Job ID = 6455956 SRX = SRX3068989 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:29:37 prefetch.2.10.7: 1) Downloading 'SRR5907465'... 2020-06-21T10:29:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:52 prefetch.2.10.7: 1) 'SRR5907465' was downloaded successfully Read 20673809 spots for SRR5907465/SRR5907465.sra Written 20673809 spots for SRR5907465/SRR5907465.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: 00:04:16 20673809 reads; of these: 20673809 (100.00%) were unpaired; of these: 3090092 (14.95%) aligned 0 times 15401808 (74.50%) aligned exactly 1 time 2181909 (10.55%) aligned >1 times 85.05% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 9381110 / 17583717 = 0.5335 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 19:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.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 19:41:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:41:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:06: 1000000 INFO @ Sun, 21 Jun 2020 19:42:13: 2000000 INFO @ Sun, 21 Jun 2020 19:42:21: 3000000 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 19:42:28: 4000000 INFO @ Sun, 21 Jun 2020 19:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.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 19:42:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:36: 5000000 INFO @ Sun, 21 Jun 2020 19:42:37: 1000000 INFO @ Sun, 21 Jun 2020 19:42:44: 6000000 INFO @ Sun, 21 Jun 2020 19:42:44: 2000000 INFO @ Sun, 21 Jun 2020 19:42:52: 3000000 INFO @ Sun, 21 Jun 2020 19:42:52: 7000000 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 19:42:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.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 19:42:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:00: 4000000 INFO @ Sun, 21 Jun 2020 19:43:00: 8000000 INFO @ Sun, 21 Jun 2020 19:43:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:43:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:43:02: #1 total tags in treatment: 8202607 INFO @ Sun, 21 Jun 2020 19:43:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:02: #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 19:43:02: #1 tags after filtering in treatment: 8202591 INFO @ Sun, 21 Jun 2020 19:43:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:03: #2 number of paired peaks: 3008 INFO @ Sun, 21 Jun 2020 19:43:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:03: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 19:43:03: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 19:43:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.05_model.r INFO @ Sun, 21 Jun 2020 19:43:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:43:07: 1000000 INFO @ Sun, 21 Jun 2020 19:43:07: 5000000 INFO @ Sun, 21 Jun 2020 19:43:13: 2000000 INFO @ Sun, 21 Jun 2020 19:43:14: 6000000 INFO @ Sun, 21 Jun 2020 19:43:20: 3000000 INFO @ Sun, 21 Jun 2020 19:43:21: 7000000 INFO @ Sun, 21 Jun 2020 19:43:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:27: 4000000 INFO @ Sun, 21 Jun 2020 19:43:27: 8000000 INFO @ Sun, 21 Jun 2020 19:43:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:43:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:43:29: #1 total tags in treatment: 8202607 INFO @ Sun, 21 Jun 2020 19:43:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:29: #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 19:43:29: #1 tags after filtering in treatment: 8202591 INFO @ Sun, 21 Jun 2020 19:43:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:30: #2 number of paired peaks: 3008 INFO @ Sun, 21 Jun 2020 19:43:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:30: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 19:43:30: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 19:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.10_model.r INFO @ Sun, 21 Jun 2020 19:43:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:43:33: 5000000 INFO @ Sun, 21 Jun 2020 19:43:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.05_summits.bed INFO @ Sun, 21 Jun 2020 19:43:34: Done! pass1 - making usageList (491 chroms): 2 millis pass2 - checking and writing primary data (8452 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:43:40: 6000000 INFO @ Sun, 21 Jun 2020 19:43:46: 7000000 INFO @ Sun, 21 Jun 2020 19:43:52: 8000000 INFO @ Sun, 21 Jun 2020 19:43:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:43:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:43:53: #1 total tags in treatment: 8202607 INFO @ Sun, 21 Jun 2020 19:43:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:53: #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 19:43:54: #1 tags after filtering in treatment: 8202591 INFO @ Sun, 21 Jun 2020 19:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:55: #2 number of paired peaks: 3008 INFO @ Sun, 21 Jun 2020 19:43:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:55: #2 predicted fragment length is 206 bps INFO @ Sun, 21 Jun 2020 19:43:55: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 21 Jun 2020 19:43:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.20_model.r INFO @ Sun, 21 Jun 2020 19:43:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:44:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.10_summits.bed INFO @ Sun, 21 Jun 2020 19:44:02: Done! pass1 - making usageList (432 chroms): 2 millis pass2 - checking and writing primary data (5568 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:44:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068989/SRX3068989.20_summits.bed INFO @ Sun, 21 Jun 2020 19:44:27: Done! pass1 - making usageList (331 chroms): 2 millis pass2 - checking and writing primary data (3109 records, 4 fields): 12 millis CompletedMACS2peakCalling