Job ID = 6452397 SRX = SRX013034 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:36:12 prefetch.2.10.7: 1) Downloading 'SRR030300'... 2020-06-21T07:36:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:37:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:37:08 prefetch.2.10.7: 'SRR030300' is valid 2020-06-21T07:37:08 prefetch.2.10.7: 1) 'SRR030300' was downloaded successfully Read 5808194 spots for SRR030300/SRR030300.sra Written 5808194 spots for SRR030300/SRR030300.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: 00:01:00 5808194 reads; of these: 5808194 (100.00%) were unpaired; of these: 310034 (5.34%) aligned 0 times 5183115 (89.24%) aligned exactly 1 time 315045 (5.42%) aligned >1 times 94.66% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 524968 / 5498160 = 0.0955 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 16:40:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.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 16:40:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:40:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:10: 1000000 INFO @ Sun, 21 Jun 2020 16:40:16: 2000000 INFO @ Sun, 21 Jun 2020 16:40:22: 3000000 INFO @ Sun, 21 Jun 2020 16:40:28: 4000000 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 16:40:33: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:40:33: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:40:33: #1 total tags in treatment: 4973192 INFO @ Sun, 21 Jun 2020 16:40:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:40:33: #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 16:40:34: #1 tags after filtering in treatment: 4972531 INFO @ Sun, 21 Jun 2020 16:40:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:40:34: #1 finished! INFO @ Sun, 21 Jun 2020 16:40:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:40:34: #2 number of paired peaks: 4933 INFO @ Sun, 21 Jun 2020 16:40:34: start model_add_line... INFO @ Sun, 21 Jun 2020 16:40:34: start X-correlation... INFO @ Sun, 21 Jun 2020 16:40:34: end of X-cor INFO @ Sun, 21 Jun 2020 16:40:34: #2 finished! INFO @ Sun, 21 Jun 2020 16:40:34: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 16:40:34: #2 alternative fragment length(s) may be 131 bps INFO @ Sun, 21 Jun 2020 16:40:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.05_model.r INFO @ Sun, 21 Jun 2020 16:40:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:40:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:40:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.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 16:40:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:40:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:40: 1000000 INFO @ Sun, 21 Jun 2020 16:40:46: 2000000 INFO @ Sun, 21 Jun 2020 16:40:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:40:52: 3000000 INFO @ Sun, 21 Jun 2020 16:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.05_summits.bed INFO @ Sun, 21 Jun 2020 16:40:55: Done! pass1 - making usageList (48 chroms): 2 millis pass2 - checking and writing primary data (10814 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:40:59: 4000000 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 16:41:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.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 16:41:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:41:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:41:05: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:05: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:05: #1 total tags in treatment: 4973192 INFO @ Sun, 21 Jun 2020 16:41:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:05: #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 16:41:05: #1 tags after filtering in treatment: 4972531 INFO @ Sun, 21 Jun 2020 16:41:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:05: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:06: #2 number of paired peaks: 4933 INFO @ Sun, 21 Jun 2020 16:41:06: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:06: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:06: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:06: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:06: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 16:41:06: #2 alternative fragment length(s) may be 131 bps INFO @ Sun, 21 Jun 2020 16:41:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.10_model.r INFO @ Sun, 21 Jun 2020 16:41:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:41:10: 1000000 INFO @ Sun, 21 Jun 2020 16:41:16: 2000000 INFO @ Sun, 21 Jun 2020 16:41:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:41:23: 3000000 INFO @ Sun, 21 Jun 2020 16:41:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.10_summits.bed INFO @ Sun, 21 Jun 2020 16:41:27: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (5201 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:41:29: 4000000 INFO @ Sun, 21 Jun 2020 16:41:35: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:41:35: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:41:35: #1 total tags in treatment: 4973192 INFO @ Sun, 21 Jun 2020 16:41:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:41:35: #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 16:41:35: #1 tags after filtering in treatment: 4972531 INFO @ Sun, 21 Jun 2020 16:41:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:41:35: #1 finished! INFO @ Sun, 21 Jun 2020 16:41:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:41:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:41:36: #2 number of paired peaks: 4933 INFO @ Sun, 21 Jun 2020 16:41:36: start model_add_line... INFO @ Sun, 21 Jun 2020 16:41:36: start X-correlation... INFO @ Sun, 21 Jun 2020 16:41:36: end of X-cor INFO @ Sun, 21 Jun 2020 16:41:36: #2 finished! INFO @ Sun, 21 Jun 2020 16:41:36: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 16:41:36: #2 alternative fragment length(s) may be 131 bps INFO @ Sun, 21 Jun 2020 16:41:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.20_model.r INFO @ Sun, 21 Jun 2020 16:41:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:41:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:41:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013034/SRX013034.20_summits.bed INFO @ Sun, 21 Jun 2020 16:41:56: Done! pass1 - making usageList (18 chroms): 2 millis pass2 - checking and writing primary data (2002 records, 4 fields): 3 millis CompletedMACS2peakCalling