Job ID = 6456653 SRX = SRX3873748 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:01:46 prefetch.2.10.7: 1) Downloading 'SRR6927813'... 2020-06-21T11:01:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:04:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:04:01 prefetch.2.10.7: 'SRR6927813' is valid 2020-06-21T11:04:01 prefetch.2.10.7: 1) 'SRR6927813' was downloaded successfully 2020-06-21T11:04:01 prefetch.2.10.7: 'SRR6927813' has 0 unresolved dependencies Read 13046291 spots for SRR6927813/SRR6927813.sra Written 13046291 spots for SRR6927813/SRR6927813.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: 00:02:46 13046291 reads; of these: 13046291 (100.00%) were unpaired; of these: 1725079 (13.22%) aligned 0 times 9540812 (73.13%) aligned exactly 1 time 1780400 (13.65%) aligned >1 times 86.78% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 2851678 / 11321212 = 0.2519 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 20:11:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.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 20:11:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:34: 1000000 INFO @ Sun, 21 Jun 2020 20:11:41: 2000000 INFO @ Sun, 21 Jun 2020 20:11:48: 3000000 INFO @ Sun, 21 Jun 2020 20:11:55: 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 20:11:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.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 20:11:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:12:01: 5000000 INFO @ Sun, 21 Jun 2020 20:12:03: 1000000 INFO @ Sun, 21 Jun 2020 20:12:08: 6000000 INFO @ Sun, 21 Jun 2020 20:12:08: 2000000 INFO @ Sun, 21 Jun 2020 20:12:14: 3000000 INFO @ Sun, 21 Jun 2020 20:12:15: 7000000 INFO @ Sun, 21 Jun 2020 20:12:19: 4000000 INFO @ Sun, 21 Jun 2020 20:12:22: 8000000 INFO @ Sun, 21 Jun 2020 20:12:24: 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 20:12:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:12:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:12:26: #1 total tags in treatment: 8469534 INFO @ Sun, 21 Jun 2020 20:12:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:26: #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 20:12:27: #1 tags after filtering in treatment: 8469255 INFO @ Sun, 21 Jun 2020 20:12:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.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 20:12:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:12:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:12:28: #2 number of paired peaks: 7863 INFO @ Sun, 21 Jun 2020 20:12:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:28: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 20:12:28: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 20:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.05_model.r INFO @ Sun, 21 Jun 2020 20:12:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:30: 6000000 INFO @ Sun, 21 Jun 2020 20:12:33: 1000000 INFO @ Sun, 21 Jun 2020 20:12:36: 7000000 INFO @ Sun, 21 Jun 2020 20:12:39: 2000000 INFO @ Sun, 21 Jun 2020 20:12:43: 8000000 INFO @ Sun, 21 Jun 2020 20:12:45: 3000000 INFO @ Sun, 21 Jun 2020 20:12:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:12:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:12:46: #1 total tags in treatment: 8469534 INFO @ Sun, 21 Jun 2020 20:12:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:46: #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 20:12:46: #1 tags after filtering in treatment: 8469255 INFO @ Sun, 21 Jun 2020 20:12:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:48: #2 number of paired peaks: 7863 INFO @ Sun, 21 Jun 2020 20:12:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:48: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 20:12:48: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 20:12:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.10_model.r INFO @ Sun, 21 Jun 2020 20:12:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:50: 4000000 INFO @ Sun, 21 Jun 2020 20:12:56: 5000000 INFO @ Sun, 21 Jun 2020 20:12:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:13:01: 6000000 INFO @ Sun, 21 Jun 2020 20:13:06: 7000000 INFO @ Sun, 21 Jun 2020 20:13:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.05_summits.bed INFO @ Sun, 21 Jun 2020 20:13:09: Done! pass1 - making usageList (171 chroms): 3 millis pass2 - checking and writing primary data (8152 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:13:12: 8000000 INFO @ Sun, 21 Jun 2020 20:13:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:13:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:13:15: #1 total tags in treatment: 8469534 INFO @ Sun, 21 Jun 2020 20:13:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:13:15: #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 20:13:16: #1 tags after filtering in treatment: 8469255 INFO @ Sun, 21 Jun 2020 20:13:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:13:16: #1 finished! INFO @ Sun, 21 Jun 2020 20:13:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:13:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:13:17: #2 number of paired peaks: 7863 INFO @ Sun, 21 Jun 2020 20:13:17: start model_add_line... INFO @ Sun, 21 Jun 2020 20:13:17: start X-correlation... INFO @ Sun, 21 Jun 2020 20:13:17: end of X-cor INFO @ Sun, 21 Jun 2020 20:13:17: #2 finished! INFO @ Sun, 21 Jun 2020 20:13:17: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 20:13:17: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 20:13:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.20_model.r INFO @ Sun, 21 Jun 2020 20:13:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:13:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:13:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:13:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:13:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:13:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.10_summits.bed INFO @ Sun, 21 Jun 2020 20:13:28: Done! pass1 - making usageList (144 chroms): 2 millis pass2 - checking and writing primary data (6377 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:13:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:13:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873748/SRX3873748.20_summits.bed INFO @ Sun, 21 Jun 2020 20:13:55: Done! pass1 - making usageList (111 chroms): 2 millis pass2 - checking and writing primary data (4314 records, 4 fields): 12 millis CompletedMACS2peakCalling