Job ID = 6453026 SRX = SRX100250 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:51:15 prefetch.2.10.7: 1) Downloading 'SRR351344'... 2020-06-21T07:51:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:52:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:52:13 prefetch.2.10.7: 'SRR351344' is valid 2020-06-21T07:52:13 prefetch.2.10.7: 1) 'SRR351344' was downloaded successfully Read 10437925 spots for SRR351344/SRR351344.sra Written 10437925 spots for SRR351344/SRR351344.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: 00:01:40 10437925 reads; of these: 10437925 (100.00%) were unpaired; of these: 3845661 (36.84%) aligned 0 times 5306776 (50.84%) aligned exactly 1 time 1285488 (12.32%) aligned >1 times 63.16% overall alignment rate Time searching: 00:01:40 Overall time: 00:01:40 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] 3525985 / 6592264 = 0.5349 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 16:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.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 16:55:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:55:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:55:55: 1000000 INFO @ Sun, 21 Jun 2020 16:56:00: 2000000 INFO @ Sun, 21 Jun 2020 16:56:05: 3000000 INFO @ Sun, 21 Jun 2020 16:56:06: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:56:06: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:56:06: #1 total tags in treatment: 3066279 INFO @ Sun, 21 Jun 2020 16:56:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:56:06: #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 16:56:06: #1 tags after filtering in treatment: 3066071 INFO @ Sun, 21 Jun 2020 16:56:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:56:06: #1 finished! INFO @ Sun, 21 Jun 2020 16:56:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:56:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:56:07: #2 number of paired peaks: 2656 INFO @ Sun, 21 Jun 2020 16:56:07: start model_add_line... INFO @ Sun, 21 Jun 2020 16:56:07: start X-correlation... INFO @ Sun, 21 Jun 2020 16:56:07: end of X-cor INFO @ Sun, 21 Jun 2020 16:56:07: #2 finished! INFO @ Sun, 21 Jun 2020 16:56:07: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 16:56:07: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 16:56:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.05_model.r INFO @ Sun, 21 Jun 2020 16:56:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:56:14: #3 Call peaks for each chromosome... 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 16:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.05_summits.bed INFO @ Sun, 21 Jun 2020 16:56:18: Done! pass1 - making usageList (347 chroms): 1 millis pass2 - checking and writing primary data (3174 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.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 16:56:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:56:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:56:25: 1000000 INFO @ Sun, 21 Jun 2020 16:56:30: 2000000 INFO @ Sun, 21 Jun 2020 16:56:35: 3000000 INFO @ Sun, 21 Jun 2020 16:56:36: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:56:36: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:56:36: #1 total tags in treatment: 3066279 INFO @ Sun, 21 Jun 2020 16:56:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:56:36: #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 16:56:36: #1 tags after filtering in treatment: 3066071 INFO @ Sun, 21 Jun 2020 16:56:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:56:36: #1 finished! INFO @ Sun, 21 Jun 2020 16:56:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:56:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:56:37: #2 number of paired peaks: 2656 INFO @ Sun, 21 Jun 2020 16:56:37: start model_add_line... INFO @ Sun, 21 Jun 2020 16:56:37: start X-correlation... INFO @ Sun, 21 Jun 2020 16:56:37: end of X-cor INFO @ Sun, 21 Jun 2020 16:56:37: #2 finished! INFO @ Sun, 21 Jun 2020 16:56:37: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 16:56:37: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 16:56:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.10_model.r INFO @ Sun, 21 Jun 2020 16:56:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:56:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:56:44: #3 Call peaks for each chromosome... 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 16:56:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:56:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:56:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.10_summits.bed INFO @ Sun, 21 Jun 2020 16:56:48: Done! pass1 - making usageList (248 chroms): 1 millis pass2 - checking and writing primary data (2222 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.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 16:56:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:56:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:56:55: 1000000 INFO @ Sun, 21 Jun 2020 16:57:00: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:57:06: 3000000 INFO @ Sun, 21 Jun 2020 16:57:06: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:57:06: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:57:06: #1 total tags in treatment: 3066279 INFO @ Sun, 21 Jun 2020 16:57:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:57:06: #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 16:57:06: #1 tags after filtering in treatment: 3066071 INFO @ Sun, 21 Jun 2020 16:57:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:57:06: #1 finished! INFO @ Sun, 21 Jun 2020 16:57:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:57:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:57:07: #2 number of paired peaks: 2656 INFO @ Sun, 21 Jun 2020 16:57:07: start model_add_line... INFO @ Sun, 21 Jun 2020 16:57:07: start X-correlation... INFO @ Sun, 21 Jun 2020 16:57:07: end of X-cor INFO @ Sun, 21 Jun 2020 16:57:07: #2 finished! INFO @ Sun, 21 Jun 2020 16:57:07: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 16:57:07: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 16:57:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.20_model.r INFO @ Sun, 21 Jun 2020 16:57:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:57:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:57:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:57:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:57:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:57:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX100250/SRX100250.20_summits.bed INFO @ Sun, 21 Jun 2020 16:57:18: Done! pass1 - making usageList (161 chroms): 1 millis pass2 - checking and writing primary data (1666 records, 4 fields): 7 millis CompletedMACS2peakCalling