Job ID = 6456138 SRX = SRX319058 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:39:08 prefetch.2.10.7: 1) Downloading 'SRR927435'... 2020-06-21T10:39:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:43:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:43:39 prefetch.2.10.7: 1) 'SRR927435' was downloaded successfully Read 35900825 spots for SRR927435/SRR927435.sra Written 35900825 spots for SRR927435/SRR927435.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: 00:04:26 35900825 reads; of these: 35900825 (100.00%) were unpaired; of these: 15669223 (43.65%) aligned 0 times 18039491 (50.25%) aligned exactly 1 time 2192111 (6.11%) aligned >1 times 56.35% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 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] 10292470 / 20231602 = 0.5087 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 19:53:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.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 19:53:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:51: 1000000 INFO @ Sun, 21 Jun 2020 19:53:56: 2000000 INFO @ Sun, 21 Jun 2020 19:54:01: 3000000 INFO @ Sun, 21 Jun 2020 19:54:06: 4000000 INFO @ Sun, 21 Jun 2020 19:54:11: 5000000 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 19:54:16: 6000000 INFO @ Sun, 21 Jun 2020 19:54:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.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 19:54:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:21: 7000000 INFO @ Sun, 21 Jun 2020 19:54:22: 1000000 INFO @ Sun, 21 Jun 2020 19:54:27: 8000000 INFO @ Sun, 21 Jun 2020 19:54:27: 2000000 INFO @ Sun, 21 Jun 2020 19:54:33: 9000000 INFO @ Sun, 21 Jun 2020 19:54:33: 3000000 INFO @ Sun, 21 Jun 2020 19:54:38: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:54:38: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:54:38: #1 total tags in treatment: 9939132 INFO @ Sun, 21 Jun 2020 19:54:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:38: #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 19:54:38: 4000000 INFO @ Sun, 21 Jun 2020 19:54:39: #1 tags after filtering in treatment: 9939050 INFO @ Sun, 21 Jun 2020 19:54:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:39: #2 number of paired peaks: 1058 INFO @ Sun, 21 Jun 2020 19:54:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:39: #2 predicted fragment length is 272 bps INFO @ Sun, 21 Jun 2020 19:54:39: #2 alternative fragment length(s) may be 272 bps INFO @ Sun, 21 Jun 2020 19:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.05_model.r INFO @ Sun, 21 Jun 2020 19:54:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:44: 5000000 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 19:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.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 19:54:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:49: 6000000 INFO @ Sun, 21 Jun 2020 19:54:51: 1000000 INFO @ Sun, 21 Jun 2020 19:54:54: 7000000 INFO @ Sun, 21 Jun 2020 19:54:57: 2000000 INFO @ Sun, 21 Jun 2020 19:55:00: 8000000 INFO @ Sun, 21 Jun 2020 19:55:02: 3000000 INFO @ Sun, 21 Jun 2020 19:55:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:05: 9000000 INFO @ Sun, 21 Jun 2020 19:55:08: 4000000 INFO @ Sun, 21 Jun 2020 19:55:11: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:55:11: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:55:11: #1 total tags in treatment: 9939132 INFO @ Sun, 21 Jun 2020 19:55:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:11: #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 19:55:11: #1 tags after filtering in treatment: 9939050 INFO @ Sun, 21 Jun 2020 19:55:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:12: #2 number of paired peaks: 1058 INFO @ Sun, 21 Jun 2020 19:55:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:12: #2 predicted fragment length is 272 bps INFO @ Sun, 21 Jun 2020 19:55:12: #2 alternative fragment length(s) may be 272 bps INFO @ Sun, 21 Jun 2020 19:55:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.10_model.r INFO @ Sun, 21 Jun 2020 19:55:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:13: 5000000 INFO @ Sun, 21 Jun 2020 19:55:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:18: 6000000 INFO @ Sun, 21 Jun 2020 19:55:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.05_summits.bed INFO @ Sun, 21 Jun 2020 19:55:18: Done! pass1 - making usageList (311 chroms): 2 millis pass2 - checking and writing primary data (13054 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:55:23: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:55:28: 8000000 INFO @ Sun, 21 Jun 2020 19:55:33: 9000000 INFO @ Sun, 21 Jun 2020 19:55:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:38: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:55:38: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:55:38: #1 total tags in treatment: 9939132 INFO @ Sun, 21 Jun 2020 19:55:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:38: #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 19:55:39: #1 tags after filtering in treatment: 9939050 INFO @ Sun, 21 Jun 2020 19:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:39: #2 number of paired peaks: 1058 INFO @ Sun, 21 Jun 2020 19:55:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:40: #2 predicted fragment length is 272 bps INFO @ Sun, 21 Jun 2020 19:55:40: #2 alternative fragment length(s) may be 272 bps INFO @ Sun, 21 Jun 2020 19:55:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.20_model.r INFO @ Sun, 21 Jun 2020 19:55:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.10_summits.bed INFO @ Sun, 21 Jun 2020 19:55:51: Done! pass1 - making usageList (231 chroms): 2 millis pass2 - checking and writing primary data (6340 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:56:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX319058/SRX319058.20_summits.bed INFO @ Sun, 21 Jun 2020 19:56:18: Done! pass1 - making usageList (153 chroms): 1 millis pass2 - checking and writing primary data (2474 records, 4 fields): 9 millis CompletedMACS2peakCalling