Job ID = 6455203 SRX = SRX2832098 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:49:55 prefetch.2.10.7: 1) Downloading 'SRR5573762'... 2020-06-21T09:49:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:51:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:51:16 prefetch.2.10.7: 'SRR5573762' is valid 2020-06-21T09:51:16 prefetch.2.10.7: 1) 'SRR5573762' was downloaded successfully Read 9752267 spots for SRR5573762/SRR5573762.sra Written 9752267 spots for SRR5573762/SRR5573762.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: 00:03:10 9752267 reads; of these: 9752267 (100.00%) were unpaired; of these: 547017 (5.61%) aligned 0 times 6314824 (64.75%) aligned exactly 1 time 2890426 (29.64%) aligned >1 times 94.39% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 1948674 / 9205250 = 0.2117 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 18:57:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.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 18:57:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:40: 1000000 INFO @ Sun, 21 Jun 2020 18:57:45: 2000000 INFO @ Sun, 21 Jun 2020 18:57:51: 3000000 INFO @ Sun, 21 Jun 2020 18:57:56: 4000000 INFO @ Sun, 21 Jun 2020 18:58:02: 5000000 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 18:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.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 18:58:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:08: 6000000 INFO @ Sun, 21 Jun 2020 18:58:11: 1000000 INFO @ Sun, 21 Jun 2020 18:58:14: 7000000 INFO @ Sun, 21 Jun 2020 18:58:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:16: #1 total tags in treatment: 7256576 INFO @ Sun, 21 Jun 2020 18:58:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:16: #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 18:58:16: #1 tags after filtering in treatment: 7256414 INFO @ Sun, 21 Jun 2020 18:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:17: 2000000 INFO @ Sun, 21 Jun 2020 18:58:17: #2 number of paired peaks: 1173 INFO @ Sun, 21 Jun 2020 18:58:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:17: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 18:58:17: #2 alternative fragment length(s) may be 218 bps INFO @ Sun, 21 Jun 2020 18:58:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.05_model.r INFO @ Sun, 21 Jun 2020 18:58:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:23: 3000000 INFO @ Sun, 21 Jun 2020 18:58:28: 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 18:58:34: 5000000 INFO @ Sun, 21 Jun 2020 18:58:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.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 18:58:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:41: 6000000 INFO @ Sun, 21 Jun 2020 18:58:41: 1000000 INFO @ Sun, 21 Jun 2020 18:58:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.05_summits.bed INFO @ Sun, 21 Jun 2020 18:58:44: Done! pass1 - making usageList (595 chroms): 2 millis pass2 - checking and writing primary data (5839 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:48: 7000000 INFO @ Sun, 21 Jun 2020 18:58:48: 2000000 INFO @ Sun, 21 Jun 2020 18:58:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:49: #1 total tags in treatment: 7256576 INFO @ Sun, 21 Jun 2020 18:58:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:49: #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 18:58:50: #1 tags after filtering in treatment: 7256414 INFO @ Sun, 21 Jun 2020 18:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:50: #2 number of paired peaks: 1173 INFO @ Sun, 21 Jun 2020 18:58:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:50: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 18:58:50: #2 alternative fragment length(s) may be 218 bps INFO @ Sun, 21 Jun 2020 18:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.10_model.r INFO @ Sun, 21 Jun 2020 18:58:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:53: 3000000 INFO @ Sun, 21 Jun 2020 18:59:00: 4000000 INFO @ Sun, 21 Jun 2020 18:59:06: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:59:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:12: 6000000 INFO @ Sun, 21 Jun 2020 18:59:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.10_summits.bed INFO @ Sun, 21 Jun 2020 18:59:16: Done! pass1 - making usageList (503 chroms): 1 millis pass2 - checking and writing primary data (2504 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:59:19: 7000000 INFO @ Sun, 21 Jun 2020 18:59:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:59:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:59:20: #1 total tags in treatment: 7256576 INFO @ Sun, 21 Jun 2020 18:59:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:20: #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 18:59:21: #1 tags after filtering in treatment: 7256414 INFO @ Sun, 21 Jun 2020 18:59:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:21: #2 number of paired peaks: 1173 INFO @ Sun, 21 Jun 2020 18:59:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:21: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 18:59:21: #2 alternative fragment length(s) may be 218 bps INFO @ Sun, 21 Jun 2020 18:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.20_model.r INFO @ Sun, 21 Jun 2020 18:59:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:59:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2832098/SRX2832098.20_summits.bed INFO @ Sun, 21 Jun 2020 18:59:48: Done! pass1 - making usageList (295 chroms): 1 millis pass2 - checking and writing primary data (862 records, 4 fields): 10 millis CompletedMACS2peakCalling