Job ID = 6456644 SRX = SRX3873734 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:59:31 prefetch.2.10.7: 1) Downloading 'SRR6927799'... 2020-06-21T10:59:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:01:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:01:13 prefetch.2.10.7: 'SRR6927799' is valid 2020-06-21T11:01:13 prefetch.2.10.7: 1) 'SRR6927799' was downloaded successfully 2020-06-21T11:01:13 prefetch.2.10.7: 'SRR6927799' has 0 unresolved dependencies Read 14470269 spots for SRR6927799/SRR6927799.sra Written 14470269 spots for SRR6927799/SRR6927799.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: 00:03:21 14470269 reads; of these: 14470269 (100.00%) were unpaired; of these: 1549939 (10.71%) aligned 0 times 10948376 (75.66%) aligned exactly 1 time 1971954 (13.63%) aligned >1 times 89.29% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 3283270 / 12920330 = 0.2541 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 20:08:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.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 20:08:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:05: 1000000 INFO @ Sun, 21 Jun 2020 20:09:11: 2000000 INFO @ Sun, 21 Jun 2020 20:09:17: 3000000 INFO @ Sun, 21 Jun 2020 20:09:24: 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 20:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.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 20:09:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:30: 5000000 INFO @ Sun, 21 Jun 2020 20:09:36: 1000000 INFO @ Sun, 21 Jun 2020 20:09:38: 6000000 INFO @ Sun, 21 Jun 2020 20:09:45: 2000000 INFO @ Sun, 21 Jun 2020 20:09:45: 7000000 INFO @ Sun, 21 Jun 2020 20:09:53: 8000000 INFO @ Sun, 21 Jun 2020 20:09:53: 3000000 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 20:09:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.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 20:09:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:01: 4000000 INFO @ Sun, 21 Jun 2020 20:10:01: 9000000 INFO @ Sun, 21 Jun 2020 20:10:06: 1000000 INFO @ Sun, 21 Jun 2020 20:10:06: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:10:06: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:10:06: #1 total tags in treatment: 9637060 INFO @ Sun, 21 Jun 2020 20:10:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:06: #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 20:10:06: #1 tags after filtering in treatment: 9636778 INFO @ Sun, 21 Jun 2020 20:10:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:08: #2 number of paired peaks: 8160 INFO @ Sun, 21 Jun 2020 20:10:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:08: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 20:10:08: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 20:10:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.05_model.r INFO @ Sun, 21 Jun 2020 20:10:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:09: 5000000 INFO @ Sun, 21 Jun 2020 20:10:13: 2000000 INFO @ Sun, 21 Jun 2020 20:10:17: 6000000 INFO @ Sun, 21 Jun 2020 20:10:20: 3000000 INFO @ Sun, 21 Jun 2020 20:10:25: 7000000 INFO @ Sun, 21 Jun 2020 20:10:28: 4000000 INFO @ Sun, 21 Jun 2020 20:10:32: 8000000 INFO @ Sun, 21 Jun 2020 20:10:35: 5000000 INFO @ Sun, 21 Jun 2020 20:10:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:41: 9000000 INFO @ Sun, 21 Jun 2020 20:10:43: 6000000 INFO @ Sun, 21 Jun 2020 20:10:46: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:10:46: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:10:46: #1 total tags in treatment: 9637060 INFO @ Sun, 21 Jun 2020 20:10:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:46: #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 20:10:46: #1 tags after filtering in treatment: 9636778 INFO @ Sun, 21 Jun 2020 20:10:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:47: #2 number of paired peaks: 8160 INFO @ Sun, 21 Jun 2020 20:10:47: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:48: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 20:10:48: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 20:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.10_model.r INFO @ Sun, 21 Jun 2020 20:10:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:10:49: 7000000 INFO @ Sun, 21 Jun 2020 20:10:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.05_summits.bed INFO @ Sun, 21 Jun 2020 20:10:52: Done! pass1 - making usageList (158 chroms): 2 millis pass2 - checking and writing primary data (9623 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:10:56: 8000000 INFO @ Sun, 21 Jun 2020 20:11:02: 9000000 INFO @ Sun, 21 Jun 2020 20:11:06: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:11:06: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:11:06: #1 total tags in treatment: 9637060 INFO @ Sun, 21 Jun 2020 20:11:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:06: #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 20:11:06: #1 tags after filtering in treatment: 9636778 INFO @ Sun, 21 Jun 2020 20:11:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:08: #2 number of paired peaks: 8160 INFO @ Sun, 21 Jun 2020 20:11:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:08: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 20:11:08: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 20:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.20_model.r INFO @ Sun, 21 Jun 2020 20:11:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:11:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.10_summits.bed INFO @ Sun, 21 Jun 2020 20:11:32: Done! pass1 - making usageList (137 chroms): 2 millis pass2 - checking and writing primary data (7669 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:11:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873734/SRX3873734.20_summits.bed INFO @ Sun, 21 Jun 2020 20:11:52: Done! pass1 - making usageList (118 chroms): 2 millis pass2 - checking and writing primary data (5492 records, 4 fields): 10 millis CompletedMACS2peakCalling