Job ID = 6452936 SRX = SRX050602 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:00:12 prefetch.2.10.7: 1) Downloading 'SRR139084'... 2020-06-21T08:00:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:00:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:01:00 prefetch.2.10.7: 'SRR139084' is valid 2020-06-21T08:01:00 prefetch.2.10.7: 1) 'SRR139084' was downloaded successfully Read 5715475 spots for SRR139084/SRR139084.sra Written 5715475 spots for SRR139084/SRR139084.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: 00:01:02 5715475 reads; of these: 5715475 (100.00%) were unpaired; of these: 177685 (3.11%) aligned 0 times 4550427 (79.62%) aligned exactly 1 time 987363 (17.28%) aligned >1 times 96.89% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 440079 / 5537790 = 0.0795 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 17:03:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.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 17:03:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:03:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:04:02: 1000000 INFO @ Sun, 21 Jun 2020 17:04:06: 2000000 INFO @ Sun, 21 Jun 2020 17:04:11: 3000000 INFO @ Sun, 21 Jun 2020 17:04:16: 4000000 INFO @ Sun, 21 Jun 2020 17:04:21: 5000000 INFO @ Sun, 21 Jun 2020 17:04:21: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:04:21: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:04:21: #1 total tags in treatment: 5097711 INFO @ Sun, 21 Jun 2020 17:04:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:04:21: #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 17:04:22: #1 tags after filtering in treatment: 5097617 INFO @ Sun, 21 Jun 2020 17:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:04:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:04:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:04:22: #2 number of paired peaks: 1275 INFO @ Sun, 21 Jun 2020 17:04:22: start model_add_line... INFO @ Sun, 21 Jun 2020 17:04:22: start X-correlation... INFO @ Sun, 21 Jun 2020 17:04:22: end of X-cor INFO @ Sun, 21 Jun 2020 17:04:22: #2 finished! INFO @ Sun, 21 Jun 2020 17:04:22: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 17:04:22: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 17:04:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.05_model.r INFO @ Sun, 21 Jun 2020 17:04:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:04:22: #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 17:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.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 17:04:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:04:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:04:32: 1000000 INFO @ Sun, 21 Jun 2020 17:04:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:04:36: 2000000 INFO @ Sun, 21 Jun 2020 17:04:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:04:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:04:40: 3000000 INFO @ Sun, 21 Jun 2020 17:04:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.05_summits.bed INFO @ Sun, 21 Jun 2020 17:04:40: Done! pass1 - making usageList (206 chroms): 2 millis pass2 - checking and writing primary data (3748 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:04:45: 4000000 INFO @ Sun, 21 Jun 2020 17:04:50: 5000000 INFO @ Sun, 21 Jun 2020 17:04:50: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:04:50: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:04:50: #1 total tags in treatment: 5097711 INFO @ Sun, 21 Jun 2020 17:04:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:04:50: #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 17:04:51: #1 tags after filtering in treatment: 5097617 INFO @ Sun, 21 Jun 2020 17:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:04:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:04:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:04:51: #2 number of paired peaks: 1275 INFO @ Sun, 21 Jun 2020 17:04:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:04:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:04:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:04:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:04:51: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 17:04:51: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 17:04:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.10_model.r INFO @ Sun, 21 Jun 2020 17:04:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:04:51: #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 17:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.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 17:04:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:04:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:02: 1000000 INFO @ Sun, 21 Jun 2020 17:05:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:05:07: 2000000 INFO @ Sun, 21 Jun 2020 17:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.10_summits.bed INFO @ Sun, 21 Jun 2020 17:05:09: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (2129 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:05:12: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:05:17: 4000000 INFO @ Sun, 21 Jun 2020 17:05:23: 5000000 INFO @ Sun, 21 Jun 2020 17:05:23: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:05:23: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:05:23: #1 total tags in treatment: 5097711 INFO @ Sun, 21 Jun 2020 17:05:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:05:23: #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 17:05:24: #1 tags after filtering in treatment: 5097617 INFO @ Sun, 21 Jun 2020 17:05:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:05:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:05:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:05:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:05:24: #2 number of paired peaks: 1275 INFO @ Sun, 21 Jun 2020 17:05:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:05:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:05:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:05:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:05:24: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 17:05:24: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 17:05:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.20_model.r INFO @ Sun, 21 Jun 2020 17:05:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:05:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:05:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:05:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:05:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:05:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050602/SRX050602.20_summits.bed INFO @ Sun, 21 Jun 2020 17:05:43: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (1182 records, 4 fields): 5 millis CompletedMACS2peakCalling