 Jun 2020 17:01:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:01:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:01:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:01:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:01:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:01:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025488/SRX025488.20_summits.bed INFO @ Sun, 21 Jun 2020 17:01:13: Done! pass1 - making usageList (49 chroms): 0 millis pass2 - checking and writing primary data (75 records, 4 fields): 3 millis CompletedMACS2peakCalling