Job ID = 6458606 SRX = SRX5343138 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:43:37 prefetch.2.10.7: 1) Downloading 'SRR8540838'... 2020-06-21T12:43:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:47:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:47:40 prefetch.2.10.7: 1) 'SRR8540838' was downloaded successfully 2020-06-21T12:47:40 prefetch.2.10.7: 'SRR8540838' has 0 unresolved dependencies Read 24105087 spots for SRR8540838/SRR8540838.sra Written 24105087 spots for SRR8540838/SRR8540838.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: 00:06:02 24105087 reads; of these: 24105087 (100.00%) were unpaired; of these: 7339456 (30.45%) aligned 0 times 13841420 (57.42%) aligned exactly 1 time 2924211 (12.13%) aligned >1 times 69.55% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8568101 / 16765631 = 0.5111 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 21:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.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 21:59:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:07: 1000000 INFO @ Sun, 21 Jun 2020 21:59:12: 2000000 INFO @ Sun, 21 Jun 2020 21:59:17: 3000000 INFO @ Sun, 21 Jun 2020 21:59:22: 4000000 INFO @ Sun, 21 Jun 2020 21:59:28: 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 21:59:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.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 21:59:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:33: 6000000 INFO @ Sun, 21 Jun 2020 21:59:37: 1000000 INFO @ Sun, 21 Jun 2020 21:59:39: 7000000 INFO @ Sun, 21 Jun 2020 21:59:42: 2000000 INFO @ Sun, 21 Jun 2020 21:59:44: 8000000 INFO @ Sun, 21 Jun 2020 21:59:45: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:59:45: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:59:45: #1 total tags in treatment: 8197530 INFO @ Sun, 21 Jun 2020 21:59:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:45: #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 21:59:46: #1 tags after filtering in treatment: 8197528 INFO @ Sun, 21 Jun 2020 21:59:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:46: #2 number of paired peaks: 1055 INFO @ Sun, 21 Jun 2020 21:59:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:46: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 21:59:46: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 21:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.05_model.r INFO @ Sun, 21 Jun 2020 21:59:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:47: 3000000 INFO @ Sun, 21 Jun 2020 21:59:52: 4000000 INFO @ Sun, 21 Jun 2020 21:59:57: 5000000 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 22:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.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 22:00:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:03: 6000000 INFO @ Sun, 21 Jun 2020 22:00:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:07: 1000000 INFO @ Sun, 21 Jun 2020 22:00:08: 7000000 INFO @ Sun, 21 Jun 2020 22:00:13: 2000000 INFO @ Sun, 21 Jun 2020 22:00:14: 8000000 INFO @ Sun, 21 Jun 2020 22:00:15: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:00:15: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:00:15: #1 total tags in treatment: 8197530 INFO @ Sun, 21 Jun 2020 22:00:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:15: #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 22:00:15: #1 tags after filtering in treatment: 8197528 INFO @ Sun, 21 Jun 2020 22:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:15: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:16: #2 number of paired peaks: 1055 INFO @ Sun, 21 Jun 2020 22:00:16: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.05_summits.bed INFO @ Sun, 21 Jun 2020 22:00:16: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:16: Done! INFO @ Sun, 21 Jun 2020 22:00:16: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:16: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:16: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 22:00:16: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 22:00:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.10_model.r INFO @ Sun, 21 Jun 2020 22:00:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:16: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (533 chroms): 2 millis pass2 - checking and writing primary data (6607 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:18: 3000000 INFO @ Sun, 21 Jun 2020 22:00:23: 4000000 INFO @ Sun, 21 Jun 2020 22:00:28: 5000000 INFO @ Sun, 21 Jun 2020 22:00:34: 6000000 INFO @ Sun, 21 Jun 2020 22:00:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:39: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:00:45: 8000000 INFO @ Sun, 21 Jun 2020 22:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.10_summits.bed INFO @ Sun, 21 Jun 2020 22:00:45: Done! pass1 - making usageList (351 chroms): 2 millis pass2 - checking and writing primary data (3022 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:46: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:00:46: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:00:46: #1 total tags in treatment: 8197530 INFO @ Sun, 21 Jun 2020 22:00:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:46: #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 22:00:46: #1 tags after filtering in treatment: 8197528 INFO @ Sun, 21 Jun 2020 22:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:46: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:47: #2 number of paired peaks: 1055 INFO @ Sun, 21 Jun 2020 22:00:47: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:47: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:47: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:47: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:47: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 22:00:47: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 22:00:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.20_model.r INFO @ Sun, 21 Jun 2020 22:00:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:01:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343138/SRX5343138.20_summits.bed INFO @ Sun, 21 Jun 2020 22:01:17: Done! pass1 - making usageList (147 chroms): 1 millis pass2 - checking and writing primary data (820 records, 4 fields): 6 millis CompletedMACS2peakCalling