Job ID = 6455612 SRX = SRX287928 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:12:37 prefetch.2.10.7: 1) Downloading 'SRR870117'... 2020-06-21T10:12:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:16:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:16:49 prefetch.2.10.7: 1) 'SRR870117' was downloaded successfully Read 19744483 spots for SRR870117/SRR870117.sra Written 19744483 spots for SRR870117/SRR870117.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: 00:05:35 19744483 reads; of these: 19744483 (100.00%) were unpaired; of these: 1360488 (6.89%) aligned 0 times 13127753 (66.49%) aligned exactly 1 time 5256242 (26.62%) aligned >1 times 93.11% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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] 5382768 / 18383995 = 0.2928 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 19:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.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 19:27:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:58: 1000000 INFO @ Sun, 21 Jun 2020 19:28:04: 2000000 INFO @ Sun, 21 Jun 2020 19:28:09: 3000000 INFO @ Sun, 21 Jun 2020 19:28:15: 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 19:28:21: 5000000 INFO @ Sun, 21 Jun 2020 19:28:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.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 19:28:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:27: 6000000 INFO @ Sun, 21 Jun 2020 19:28:29: 1000000 INFO @ Sun, 21 Jun 2020 19:28:33: 7000000 INFO @ Sun, 21 Jun 2020 19:28:35: 2000000 INFO @ Sun, 21 Jun 2020 19:28:39: 8000000 INFO @ Sun, 21 Jun 2020 19:28:41: 3000000 INFO @ Sun, 21 Jun 2020 19:28:45: 9000000 INFO @ Sun, 21 Jun 2020 19:28:47: 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 19:28:52: 10000000 INFO @ Sun, 21 Jun 2020 19:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.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 19:28:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:53: 5000000 INFO @ Sun, 21 Jun 2020 19:28:59: 11000000 INFO @ Sun, 21 Jun 2020 19:29:00: 1000000 INFO @ Sun, 21 Jun 2020 19:29:00: 6000000 INFO @ Sun, 21 Jun 2020 19:29:06: 12000000 INFO @ Sun, 21 Jun 2020 19:29:07: 7000000 INFO @ Sun, 21 Jun 2020 19:29:07: 2000000 INFO @ Sun, 21 Jun 2020 19:29:13: 13000000 INFO @ Sun, 21 Jun 2020 19:29:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:13: #1 total tags in treatment: 13001227 INFO @ Sun, 21 Jun 2020 19:29:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:13: #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 19:29:14: #1 tags after filtering in treatment: 13001227 INFO @ Sun, 21 Jun 2020 19:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:14: 8000000 INFO @ Sun, 21 Jun 2020 19:29:15: #2 number of paired peaks: 1150 INFO @ Sun, 21 Jun 2020 19:29:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:15: 3000000 INFO @ Sun, 21 Jun 2020 19:29:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:15: #2 predicted fragment length is 233 bps INFO @ Sun, 21 Jun 2020 19:29:15: #2 alternative fragment length(s) may be 233 bps INFO @ Sun, 21 Jun 2020 19:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.05_model.r INFO @ Sun, 21 Jun 2020 19:29:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:21: 9000000 INFO @ Sun, 21 Jun 2020 19:29:22: 4000000 INFO @ Sun, 21 Jun 2020 19:29:28: 10000000 INFO @ Sun, 21 Jun 2020 19:29:30: 5000000 INFO @ Sun, 21 Jun 2020 19:29:35: 11000000 INFO @ Sun, 21 Jun 2020 19:29:37: 6000000 INFO @ Sun, 21 Jun 2020 19:29:42: 12000000 INFO @ Sun, 21 Jun 2020 19:29:44: 7000000 INFO @ Sun, 21 Jun 2020 19:29:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:49: 13000000 INFO @ Sun, 21 Jun 2020 19:29:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:50: #1 total tags in treatment: 13001227 INFO @ Sun, 21 Jun 2020 19:29:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:50: #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 19:29:50: #1 tags after filtering in treatment: 13001227 INFO @ Sun, 21 Jun 2020 19:29:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:51: #2 number of paired peaks: 1150 INFO @ Sun, 21 Jun 2020 19:29:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:51: #2 predicted fragment length is 233 bps INFO @ Sun, 21 Jun 2020 19:29:51: #2 alternative fragment length(s) may be 233 bps INFO @ Sun, 21 Jun 2020 19:29:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.10_model.r INFO @ Sun, 21 Jun 2020 19:29:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:51: 8000000 INFO @ Sun, 21 Jun 2020 19:29:58: 9000000 INFO @ Sun, 21 Jun 2020 19:30:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.05_summits.bed INFO @ Sun, 21 Jun 2020 19:30:00: Done! pass1 - making usageList (674 chroms): 1 millis pass2 - checking and writing primary data (1366 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:30:05: 10000000 INFO @ Sun, 21 Jun 2020 19:30:12: 11000000 INFO @ Sun, 21 Jun 2020 19:30:19: 12000000 INFO @ Sun, 21 Jun 2020 19:30:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:26: 13000000 INFO @ Sun, 21 Jun 2020 19:30:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:26: #1 total tags in treatment: 13001227 INFO @ Sun, 21 Jun 2020 19:30:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:26: #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 19:30:27: #1 tags after filtering in treatment: 13001227 INFO @ Sun, 21 Jun 2020 19:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:28: #2 number of paired peaks: 1150 INFO @ Sun, 21 Jun 2020 19:30:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:28: #2 predicted fragment length is 233 bps INFO @ Sun, 21 Jun 2020 19:30:28: #2 alternative fragment length(s) may be 233 bps INFO @ Sun, 21 Jun 2020 19:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.20_model.r INFO @ Sun, 21 Jun 2020 19:30:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.10_summits.bed INFO @ Sun, 21 Jun 2020 19:30:35: Done! pass1 - making usageList (600 chroms): 1 millis pass2 - checking and writing primary data (1083 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287928/SRX287928.20_summits.bed INFO @ Sun, 21 Jun 2020 19:31:09: Done! pass1 - making usageList (508 chroms): 1 millis pass2 - checking and writing primary data (863 records, 4 fields): 15 millis CompletedMACS2peakCalling