Job ID = 6457054 SRX = SRX4375822 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:14:39 prefetch.2.10.7: 1) Downloading 'SRR7506476'... 2020-06-21T11:14:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:17:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:17:11 prefetch.2.10.7: 1) 'SRR7506476' was downloaded successfully Read 22013082 spots for SRR7506476/SRR7506476.sra Written 22013082 spots for SRR7506476/SRR7506476.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: 00:03:51 22013082 reads; of these: 22013082 (100.00%) were unpaired; of these: 9709237 (44.11%) aligned 0 times 9865377 (44.82%) aligned exactly 1 time 2438468 (11.08%) aligned >1 times 55.89% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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] 7735664 / 12303845 = 0.6287 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 20:24:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.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 20:24:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:04: 1000000 INFO @ Sun, 21 Jun 2020 20:25:10: 2000000 INFO @ Sun, 21 Jun 2020 20:25:15: 3000000 INFO @ Sun, 21 Jun 2020 20:25:22: 4000000 INFO @ Sun, 21 Jun 2020 20:25:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:25:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:25:25: #1 total tags in treatment: 4568181 INFO @ Sun, 21 Jun 2020 20:25:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:25: #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 20:25:26: #1 tags after filtering in treatment: 4567940 INFO @ Sun, 21 Jun 2020 20:25:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:26: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:26: #2 looking for paired plus/minus strand peaks... 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 20:25:26: #2 number of paired peaks: 6942 INFO @ Sun, 21 Jun 2020 20:25:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:26: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:26: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:26: #2 predicted fragment length is 241 bps INFO @ Sun, 21 Jun 2020 20:25:26: #2 alternative fragment length(s) may be 241 bps INFO @ Sun, 21 Jun 2020 20:25:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.05_model.r INFO @ Sun, 21 Jun 2020 20:25:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:25:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.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 20:25:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:34: 1000000 INFO @ Sun, 21 Jun 2020 20:25:40: 2000000 INFO @ Sun, 21 Jun 2020 20:25:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:25:46: 3000000 INFO @ Sun, 21 Jun 2020 20:25:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:25:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:25:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.05_summits.bed INFO @ Sun, 21 Jun 2020 20:25:48: Done! pass1 - making usageList (374 chroms): 2 millis pass2 - checking and writing primary data (7652 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:25:52: 4000000 INFO @ Sun, 21 Jun 2020 20:25:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:25:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:25:55: #1 total tags in treatment: 4568181 INFO @ Sun, 21 Jun 2020 20:25:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Sun, 21 Jun 2020 20:25:56: #1 tags after filtering in treatment: 4567940 INFO @ Sun, 21 Jun 2020 20:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:56: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:56: #2 looking for paired plus/minus strand peaks... 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 20:25:56: #2 number of paired peaks: 6942 INFO @ Sun, 21 Jun 2020 20:25:56: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:57: #2 predicted fragment length is 241 bps INFO @ Sun, 21 Jun 2020 20:25:57: #2 alternative fragment length(s) may be 241 bps INFO @ Sun, 21 Jun 2020 20:25:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.10_model.r INFO @ Sun, 21 Jun 2020 20:25:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:25:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.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 20:25:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:04: 1000000 INFO @ Sun, 21 Jun 2020 20:26:10: 2000000 INFO @ Sun, 21 Jun 2020 20:26:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:16: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:26:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.10_summits.bed INFO @ Sun, 21 Jun 2020 20:26:19: Done! pass1 - making usageList (209 chroms): 2 millis pass2 - checking and writing primary data (6240 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:26:22: 4000000 INFO @ Sun, 21 Jun 2020 20:26:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:26:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:26:26: #1 total tags in treatment: 4568181 INFO @ Sun, 21 Jun 2020 20:26:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:26: #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 20:26:26: #1 tags after filtering in treatment: 4567940 INFO @ Sun, 21 Jun 2020 20:26:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:26: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:27: #2 number of paired peaks: 6942 INFO @ Sun, 21 Jun 2020 20:26:27: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:27: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:27: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:27: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:27: #2 predicted fragment length is 241 bps INFO @ Sun, 21 Jun 2020 20:26:27: #2 alternative fragment length(s) may be 241 bps INFO @ Sun, 21 Jun 2020 20:26:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.20_model.r INFO @ Sun, 21 Jun 2020 20:26:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:26:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375822/SRX4375822.20_summits.bed INFO @ Sun, 21 Jun 2020 20:26:48: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (4811 records, 4 fields): 9 millis CompletedMACS2peakCalling