Job ID = 12264856 SRX = SRX3032255 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16917848 spots for SRR5863945/SRR5863945.sra Written 16917848 spots for SRR5863945/SRR5863945.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265039 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:58 16917848 reads; of these: 16917848 (100.00%) were unpaired; of these: 6943924 (41.04%) aligned 0 times 5073092 (29.99%) aligned exactly 1 time 4900832 (28.97%) aligned >1 times 58.96% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 5453570 / 9973924 = 0.5468 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 05:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.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 @ Sat, 03 Apr 2021 05:59:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:59:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:00: 1000000 INFO @ Sat, 03 Apr 2021 06:00:07: 2000000 INFO @ Sat, 03 Apr 2021 06:00:14: 3000000 INFO @ Sat, 03 Apr 2021 06:00:21: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:00:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.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 @ Sat, 03 Apr 2021 06:00:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:24: #1 tag size is determined as 20 bps INFO @ Sat, 03 Apr 2021 06:00:24: #1 tag size = 20 INFO @ Sat, 03 Apr 2021 06:00:24: #1 total tags in treatment: 4520354 INFO @ Sat, 03 Apr 2021 06:00:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:00:24: #1 tags after filtering in treatment: 4520354 INFO @ Sat, 03 Apr 2021 06:00:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:24: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:24: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:00:25: #2 number of paired peaks: 2372 INFO @ Sat, 03 Apr 2021 06:00:25: start model_add_line... INFO @ Sat, 03 Apr 2021 06:00:25: start X-correlation... INFO @ Sat, 03 Apr 2021 06:00:25: end of X-cor INFO @ Sat, 03 Apr 2021 06:00:25: #2 finished! INFO @ Sat, 03 Apr 2021 06:00:25: #2 predicted fragment length is 64 bps INFO @ Sat, 03 Apr 2021 06:00:25: #2 alternative fragment length(s) may be 64 bps INFO @ Sat, 03 Apr 2021 06:00:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.05_model.r INFO @ Sat, 03 Apr 2021 06:00:25: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:00:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:00:30: 1000000 INFO @ Sat, 03 Apr 2021 06:00:37: 2000000 INFO @ Sat, 03 Apr 2021 06:00:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:00:44: 3000000 INFO @ Sat, 03 Apr 2021 06:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.05_summits.bed INFO @ Sat, 03 Apr 2021 06:00:46: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (11315 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 03 Apr 2021 06:00:51: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:00:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.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 @ Sat, 03 Apr 2021 06:00:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:54: #1 tag size is determined as 20 bps INFO @ Sat, 03 Apr 2021 06:00:54: #1 tag size = 20 INFO @ Sat, 03 Apr 2021 06:00:54: #1 total tags in treatment: 4520354 INFO @ Sat, 03 Apr 2021 06:00:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:00:55: #1 tags after filtering in treatment: 4520354 INFO @ Sat, 03 Apr 2021 06:00:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:55: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:00:55: #2 number of paired peaks: 2372 INFO @ Sat, 03 Apr 2021 06:00:55: start model_add_line... INFO @ Sat, 03 Apr 2021 06:00:55: start X-correlation... INFO @ Sat, 03 Apr 2021 06:00:55: end of X-cor INFO @ Sat, 03 Apr 2021 06:00:55: #2 finished! INFO @ Sat, 03 Apr 2021 06:00:55: #2 predicted fragment length is 64 bps INFO @ Sat, 03 Apr 2021 06:00:55: #2 alternative fragment length(s) may be 64 bps INFO @ Sat, 03 Apr 2021 06:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.10_model.r INFO @ Sat, 03 Apr 2021 06:00:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:01:01: 1000000 INFO @ Sat, 03 Apr 2021 06:01:07: 2000000 INFO @ Sat, 03 Apr 2021 06:01:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:14: 3000000 INFO @ Sat, 03 Apr 2021 06:01:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.10_summits.bed INFO @ Sat, 03 Apr 2021 06:01:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4826 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:01:21: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:01:24: #1 tag size is determined as 20 bps INFO @ Sat, 03 Apr 2021 06:01:24: #1 tag size = 20 INFO @ Sat, 03 Apr 2021 06:01:24: #1 total tags in treatment: 4520354 INFO @ Sat, 03 Apr 2021 06:01:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:01:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:01:24: #1 tags after filtering in treatment: 4520354 INFO @ Sat, 03 Apr 2021 06:01:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:01:24: #1 finished! INFO @ Sat, 03 Apr 2021 06:01:24: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:01:25: #2 number of paired peaks: 2372 INFO @ Sat, 03 Apr 2021 06:01:25: start model_add_line... INFO @ Sat, 03 Apr 2021 06:01:25: start X-correlation... INFO @ Sat, 03 Apr 2021 06:01:25: end of X-cor INFO @ Sat, 03 Apr 2021 06:01:25: #2 finished! INFO @ Sat, 03 Apr 2021 06:01:25: #2 predicted fragment length is 64 bps INFO @ Sat, 03 Apr 2021 06:01:25: #2 alternative fragment length(s) may be 64 bps INFO @ Sat, 03 Apr 2021 06:01:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.20_model.r INFO @ Sat, 03 Apr 2021 06:01:25: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:01:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:01:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032255/SRX3032255.20_summits.bed INFO @ Sat, 03 Apr 2021 06:01:45: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (685 records, 4 fields): 3 millis CompletedMACS2peakCalling