Job ID = 6454082 SRX = SRX181427 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:48:49 prefetch.2.10.7: 1) Downloading 'SRR548164'... 2020-06-21T08:48:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:51:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:51:35 prefetch.2.10.7: 'SRR548164' is valid 2020-06-21T08:51:35 prefetch.2.10.7: 1) 'SRR548164' was downloaded successfully Read 13855161 spots for SRR548164/SRR548164.sra Written 13855161 spots for SRR548164/SRR548164.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: 00:02:03 13855161 reads; of these: 13855161 (100.00%) were unpaired; of these: 2448559 (17.67%) aligned 0 times 10337178 (74.61%) aligned exactly 1 time 1069424 (7.72%) aligned >1 times 82.33% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 2590267 / 11406602 = 0.2271 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 17:56:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.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 17:56:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:58: 1000000 INFO @ Sun, 21 Jun 2020 17:57:05: 2000000 INFO @ Sun, 21 Jun 2020 17:57:11: 3000000 INFO @ Sun, 21 Jun 2020 17:57:17: 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 17:57:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.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 17:57:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:24: 5000000 INFO @ Sun, 21 Jun 2020 17:57:28: 1000000 INFO @ Sun, 21 Jun 2020 17:57:31: 6000000 INFO @ Sun, 21 Jun 2020 17:57:34: 2000000 INFO @ Sun, 21 Jun 2020 17:57:38: 7000000 INFO @ Sun, 21 Jun 2020 17:57:40: 3000000 INFO @ Sun, 21 Jun 2020 17:57:45: 8000000 INFO @ Sun, 21 Jun 2020 17:57:46: 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 17:57:51: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:57:51: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:57:51: #1 total tags in treatment: 8816335 INFO @ Sun, 21 Jun 2020 17:57:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:51: #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 17:57:51: #1 tags after filtering in treatment: 8816294 INFO @ Sun, 21 Jun 2020 17:57:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.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 17:57:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:52: 5000000 INFO @ Sun, 21 Jun 2020 17:57:52: #2 number of paired peaks: 1796 INFO @ Sun, 21 Jun 2020 17:57:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:52: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 17:57:52: #2 alternative fragment length(s) may be 125 bps INFO @ Sun, 21 Jun 2020 17:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.05_model.r INFO @ Sun, 21 Jun 2020 17:57:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:57:58: 1000000 INFO @ Sun, 21 Jun 2020 17:57:58: 6000000 INFO @ Sun, 21 Jun 2020 17:58:04: 7000000 INFO @ Sun, 21 Jun 2020 17:58:04: 2000000 INFO @ Sun, 21 Jun 2020 17:58:10: 3000000 INFO @ Sun, 21 Jun 2020 17:58:10: 8000000 INFO @ Sun, 21 Jun 2020 17:58:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:58:15: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:58:15: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:58:15: #1 total tags in treatment: 8816335 INFO @ Sun, 21 Jun 2020 17:58:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:15: #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 17:58:15: #1 tags after filtering in treatment: 8816294 INFO @ Sun, 21 Jun 2020 17:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:15: 4000000 INFO @ Sun, 21 Jun 2020 17:58:16: #2 number of paired peaks: 1796 INFO @ Sun, 21 Jun 2020 17:58:16: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:16: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:16: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:16: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:16: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 17:58:16: #2 alternative fragment length(s) may be 125 bps INFO @ Sun, 21 Jun 2020 17:58:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.10_model.r INFO @ Sun, 21 Jun 2020 17:58:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:58:21: 5000000 INFO @ Sun, 21 Jun 2020 17:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.05_summits.bed INFO @ Sun, 21 Jun 2020 17:58:25: Done! pass1 - making usageList (136 chroms): 2 millis pass2 - checking and writing primary data (8235 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:58:26: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:58:31: 7000000 INFO @ Sun, 21 Jun 2020 17:58:37: 8000000 INFO @ Sun, 21 Jun 2020 17:58:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:58:41: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:58:41: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:58:41: #1 total tags in treatment: 8816335 INFO @ Sun, 21 Jun 2020 17:58:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:41: #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 17:58:42: #1 tags after filtering in treatment: 8816294 INFO @ Sun, 21 Jun 2020 17:58:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:42: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:42: #2 number of paired peaks: 1796 INFO @ Sun, 21 Jun 2020 17:58:42: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:43: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:43: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:43: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:43: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 17:58:43: #2 alternative fragment length(s) may be 125 bps INFO @ Sun, 21 Jun 2020 17:58:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.20_model.r INFO @ Sun, 21 Jun 2020 17:58:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:58:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.10_summits.bed INFO @ Sun, 21 Jun 2020 17:58:48: Done! pass1 - making usageList (106 chroms): 1 millis pass2 - checking and writing primary data (4211 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:59:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181427/SRX181427.20_summits.bed INFO @ Sun, 21 Jun 2020 17:59:13: Done! pass1 - making usageList (90 chroms): 1 millis pass2 - checking and writing primary data (1372 records, 4 fields): 5 millis CompletedMACS2peakCalling