Job ID = 6458379 SRX = SRX507391 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:44:07 prefetch.2.10.7: 1) Downloading 'SRR1213178'... 2020-06-21T12:44:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:45:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:45:04 prefetch.2.10.7: 'SRR1213178' is valid 2020-06-21T12:45:04 prefetch.2.10.7: 1) 'SRR1213178' was downloaded successfully Read 9777717 spots for SRR1213178/SRR1213178.sra Written 9777717 spots for SRR1213178/SRR1213178.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: 00:02:01 9777717 reads; of these: 9777717 (100.00%) were unpaired; of these: 374857 (3.83%) aligned 0 times 8021815 (82.04%) aligned exactly 1 time 1381045 (14.12%) aligned >1 times 96.17% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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_rmdupse_core] 2523881 / 9402860 = 0.2684 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 21:50:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.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 21:50:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:12: 1000000 INFO @ Sun, 21 Jun 2020 21:50:18: 2000000 INFO @ Sun, 21 Jun 2020 21:50:24: 3000000 INFO @ Sun, 21 Jun 2020 21:50:30: 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 21:50:36: 5000000 INFO @ Sun, 21 Jun 2020 21:50:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.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 21:50:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:42: 1000000 INFO @ Sun, 21 Jun 2020 21:50:42: 6000000 INFO @ Sun, 21 Jun 2020 21:50:48: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:50:48: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:50:48: #1 total tags in treatment: 6878979 INFO @ Sun, 21 Jun 2020 21:50:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:50:48: #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 21:50:48: 2000000 INFO @ Sun, 21 Jun 2020 21:50:48: #1 tags after filtering in treatment: 6878836 INFO @ Sun, 21 Jun 2020 21:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:50:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:50:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:50:49: #2 number of paired peaks: 1197 INFO @ Sun, 21 Jun 2020 21:50:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:50:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:50:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:50:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:50:49: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 21:50:49: #2 alternative fragment length(s) may be 4,154 bps INFO @ Sun, 21 Jun 2020 21:50:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.05_model.r INFO @ Sun, 21 Jun 2020 21:50:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:50:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:50:54: 3000000 INFO @ Sun, 21 Jun 2020 21:51:00: 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 21:51:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:06: 5000000 INFO @ Sun, 21 Jun 2020 21:51:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.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 21:51:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:12: 1000000 INFO @ Sun, 21 Jun 2020 21:51:12: 6000000 INFO @ Sun, 21 Jun 2020 21:51:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:51:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:51:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.05_summits.bed INFO @ Sun, 21 Jun 2020 21:51:14: Done! pass1 - making usageList (234 chroms): 2 millis pass2 - checking and writing primary data (6435 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:51:18: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:51:18: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:51:18: #1 total tags in treatment: 6878979 INFO @ Sun, 21 Jun 2020 21:51:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:18: #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 21:51:18: 2000000 INFO @ Sun, 21 Jun 2020 21:51:18: #1 tags after filtering in treatment: 6878836 INFO @ Sun, 21 Jun 2020 21:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:19: #2 number of paired peaks: 1197 INFO @ Sun, 21 Jun 2020 21:51:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:19: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 21:51:19: #2 alternative fragment length(s) may be 4,154 bps INFO @ Sun, 21 Jun 2020 21:51:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.10_model.r INFO @ Sun, 21 Jun 2020 21:51:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:24: 3000000 INFO @ Sun, 21 Jun 2020 21:51:29: 4000000 INFO @ Sun, 21 Jun 2020 21:51:35: 5000000 INFO @ Sun, 21 Jun 2020 21:51:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:41: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:51:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:51:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:51:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.10_summits.bed INFO @ Sun, 21 Jun 2020 21:51:44: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (2379 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:51:46: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:51:46: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:51:46: #1 total tags in treatment: 6878979 INFO @ Sun, 21 Jun 2020 21:51:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:46: #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 21:51:46: #1 tags after filtering in treatment: 6878836 INFO @ Sun, 21 Jun 2020 21:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:47: #2 number of paired peaks: 1197 INFO @ Sun, 21 Jun 2020 21:51:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:47: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 21:51:47: #2 alternative fragment length(s) may be 4,154 bps INFO @ Sun, 21 Jun 2020 21:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.20_model.r INFO @ Sun, 21 Jun 2020 21:51:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:52:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507391/SRX507391.20_summits.bed INFO @ Sun, 21 Jun 2020 21:52:12: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 4 millis CompletedMACS2peakCalling