Job ID = 6454688 SRX = SRX2520637 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:25:59 prefetch.2.10.7: 1) Downloading 'SRR5206756'... 2020-06-21T09:25:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:11 prefetch.2.10.7: 1) 'SRR5206756' was downloaded successfully Read 37598583 spots for SRR5206756/SRR5206756.sra Written 37598583 spots for SRR5206756/SRR5206756.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:14 37598583 reads; of these: 37598583 (100.00%) were unpaired; of these: 8930478 (23.75%) aligned 0 times 21172619 (56.31%) aligned exactly 1 time 7495486 (19.94%) aligned >1 times 76.25% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 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] 10160194 / 28668105 = 0.3544 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 18:49:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.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 18:49:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:49: 1000000 INFO @ Sun, 21 Jun 2020 18:49:54: 2000000 INFO @ Sun, 21 Jun 2020 18:49:59: 3000000 INFO @ Sun, 21 Jun 2020 18:50:04: 4000000 INFO @ Sun, 21 Jun 2020 18:50:08: 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 18:50:13: 6000000 INFO @ Sun, 21 Jun 2020 18:50:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.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 18:50:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:19: 7000000 INFO @ Sun, 21 Jun 2020 18:50:19: 1000000 INFO @ Sun, 21 Jun 2020 18:50:24: 8000000 INFO @ Sun, 21 Jun 2020 18:50:24: 2000000 INFO @ Sun, 21 Jun 2020 18:50:29: 9000000 INFO @ Sun, 21 Jun 2020 18:50:30: 3000000 INFO @ Sun, 21 Jun 2020 18:50:34: 10000000 INFO @ Sun, 21 Jun 2020 18:50:35: 4000000 INFO @ Sun, 21 Jun 2020 18:50:40: 11000000 INFO @ Sun, 21 Jun 2020 18:50:40: 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 18:50:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.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 18:50:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:45: 12000000 INFO @ Sun, 21 Jun 2020 18:50:45: 6000000 INFO @ Sun, 21 Jun 2020 18:50:50: 1000000 INFO @ Sun, 21 Jun 2020 18:50:50: 13000000 INFO @ Sun, 21 Jun 2020 18:50:50: 7000000 INFO @ Sun, 21 Jun 2020 18:50:56: 8000000 INFO @ Sun, 21 Jun 2020 18:50:56: 14000000 INFO @ Sun, 21 Jun 2020 18:50:56: 2000000 INFO @ Sun, 21 Jun 2020 18:51:01: 15000000 INFO @ Sun, 21 Jun 2020 18:51:01: 9000000 INFO @ Sun, 21 Jun 2020 18:51:03: 3000000 INFO @ Sun, 21 Jun 2020 18:51:07: 10000000 INFO @ Sun, 21 Jun 2020 18:51:07: 16000000 INFO @ Sun, 21 Jun 2020 18:51:09: 4000000 INFO @ Sun, 21 Jun 2020 18:51:12: 11000000 INFO @ Sun, 21 Jun 2020 18:51:12: 17000000 INFO @ Sun, 21 Jun 2020 18:51:15: 5000000 INFO @ Sun, 21 Jun 2020 18:51:17: 12000000 INFO @ Sun, 21 Jun 2020 18:51:18: 18000000 INFO @ Sun, 21 Jun 2020 18:51:21: 6000000 INFO @ Sun, 21 Jun 2020 18:51:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:51:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:51:21: #1 total tags in treatment: 18507911 INFO @ Sun, 21 Jun 2020 18:51:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:21: #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 18:51:21: #1 tags after filtering in treatment: 18507827 INFO @ Sun, 21 Jun 2020 18:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:23: #2 number of paired peaks: 1019 INFO @ Sun, 21 Jun 2020 18:51:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:23: 13000000 INFO @ Sun, 21 Jun 2020 18:51:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:23: #2 predicted fragment length is 190 bps INFO @ Sun, 21 Jun 2020 18:51:23: #2 alternative fragment length(s) may be 4,190 bps INFO @ Sun, 21 Jun 2020 18:51:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.05_model.r INFO @ Sun, 21 Jun 2020 18:51:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:27: 7000000 INFO @ Sun, 21 Jun 2020 18:51:28: 14000000 INFO @ Sun, 21 Jun 2020 18:51:33: 8000000 INFO @ Sun, 21 Jun 2020 18:51:34: 15000000 INFO @ Sun, 21 Jun 2020 18:51:39: 16000000 INFO @ Sun, 21 Jun 2020 18:51:40: 9000000 INFO @ Sun, 21 Jun 2020 18:51:45: 17000000 INFO @ Sun, 21 Jun 2020 18:51:46: 10000000 INFO @ Sun, 21 Jun 2020 18:51:50: 18000000 INFO @ Sun, 21 Jun 2020 18:51:52: 11000000 INFO @ Sun, 21 Jun 2020 18:51:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:51:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:51:53: #1 total tags in treatment: 18507911 INFO @ Sun, 21 Jun 2020 18:51:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:53: #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 18:51:54: #1 tags after filtering in treatment: 18507827 INFO @ Sun, 21 Jun 2020 18:51:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:55: #2 number of paired peaks: 1019 INFO @ Sun, 21 Jun 2020 18:51:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:55: #2 predicted fragment length is 190 bps INFO @ Sun, 21 Jun 2020 18:51:55: #2 alternative fragment length(s) may be 4,190 bps INFO @ Sun, 21 Jun 2020 18:51:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.10_model.r INFO @ Sun, 21 Jun 2020 18:51:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:59: 12000000 INFO @ Sun, 21 Jun 2020 18:52:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:05: 13000000 INFO @ Sun, 21 Jun 2020 18:52:11: 14000000 INFO @ Sun, 21 Jun 2020 18:52:18: 15000000 INFO @ Sun, 21 Jun 2020 18:52:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.05_summits.bed INFO @ Sun, 21 Jun 2020 18:52:24: Done! INFO @ Sun, 21 Jun 2020 18:52:24: 16000000 pass1 - making usageList (591 chroms): 1 millis pass2 - checking and writing primary data (4644 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:31: 17000000 INFO @ Sun, 21 Jun 2020 18:52:37: 18000000 INFO @ Sun, 21 Jun 2020 18:52:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:52:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:52:41: #1 total tags in treatment: 18507911 INFO @ Sun, 21 Jun 2020 18:52:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:41: #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 18:52:41: #1 tags after filtering in treatment: 18507827 INFO @ Sun, 21 Jun 2020 18:52:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:43: #2 number of paired peaks: 1019 INFO @ Sun, 21 Jun 2020 18:52:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:43: #2 predicted fragment length is 190 bps INFO @ Sun, 21 Jun 2020 18:52:43: #2 alternative fragment length(s) may be 4,190 bps INFO @ Sun, 21 Jun 2020 18:52:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.20_model.r INFO @ Sun, 21 Jun 2020 18:52:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.10_summits.bed INFO @ Sun, 21 Jun 2020 18:52:58: Done! pass1 - making usageList (504 chroms): 1 millis pass2 - checking and writing primary data (2954 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:53:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520637/SRX2520637.20_summits.bed INFO @ Sun, 21 Jun 2020 18:53:45: Done! pass1 - making usageList (379 chroms): 1 millis pass2 - checking and writing primary data (1660 records, 4 fields): 12 millis CompletedMACS2peakCalling