Job ID = 6454909 SRX = SRX2592494 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:47:40 prefetch.2.10.7: 1) Downloading 'SRR5289771'... 2020-06-21T09:47:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:47:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:47:55 prefetch.2.10.7: 'SRR5289771' is valid 2020-06-21T09:47:55 prefetch.2.10.7: 1) 'SRR5289771' was downloaded successfully Read 314487 spots for SRR5289771/SRR5289771.sra Written 314487 spots for SRR5289771/SRR5289771.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: 00:00:04 314487 reads; of these: 314487 (100.00%) were unpaired; of these: 139942 (44.50%) aligned 0 times 150793 (47.95%) aligned exactly 1 time 23752 (7.55%) aligned >1 times 55.50% overall alignment rate Time searching: 00:00:04 Overall time: 00:00:04 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] 5401 / 174545 = 0.0309 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 18:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.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 18:48:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:48:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:48:37: #1 total tags in treatment: 169144 INFO @ Sun, 21 Jun 2020 18:48:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:37: #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 18:48:37: #1 tags after filtering in treatment: 168573 INFO @ Sun, 21 Jun 2020 18:48:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:37: #2 number of paired peaks: 5449 INFO @ Sun, 21 Jun 2020 18:48:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:37: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 18:48:37: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 18:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.05_model.r INFO @ Sun, 21 Jun 2020 18:48:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.05_summits.bed INFO @ Sun, 21 Jun 2020 18:48:38: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (279 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 18:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.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 18:49:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:49:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:49:07: #1 total tags in treatment: 169144 INFO @ Sun, 21 Jun 2020 18:49:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:07: #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 18:49:07: #1 tags after filtering in treatment: 168573 INFO @ Sun, 21 Jun 2020 18:49:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:07: #2 number of paired peaks: 5449 INFO @ Sun, 21 Jun 2020 18:49:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:07: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 18:49:07: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 18:49:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.10_model.r INFO @ Sun, 21 Jun 2020 18:49:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.10_summits.bed INFO @ Sun, 21 Jun 2020 18:49:08: Done! pass1 - making usageList (21 chroms): 1 millis pass2 - checking and writing primary data (65 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... INFO @ Sun, 21 Jun 2020 18:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.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 18:49:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:36: #1 read treatment tags... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:49:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:49:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:49:37: #1 total tags in treatment: 169144 INFO @ Sun, 21 Jun 2020 18:49:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:37: #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 18:49:37: #1 tags after filtering in treatment: 168573 INFO @ Sun, 21 Jun 2020 18:49:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:37: #2 number of paired peaks: 5449 INFO @ Sun, 21 Jun 2020 18:49:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:37: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 18:49:37: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 18:49:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.20_model.r INFO @ Sun, 21 Jun 2020 18:49:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592494/SRX2592494.20_summits.bed INFO @ Sun, 21 Jun 2020 18:49:38: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (23 records, 4 fields): 2 millis CompletedMACS2peakCalling