Job ID = 6452450 SRX = SRX013069 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:34:57 prefetch.2.10.7: 1) Downloading 'SRR030335'... 2020-06-21T07:34:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:36:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:36:05 prefetch.2.10.7: 'SRR030335' is valid 2020-06-21T07:36:05 prefetch.2.10.7: 1) 'SRR030335' was downloaded successfully Read 7359017 spots for SRR030335/SRR030335.sra Written 7359017 spots for SRR030335/SRR030335.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: 00:01:09 7359017 reads; of these: 7359017 (100.00%) were unpaired; of these: 1377418 (18.72%) aligned 0 times 5341503 (72.58%) aligned exactly 1 time 640096 (8.70%) aligned >1 times 81.28% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 2251831 / 5981599 = 0.3765 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 16:39:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.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 16:39:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:39:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:39:21: 1000000 INFO @ Sun, 21 Jun 2020 16:39:26: 2000000 INFO @ Sun, 21 Jun 2020 16:39:31: 3000000 INFO @ Sun, 21 Jun 2020 16:39:35: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:39:35: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:39:35: #1 total tags in treatment: 3729768 INFO @ Sun, 21 Jun 2020 16:39:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:39:35: #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 16:39:35: #1 tags after filtering in treatment: 3729559 INFO @ Sun, 21 Jun 2020 16:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:39:35: #1 finished! INFO @ Sun, 21 Jun 2020 16:39:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:39:36: #2 number of paired peaks: 4178 INFO @ Sun, 21 Jun 2020 16:39:36: start model_add_line... INFO @ Sun, 21 Jun 2020 16:39:36: start X-correlation... INFO @ Sun, 21 Jun 2020 16:39:36: end of X-cor INFO @ Sun, 21 Jun 2020 16:39:36: #2 finished! INFO @ Sun, 21 Jun 2020 16:39:36: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 16:39:36: #2 alternative fragment length(s) may be 213,597 bps INFO @ Sun, 21 Jun 2020 16:39:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.05_model.r INFO @ Sun, 21 Jun 2020 16:39:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:39:36: #3 Pre-compute pvalue-qvalue table... 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 16:39:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.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 16:39:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:39:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:39:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:39:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:39:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.05_summits.bed INFO @ Sun, 21 Jun 2020 16:39:51: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (5811 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:39:51: 1000000 INFO @ Sun, 21 Jun 2020 16:39:57: 2000000 INFO @ Sun, 21 Jun 2020 16:40:02: 3000000 INFO @ Sun, 21 Jun 2020 16:40:06: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:40:06: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:40:06: #1 total tags in treatment: 3729768 INFO @ Sun, 21 Jun 2020 16:40:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:40:06: #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 16:40:06: #1 tags after filtering in treatment: 3729559 INFO @ Sun, 21 Jun 2020 16:40:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:40:06: #1 finished! INFO @ Sun, 21 Jun 2020 16:40:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:40:07: #2 number of paired peaks: 4178 INFO @ Sun, 21 Jun 2020 16:40:07: start model_add_line... INFO @ Sun, 21 Jun 2020 16:40:07: start X-correlation... INFO @ Sun, 21 Jun 2020 16:40:07: end of X-cor INFO @ Sun, 21 Jun 2020 16:40:07: #2 finished! INFO @ Sun, 21 Jun 2020 16:40:07: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 16:40:07: #2 alternative fragment length(s) may be 213,597 bps INFO @ Sun, 21 Jun 2020 16:40:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.10_model.r INFO @ Sun, 21 Jun 2020 16:40:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:40:07: #3 Pre-compute pvalue-qvalue table... 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 16:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.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 16:40:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:40:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:40:21: 1000000 INFO @ Sun, 21 Jun 2020 16:40:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:40:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:40:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.10_summits.bed INFO @ Sun, 21 Jun 2020 16:40:22: Done! pass1 - making usageList (65 chroms): 1 millis pass2 - checking and writing primary data (4417 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:40:26: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:40:31: 3000000 INFO @ Sun, 21 Jun 2020 16:40:35: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:40:35: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:40:35: #1 total tags in treatment: 3729768 INFO @ Sun, 21 Jun 2020 16:40:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:40:35: #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 16:40:35: #1 tags after filtering in treatment: 3729559 INFO @ Sun, 21 Jun 2020 16:40:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:40:35: #1 finished! INFO @ Sun, 21 Jun 2020 16:40:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:40:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:40:36: #2 number of paired peaks: 4178 INFO @ Sun, 21 Jun 2020 16:40:36: start model_add_line... INFO @ Sun, 21 Jun 2020 16:40:36: start X-correlation... INFO @ Sun, 21 Jun 2020 16:40:36: end of X-cor INFO @ Sun, 21 Jun 2020 16:40:36: #2 finished! INFO @ Sun, 21 Jun 2020 16:40:36: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 16:40:36: #2 alternative fragment length(s) may be 213,597 bps INFO @ Sun, 21 Jun 2020 16:40:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.20_model.r INFO @ Sun, 21 Jun 2020 16:40:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:40:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:40:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013069/SRX013069.20_summits.bed INFO @ Sun, 21 Jun 2020 16:40:51: Done! pass1 - making usageList (48 chroms): 2 millis pass2 - checking and writing primary data (2959 records, 4 fields): 6 millis CompletedMACS2peakCalling