Job ID = 6452806 SRX = SRX040609 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:55:30 prefetch.2.10.7: 1) Downloading 'SRR097978'... 2020-06-21T07:55:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:59:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:59:47 prefetch.2.10.7: 'SRR097978' is valid 2020-06-21T07:59:47 prefetch.2.10.7: 1) 'SRR097978' was downloaded successfully Read 15781499 spots for SRR097978/SRR097978.sra Written 15781499 spots for SRR097978/SRR097978.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: 00:00:01 Multiseed full-index search: 00:02:23 15781499 reads; of these: 15781499 (100.00%) were unpaired; of these: 895229 (5.67%) aligned 0 times 14257828 (90.35%) aligned exactly 1 time 628442 (3.98%) aligned >1 times 94.33% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 7965601 / 14886270 = 0.5351 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 17:06:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.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 17:06:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:06:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:06:14: 1000000 INFO @ Sun, 21 Jun 2020 17:06:19: 2000000 INFO @ Sun, 21 Jun 2020 17:06:24: 3000000 INFO @ Sun, 21 Jun 2020 17:06:29: 4000000 INFO @ Sun, 21 Jun 2020 17:06:34: 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 17:06:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.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 17:06:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:06:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:06:39: 6000000 INFO @ Sun, 21 Jun 2020 17:06:44: 1000000 INFO @ Sun, 21 Jun 2020 17:06:44: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:06:44: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:06:44: #1 total tags in treatment: 6920669 INFO @ Sun, 21 Jun 2020 17:06:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:06:44: #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 17:06:45: #1 tags after filtering in treatment: 6920129 INFO @ Sun, 21 Jun 2020 17:06:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:06:45: #1 finished! INFO @ Sun, 21 Jun 2020 17:06:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:06:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:06:46: #2 number of paired peaks: 11878 INFO @ Sun, 21 Jun 2020 17:06:46: start model_add_line... INFO @ Sun, 21 Jun 2020 17:06:46: start X-correlation... INFO @ Sun, 21 Jun 2020 17:06:46: end of X-cor INFO @ Sun, 21 Jun 2020 17:06:46: #2 finished! INFO @ Sun, 21 Jun 2020 17:06:46: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 17:06:46: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 17:06:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.05_model.r INFO @ Sun, 21 Jun 2020 17:06:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:06:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:06:49: 2000000 INFO @ Sun, 21 Jun 2020 17:06:54: 3000000 INFO @ Sun, 21 Jun 2020 17:06:59: 4000000 INFO @ Sun, 21 Jun 2020 17:07:04: 5000000 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 17:07:09: 6000000 INFO @ Sun, 21 Jun 2020 17:07:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.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 17:07:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:07:14: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:07:14: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:07:14: #1 total tags in treatment: 6920669 INFO @ Sun, 21 Jun 2020 17:07:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:07:14: #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 17:07:14: #1 tags after filtering in treatment: 6920129 INFO @ Sun, 21 Jun 2020 17:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:07:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:07:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:07:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:07:15: 1000000 INFO @ Sun, 21 Jun 2020 17:07:15: #2 number of paired peaks: 11878 INFO @ Sun, 21 Jun 2020 17:07:15: start model_add_line... INFO @ Sun, 21 Jun 2020 17:07:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:07:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:07:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:07:15: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 17:07:15: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 17:07:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.10_model.r INFO @ Sun, 21 Jun 2020 17:07:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:07:20: 2000000 INFO @ Sun, 21 Jun 2020 17:07:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:07:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:07:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.05_summits.bed INFO @ Sun, 21 Jun 2020 17:07:23: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (7641 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:07:26: 3000000 INFO @ Sun, 21 Jun 2020 17:07:31: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:07:37: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:07:43: 6000000 INFO @ Sun, 21 Jun 2020 17:07:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:07:48: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:07:48: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:07:48: #1 total tags in treatment: 6920669 INFO @ Sun, 21 Jun 2020 17:07:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:07:48: #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 17:07:49: #1 tags after filtering in treatment: 6920129 INFO @ Sun, 21 Jun 2020 17:07:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:07:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:07:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:07:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:07:50: #2 number of paired peaks: 11878 INFO @ Sun, 21 Jun 2020 17:07:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:07:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:07:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:07:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:07:50: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 17:07:50: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 17:07:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.20_model.r INFO @ Sun, 21 Jun 2020 17:07:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:07:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:07:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:07:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:07:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.10_summits.bed INFO @ Sun, 21 Jun 2020 17:07:52: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (7189 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:08:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:08:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:08:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:08:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040609/SRX040609.20_summits.bed INFO @ Sun, 21 Jun 2020 17:08:27: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (6562 records, 4 fields): 8 millis CompletedMACS2peakCalling