Job ID = 6458580 SRX = SRX5343116 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:40:11 prefetch.2.10.7: 1) Downloading 'SRR8540816'... 2020-06-21T12:40:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:44:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:44:52 prefetch.2.10.7: 1) 'SRR8540816' was downloaded successfully 2020-06-21T12:44:52 prefetch.2.10.7: 'SRR8540816' has 0 unresolved dependencies Read 25404495 spots for SRR8540816/SRR8540816.sra Written 25404495 spots for SRR8540816/SRR8540816.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: 00:07:04 25404495 reads; of these: 25404495 (100.00%) were unpaired; of these: 4260345 (16.77%) aligned 0 times 18439960 (72.59%) aligned exactly 1 time 2704190 (10.64%) aligned >1 times 83.23% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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_sort_core] merging from 12 files... [bam_rmdupse_core] 15468322 / 21144150 = 0.7316 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 21:57:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.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 21:57:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:11: 1000000 INFO @ Sun, 21 Jun 2020 21:57:16: 2000000 INFO @ Sun, 21 Jun 2020 21:57:22: 3000000 INFO @ Sun, 21 Jun 2020 21:57:28: 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 21:57:34: 5000000 INFO @ Sun, 21 Jun 2020 21:57:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.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 21:57:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:39: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:57:39: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:57:39: #1 total tags in treatment: 5675828 INFO @ Sun, 21 Jun 2020 21:57:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:57:39: #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 21:57:39: #1 tags after filtering in treatment: 5675815 INFO @ Sun, 21 Jun 2020 21:57:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:57:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:57:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:57:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:57:40: #2 number of paired peaks: 8540 INFO @ Sun, 21 Jun 2020 21:57:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:57:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:57:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:57:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:57:40: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 21:57:40: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 21:57:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.05_model.r INFO @ Sun, 21 Jun 2020 21:57:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:57:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:57:42: 1000000 INFO @ Sun, 21 Jun 2020 21:57:48: 2000000 INFO @ Sun, 21 Jun 2020 21:57:54: 3000000 INFO @ Sun, 21 Jun 2020 21:57:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:01: 4000000 INFO @ Sun, 21 Jun 2020 21:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.05_summits.bed INFO @ Sun, 21 Jun 2020 21:58:02: Done! pass1 - making usageList (435 chroms): 2 millis pass2 - checking and writing primary data (7631 records, 4 fields): 19 millis CompletedMACS2peakCalling 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 21:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.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 21:58:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:07: 5000000 INFO @ Sun, 21 Jun 2020 21:58:12: 1000000 INFO @ Sun, 21 Jun 2020 21:58:12: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:58:12: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:58:12: #1 total tags in treatment: 5675828 INFO @ Sun, 21 Jun 2020 21:58:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:12: #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 21:58:13: #1 tags after filtering in treatment: 5675815 INFO @ Sun, 21 Jun 2020 21:58:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:13: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:13: #2 number of paired peaks: 8540 INFO @ Sun, 21 Jun 2020 21:58:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:13: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 21:58:13: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 21:58:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.10_model.r INFO @ Sun, 21 Jun 2020 21:58:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:18: 2000000 INFO @ Sun, 21 Jun 2020 21:58:25: 3000000 INFO @ Sun, 21 Jun 2020 21:58:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:31: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:58:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.10_summits.bed INFO @ Sun, 21 Jun 2020 21:58:35: Done! pass1 - making usageList (261 chroms): 2 millis pass2 - checking and writing primary data (6494 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:58:38: 5000000 INFO @ Sun, 21 Jun 2020 21:58:42: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:58:42: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:58:42: #1 total tags in treatment: 5675828 INFO @ Sun, 21 Jun 2020 21:58:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:42: #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 21:58:43: #1 tags after filtering in treatment: 5675815 INFO @ Sun, 21 Jun 2020 21:58:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:43: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:43: #2 number of paired peaks: 8540 INFO @ Sun, 21 Jun 2020 21:58:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:43: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 21:58:43: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 21:58:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.20_model.r INFO @ Sun, 21 Jun 2020 21:58:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:58:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343116/SRX5343116.20_summits.bed INFO @ Sun, 21 Jun 2020 21:59:05: Done! pass1 - making usageList (127 chroms): 2 millis pass2 - checking and writing primary data (4967 records, 4 fields): 9 millis CompletedMACS2peakCalling