Job ID = 6456124 SRX = SRX318797 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:43:23 prefetch.2.10.7: 1) Downloading 'SRR927113'... 2020-06-21T10:43:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:49:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:49:19 prefetch.2.10.7: 1) 'SRR927113' was downloaded successfully Read 23636737 spots for SRR927113/SRR927113.sra Written 23636737 spots for SRR927113/SRR927113.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: 00:05:24 23636737 reads; of these: 23636737 (100.00%) were unpaired; of these: 3656717 (15.47%) aligned 0 times 15768222 (66.71%) aligned exactly 1 time 4211798 (17.82%) aligned >1 times 84.53% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 7453400 / 19980020 = 0.3730 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 20:00:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.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 20:00:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:00:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:00:25: 1000000 INFO @ Sun, 21 Jun 2020 20:00:31: 2000000 INFO @ Sun, 21 Jun 2020 20:00:37: 3000000 INFO @ Sun, 21 Jun 2020 20:00:42: 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 20:00:48: 5000000 INFO @ Sun, 21 Jun 2020 20:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.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 20:00:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:00:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:00:54: 6000000 INFO @ Sun, 21 Jun 2020 20:00:56: 1000000 INFO @ Sun, 21 Jun 2020 20:01:01: 7000000 INFO @ Sun, 21 Jun 2020 20:01:02: 2000000 INFO @ Sun, 21 Jun 2020 20:01:07: 8000000 INFO @ Sun, 21 Jun 2020 20:01:09: 3000000 INFO @ Sun, 21 Jun 2020 20:01:14: 9000000 INFO @ Sun, 21 Jun 2020 20:01:15: 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 20:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.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 20:01:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:01:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:01:20: 10000000 INFO @ Sun, 21 Jun 2020 20:01:21: 5000000 INFO @ Sun, 21 Jun 2020 20:01:26: 1000000 INFO @ Sun, 21 Jun 2020 20:01:27: 11000000 INFO @ Sun, 21 Jun 2020 20:01:28: 6000000 INFO @ Sun, 21 Jun 2020 20:01:32: 2000000 INFO @ Sun, 21 Jun 2020 20:01:33: 12000000 INFO @ Sun, 21 Jun 2020 20:01:34: 7000000 INFO @ Sun, 21 Jun 2020 20:01:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:01:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:01:37: #1 total tags in treatment: 12526620 INFO @ Sun, 21 Jun 2020 20:01:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:01:37: #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 20:01:38: #1 tags after filtering in treatment: 12526500 INFO @ Sun, 21 Jun 2020 20:01:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:01:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:01:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:01:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:01:39: 3000000 INFO @ Sun, 21 Jun 2020 20:01:39: #2 number of paired peaks: 9640 INFO @ Sun, 21 Jun 2020 20:01:39: start model_add_line... INFO @ Sun, 21 Jun 2020 20:01:39: start X-correlation... INFO @ Sun, 21 Jun 2020 20:01:39: end of X-cor INFO @ Sun, 21 Jun 2020 20:01:39: #2 finished! INFO @ Sun, 21 Jun 2020 20:01:39: #2 predicted fragment length is 228 bps INFO @ Sun, 21 Jun 2020 20:01:39: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 21 Jun 2020 20:01:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.05_model.r INFO @ Sun, 21 Jun 2020 20:01:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:01:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:01:41: 8000000 INFO @ Sun, 21 Jun 2020 20:01:45: 4000000 INFO @ Sun, 21 Jun 2020 20:01:47: 9000000 INFO @ Sun, 21 Jun 2020 20:01:52: 5000000 INFO @ Sun, 21 Jun 2020 20:01:54: 10000000 INFO @ Sun, 21 Jun 2020 20:01:58: 6000000 INFO @ Sun, 21 Jun 2020 20:02:01: 11000000 INFO @ Sun, 21 Jun 2020 20:02:05: 7000000 INFO @ Sun, 21 Jun 2020 20:02:07: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:02:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:02:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:02:11: #1 total tags in treatment: 12526620 INFO @ Sun, 21 Jun 2020 20:02:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:02:11: #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 20:02:12: 8000000 INFO @ Sun, 21 Jun 2020 20:02:12: #1 tags after filtering in treatment: 12526500 INFO @ Sun, 21 Jun 2020 20:02:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:02:12: #1 finished! INFO @ Sun, 21 Jun 2020 20:02:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:02:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:02:13: #2 number of paired peaks: 9640 INFO @ Sun, 21 Jun 2020 20:02:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:02:13: start X-correlation... INFO @ Sun, 21 Jun 2020 20:02:13: end of X-cor INFO @ Sun, 21 Jun 2020 20:02:13: #2 finished! INFO @ Sun, 21 Jun 2020 20:02:13: #2 predicted fragment length is 228 bps INFO @ Sun, 21 Jun 2020 20:02:13: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 21 Jun 2020 20:02:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.10_model.r INFO @ Sun, 21 Jun 2020 20:02:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:02:18: 9000000 INFO @ Sun, 21 Jun 2020 20:02:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:02:25: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:02:31: 11000000 INFO @ Sun, 21 Jun 2020 20:02:37: 12000000 INFO @ Sun, 21 Jun 2020 20:02:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:02:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:02:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.05_summits.bed INFO @ Sun, 21 Jun 2020 20:02:38: Done! pass1 - making usageList (401 chroms): 2 millis pass2 - checking and writing primary data (9565 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:02:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:02:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:02:40: #1 total tags in treatment: 12526620 INFO @ Sun, 21 Jun 2020 20:02:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:02:40: #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 20:02:41: #1 tags after filtering in treatment: 12526500 INFO @ Sun, 21 Jun 2020 20:02:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:02:41: #1 finished! INFO @ Sun, 21 Jun 2020 20:02:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:02:42: #2 number of paired peaks: 9640 INFO @ Sun, 21 Jun 2020 20:02:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:02:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:02:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:02:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:02:42: #2 predicted fragment length is 228 bps INFO @ Sun, 21 Jun 2020 20:02:42: #2 alternative fragment length(s) may be 228 bps INFO @ Sun, 21 Jun 2020 20:02:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.20_model.r INFO @ Sun, 21 Jun 2020 20:02:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:02:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:02:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.10_summits.bed INFO @ Sun, 21 Jun 2020 20:03:12: Done! pass1 - making usageList (260 chroms): 2 millis pass2 - checking and writing primary data (8249 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:03:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318797/SRX318797.20_summits.bed INFO @ Sun, 21 Jun 2020 20:03:40: Done! pass1 - making usageList (190 chroms): 3 millis pass2 - checking and writing primary data (6779 records, 4 fields): 12 millis CompletedMACS2peakCalling