Job ID = 6454258 SRX = SRX193333 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:49:04 prefetch.2.10.7: 1) Downloading 'SRR585066'... 2020-06-21T08:49:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:51:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:51:50 prefetch.2.10.7: 'SRR585066' is valid 2020-06-21T08:51:50 prefetch.2.10.7: 1) 'SRR585066' was downloaded successfully Read 12330945 spots for SRR585066/SRR585066.sra Written 12330945 spots for SRR585066/SRR585066.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: 00:02:48 12330945 reads; of these: 12330945 (100.00%) were unpaired; of these: 717609 (5.82%) aligned 0 times 9872174 (80.06%) aligned exactly 1 time 1741162 (14.12%) aligned >1 times 94.18% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 2142284 / 11613336 = 0.1845 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 17:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.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 17:58:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:46: 1000000 INFO @ Sun, 21 Jun 2020 17:58:52: 2000000 INFO @ Sun, 21 Jun 2020 17:58:58: 3000000 INFO @ Sun, 21 Jun 2020 17:59:04: 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 17:59:10: 5000000 INFO @ Sun, 21 Jun 2020 17:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.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 17:59:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:59:16: 6000000 INFO @ Sun, 21 Jun 2020 17:59:17: 1000000 INFO @ Sun, 21 Jun 2020 17:59:23: 7000000 INFO @ Sun, 21 Jun 2020 17:59:24: 2000000 INFO @ Sun, 21 Jun 2020 17:59:29: 8000000 INFO @ Sun, 21 Jun 2020 17:59:30: 3000000 INFO @ Sun, 21 Jun 2020 17:59:36: 9000000 INFO @ Sun, 21 Jun 2020 17:59:37: 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 17:59:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:59:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:59:39: #1 total tags in treatment: 9471052 INFO @ Sun, 21 Jun 2020 17:59:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:39: #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 17:59:39: #1 tags after filtering in treatment: 9470683 INFO @ Sun, 21 Jun 2020 17:59:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.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 17:59:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:59:41: #2 number of paired peaks: 10590 INFO @ Sun, 21 Jun 2020 17:59:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:41: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 17:59:41: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 17:59:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.05_model.r INFO @ Sun, 21 Jun 2020 17:59:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:44: 5000000 INFO @ Sun, 21 Jun 2020 17:59:48: 1000000 INFO @ Sun, 21 Jun 2020 17:59:51: 6000000 INFO @ Sun, 21 Jun 2020 17:59:54: 2000000 INFO @ Sun, 21 Jun 2020 17:59:58: 7000000 INFO @ Sun, 21 Jun 2020 18:00:01: 3000000 INFO @ Sun, 21 Jun 2020 18:00:05: 8000000 INFO @ Sun, 21 Jun 2020 18:00:08: 4000000 INFO @ Sun, 21 Jun 2020 18:00:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:12: 9000000 INFO @ Sun, 21 Jun 2020 18:00:14: 5000000 INFO @ Sun, 21 Jun 2020 18:00:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:00:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:00:15: #1 total tags in treatment: 9471052 INFO @ Sun, 21 Jun 2020 18:00:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:00:15: #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 18:00:15: #1 tags after filtering in treatment: 9470683 INFO @ Sun, 21 Jun 2020 18:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:00:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:00:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:00:17: #2 number of paired peaks: 10590 INFO @ Sun, 21 Jun 2020 18:00:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:00:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:00:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:00:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:00:17: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 18:00:17: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 18:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.10_model.r INFO @ Sun, 21 Jun 2020 18:00:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:00:21: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:00:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.05_summits.bed INFO @ Sun, 21 Jun 2020 18:00:26: Done! pass1 - making usageList (159 chroms): 3 millis pass2 - checking and writing primary data (12788 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:00:27: 7000000 INFO @ Sun, 21 Jun 2020 18:00:34: 8000000 INFO @ Sun, 21 Jun 2020 18:00:40: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:00:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:00:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:00:43: #1 total tags in treatment: 9471052 INFO @ Sun, 21 Jun 2020 18:00:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:00:43: #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 18:00:44: #1 tags after filtering in treatment: 9470683 INFO @ Sun, 21 Jun 2020 18:00:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:00:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:00:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:00:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:00:45: #2 number of paired peaks: 10590 INFO @ Sun, 21 Jun 2020 18:00:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:00:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:00:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:00:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:00:46: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 18:00:46: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 18:00:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.20_model.r INFO @ Sun, 21 Jun 2020 18:00:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:00:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.10_summits.bed INFO @ Sun, 21 Jun 2020 18:01:02: Done! pass1 - making usageList (128 chroms): 2 millis pass2 - checking and writing primary data (9180 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:01:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193333/SRX193333.20_summits.bed INFO @ Sun, 21 Jun 2020 18:01:30: Done! pass1 - making usageList (106 chroms): 1 millis pass2 - checking and writing primary data (5129 records, 4 fields): 11 millis CompletedMACS2peakCalling