Job ID = 6454803 SRX = SRX2592402 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:25:29 prefetch.2.10.7: 1) Downloading 'SRR5289679'... 2020-06-21T09:25:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:28:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:28:10 prefetch.2.10.7: 1) 'SRR5289679' was downloaded successfully Read 21542316 spots for SRR5289679/SRR5289679.sra Written 21542316 spots for SRR5289679/SRR5289679.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: 00:06:18 21542316 reads; of these: 21542316 (100.00%) were unpaired; of these: 1515216 (7.03%) aligned 0 times 16283370 (75.59%) aligned exactly 1 time 3743730 (17.38%) aligned >1 times 92.97% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 8228236 / 20027100 = 0.4109 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 18:40:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.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 18:40:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:58: 1000000 INFO @ Sun, 21 Jun 2020 18:41:04: 2000000 INFO @ Sun, 21 Jun 2020 18:41:10: 3000000 INFO @ Sun, 21 Jun 2020 18:41:16: 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 18:41:22: 5000000 INFO @ Sun, 21 Jun 2020 18:41:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.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 18:41:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:41:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:41:28: 6000000 INFO @ Sun, 21 Jun 2020 18:41:29: 1000000 INFO @ Sun, 21 Jun 2020 18:41:35: 7000000 INFO @ Sun, 21 Jun 2020 18:41:36: 2000000 INFO @ Sun, 21 Jun 2020 18:41:41: 8000000 INFO @ Sun, 21 Jun 2020 18:41:43: 3000000 INFO @ Sun, 21 Jun 2020 18:41:49: 9000000 INFO @ Sun, 21 Jun 2020 18:41:50: 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 18:41:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.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 18:41:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:41:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:41:55: 10000000 INFO @ Sun, 21 Jun 2020 18:41:57: 5000000 INFO @ Sun, 21 Jun 2020 18:42:01: 1000000 INFO @ Sun, 21 Jun 2020 18:42:03: 11000000 INFO @ Sun, 21 Jun 2020 18:42:04: 6000000 INFO @ Sun, 21 Jun 2020 18:42:09: 2000000 INFO @ Sun, 21 Jun 2020 18:42:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:42:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:42:09: #1 total tags in treatment: 11798864 INFO @ Sun, 21 Jun 2020 18:42:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:42:09: #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 18:42:09: #1 tags after filtering in treatment: 11798750 INFO @ Sun, 21 Jun 2020 18:42:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:42:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:42:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:42:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:42:11: #2 number of paired peaks: 1511 INFO @ Sun, 21 Jun 2020 18:42:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:42:11: start X-correlation... INFO @ Sun, 21 Jun 2020 18:42:11: end of X-cor INFO @ Sun, 21 Jun 2020 18:42:11: #2 finished! INFO @ Sun, 21 Jun 2020 18:42:11: #2 predicted fragment length is 179 bps INFO @ Sun, 21 Jun 2020 18:42:11: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 21 Jun 2020 18:42:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.05_model.r INFO @ Sun, 21 Jun 2020 18:42:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:42:12: 7000000 INFO @ Sun, 21 Jun 2020 18:42:17: 3000000 INFO @ Sun, 21 Jun 2020 18:42:20: 8000000 INFO @ Sun, 21 Jun 2020 18:42:25: 4000000 INFO @ Sun, 21 Jun 2020 18:42:28: 9000000 INFO @ Sun, 21 Jun 2020 18:42:32: 5000000 INFO @ Sun, 21 Jun 2020 18:42:36: 10000000 INFO @ Sun, 21 Jun 2020 18:42:40: 6000000 INFO @ Sun, 21 Jun 2020 18:42:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:42:44: 11000000 INFO @ Sun, 21 Jun 2020 18:42:49: 7000000 INFO @ Sun, 21 Jun 2020 18:42:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:42:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:42:51: #1 total tags in treatment: 11798864 INFO @ Sun, 21 Jun 2020 18:42:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:42:51: #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 18:42:51: #1 tags after filtering in treatment: 11798750 INFO @ Sun, 21 Jun 2020 18:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:42:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:42:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:42:51: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:42:52: #2 number of paired peaks: 1511 INFO @ Sun, 21 Jun 2020 18:42:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:42:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:42:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:42:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:42:53: #2 predicted fragment length is 179 bps INFO @ Sun, 21 Jun 2020 18:42:53: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 21 Jun 2020 18:42:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.10_model.r INFO @ Sun, 21 Jun 2020 18:42:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:42:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:42:56: 8000000 INFO @ Sun, 21 Jun 2020 18:42:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.05_summits.bed INFO @ Sun, 21 Jun 2020 18:43:00: Done! pass1 - making usageList (345 chroms): 4 millis pass2 - checking and writing primary data (22149 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:43:04: 9000000 INFO @ Sun, 21 Jun 2020 18:43:12: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:43:20: 11000000 INFO @ Sun, 21 Jun 2020 18:43:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:43:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:43:26: #1 total tags in treatment: 11798864 INFO @ Sun, 21 Jun 2020 18:43:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:26: #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 18:43:26: #1 tags after filtering in treatment: 11798750 INFO @ Sun, 21 Jun 2020 18:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:28: #2 number of paired peaks: 1511 INFO @ Sun, 21 Jun 2020 18:43:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:28: #2 predicted fragment length is 179 bps INFO @ Sun, 21 Jun 2020 18:43:28: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 21 Jun 2020 18:43:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.20_model.r INFO @ Sun, 21 Jun 2020 18:43:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:43:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.10_summits.bed INFO @ Sun, 21 Jun 2020 18:43:41: Done! pass1 - making usageList (243 chroms): 4 millis pass2 - checking and writing primary data (18587 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592402/SRX2592402.20_summits.bed INFO @ Sun, 21 Jun 2020 18:44:17: Done! pass1 - making usageList (162 chroms): 2 millis pass2 - checking and writing primary data (13222 records, 4 fields): 19 millis CompletedMACS2peakCalling