Job ID = 6455215 SRX = SRX287563 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:39:55 prefetch.2.10.7: 1) Downloading 'SRR869706'... 2020-06-21T09:39:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:41:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:41:30 prefetch.2.10.7: 'SRR869706' is valid 2020-06-21T09:41:30 prefetch.2.10.7: 1) 'SRR869706' was downloaded successfully Read 14126806 spots for SRR869706/SRR869706.sra Written 14126806 spots for SRR869706/SRR869706.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: 00:03:09 14126806 reads; of these: 14126806 (100.00%) were unpaired; of these: 401861 (2.84%) aligned 0 times 10019739 (70.93%) aligned exactly 1 time 3705206 (26.23%) aligned >1 times 97.16% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 1614817 / 13724945 = 0.1177 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 18:48:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.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 18:48:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:46: 1000000 INFO @ Sun, 21 Jun 2020 18:48:51: 2000000 INFO @ Sun, 21 Jun 2020 18:48:56: 3000000 INFO @ Sun, 21 Jun 2020 18:49:01: 4000000 INFO @ Sun, 21 Jun 2020 18:49:06: 5000000 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 18:49:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.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 18:49:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:12: 6000000 INFO @ Sun, 21 Jun 2020 18:49:17: 1000000 INFO @ Sun, 21 Jun 2020 18:49:17: 7000000 INFO @ Sun, 21 Jun 2020 18:49:23: 8000000 INFO @ Sun, 21 Jun 2020 18:49:23: 2000000 INFO @ Sun, 21 Jun 2020 18:49:28: 9000000 INFO @ Sun, 21 Jun 2020 18:49:30: 3000000 INFO @ Sun, 21 Jun 2020 18:49:34: 10000000 INFO @ Sun, 21 Jun 2020 18:49:36: 4000000 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 18:49:40: 11000000 INFO @ Sun, 21 Jun 2020 18:49:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.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 18:49:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:43: 5000000 INFO @ Sun, 21 Jun 2020 18:49:46: 12000000 INFO @ Sun, 21 Jun 2020 18:49:46: 1000000 INFO @ Sun, 21 Jun 2020 18:49:46: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:49:46: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:49:46: #1 total tags in treatment: 12110128 INFO @ Sun, 21 Jun 2020 18:49:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:46: #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 18:49:47: #1 tags after filtering in treatment: 12110032 INFO @ Sun, 21 Jun 2020 18:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:48: #2 number of paired peaks: 932 WARNING @ Sun, 21 Jun 2020 18:49:48: Fewer paired peaks (932) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 932 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:48: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 18:49:48: #2 alternative fragment length(s) may be 131,571 bps INFO @ Sun, 21 Jun 2020 18:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.05_model.r INFO @ Sun, 21 Jun 2020 18:49:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:49: 6000000 INFO @ Sun, 21 Jun 2020 18:49:52: 2000000 INFO @ Sun, 21 Jun 2020 18:49:55: 7000000 INFO @ Sun, 21 Jun 2020 18:49:58: 3000000 INFO @ Sun, 21 Jun 2020 18:50:02: 8000000 INFO @ Sun, 21 Jun 2020 18:50:03: 4000000 INFO @ Sun, 21 Jun 2020 18:50:08: 9000000 INFO @ Sun, 21 Jun 2020 18:50:09: 5000000 INFO @ Sun, 21 Jun 2020 18:50:14: 6000000 INFO @ Sun, 21 Jun 2020 18:50:15: 10000000 INFO @ Sun, 21 Jun 2020 18:50:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:20: 7000000 INFO @ Sun, 21 Jun 2020 18:50:21: 11000000 INFO @ Sun, 21 Jun 2020 18:50:25: 8000000 INFO @ Sun, 21 Jun 2020 18:50:28: 12000000 INFO @ Sun, 21 Jun 2020 18:50:29: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:50:29: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:50:29: #1 total tags in treatment: 12110128 INFO @ Sun, 21 Jun 2020 18:50:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:29: #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 18:50:29: #1 tags after filtering in treatment: 12110032 INFO @ Sun, 21 Jun 2020 18:50:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:29: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:30: #2 number of paired peaks: 932 WARNING @ Sun, 21 Jun 2020 18:50:30: Fewer paired peaks (932) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 932 pairs to build model! INFO @ Sun, 21 Jun 2020 18:50:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:30: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 18:50:30: #2 alternative fragment length(s) may be 131,571 bps INFO @ Sun, 21 Jun 2020 18:50:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.10_model.r INFO @ Sun, 21 Jun 2020 18:50:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:31: 9000000 INFO @ Sun, 21 Jun 2020 18:50:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.05_summits.bed INFO @ Sun, 21 Jun 2020 18:50:32: Done! pass1 - making usageList (524 chroms): 1 millis pass2 - checking and writing primary data (4852 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:50:36: 10000000 INFO @ Sun, 21 Jun 2020 18:50:41: 11000000 INFO @ Sun, 21 Jun 2020 18:50:46: 12000000 INFO @ Sun, 21 Jun 2020 18:50:47: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:50:47: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:50:47: #1 total tags in treatment: 12110128 INFO @ Sun, 21 Jun 2020 18:50:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:47: #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 18:50:48: #1 tags after filtering in treatment: 12110032 INFO @ Sun, 21 Jun 2020 18:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:48: #2 number of paired peaks: 932 WARNING @ Sun, 21 Jun 2020 18:50:48: Fewer paired peaks (932) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 932 pairs to build model! INFO @ Sun, 21 Jun 2020 18:50:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:49: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 18:50:49: #2 alternative fragment length(s) may be 131,571 bps INFO @ Sun, 21 Jun 2020 18:50:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.20_model.r INFO @ Sun, 21 Jun 2020 18:50:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:51:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.10_summits.bed INFO @ Sun, 21 Jun 2020 18:51:15: Done! pass1 - making usageList (325 chroms): 1 millis pass2 - checking and writing primary data (1494 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287563/SRX287563.20_summits.bed INFO @ Sun, 21 Jun 2020 18:51:31: Done! pass1 - making usageList (180 chroms): 1 millis pass2 - checking and writing primary data (539 records, 4 fields): 7 millis CompletedMACS2peakCalling