Job ID = 6459867 SRX = SRX914962 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:49:19 prefetch.2.10.7: 1) Downloading 'SRR1873272'... 2020-06-21T13:49:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:52:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:52:24 prefetch.2.10.7: 1) 'SRR1873272' was downloaded successfully Read 23459756 spots for SRR1873272/SRR1873272.sra Written 23459756 spots for SRR1873272/SRR1873272.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: 00:02:31 23459756 reads; of these: 23459756 (100.00%) were unpaired; of these: 17286190 (73.68%) aligned 0 times 5608536 (23.91%) aligned exactly 1 time 565030 (2.41%) aligned >1 times 26.32% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 5005100 / 6173566 = 0.8107 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 22:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.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 22:57:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:57:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:58:03: 1000000 INFO @ Sun, 21 Jun 2020 22:58:04: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:58:04: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:58:04: #1 total tags in treatment: 1168466 INFO @ Sun, 21 Jun 2020 22:58:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:58:04: #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 22:58:05: #1 tags after filtering in treatment: 1168027 INFO @ Sun, 21 Jun 2020 22:58:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:58:05: #1 finished! INFO @ Sun, 21 Jun 2020 22:58:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:58:05: #2 number of paired peaks: 1144 INFO @ Sun, 21 Jun 2020 22:58:05: start model_add_line... INFO @ Sun, 21 Jun 2020 22:58:05: start X-correlation... INFO @ Sun, 21 Jun 2020 22:58:05: end of X-cor INFO @ Sun, 21 Jun 2020 22:58:05: #2 finished! INFO @ Sun, 21 Jun 2020 22:58:05: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 22:58:05: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 22:58:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.05_model.r INFO @ Sun, 21 Jun 2020 22:58:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:58:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.05_summits.bed INFO @ Sun, 21 Jun 2020 22:58:10: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 22:58:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.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 22:58:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:58:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:58:33: 1000000 INFO @ Sun, 21 Jun 2020 22:58:34: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:58:34: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:58:34: #1 total tags in treatment: 1168466 INFO @ Sun, 21 Jun 2020 22:58:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:58:34: #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 22:58:35: #1 tags after filtering in treatment: 1168027 INFO @ Sun, 21 Jun 2020 22:58:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:58:35: #1 finished! INFO @ Sun, 21 Jun 2020 22:58:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:58:35: #2 number of paired peaks: 1144 INFO @ Sun, 21 Jun 2020 22:58:35: start model_add_line... INFO @ Sun, 21 Jun 2020 22:58:35: start X-correlation... INFO @ Sun, 21 Jun 2020 22:58:35: end of X-cor INFO @ Sun, 21 Jun 2020 22:58:35: #2 finished! INFO @ Sun, 21 Jun 2020 22:58:35: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 22:58:35: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 22:58:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.10_model.r INFO @ Sun, 21 Jun 2020 22:58:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:58:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:58:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:58:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.10_summits.bed INFO @ Sun, 21 Jun 2020 22:58:40: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (64 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 22:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.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 22:58:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:58:57: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:59:04: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:59:05: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:59:05: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:59:05: #1 total tags in treatment: 1168466 INFO @ Sun, 21 Jun 2020 22:59:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:05: #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 22:59:05: #1 tags after filtering in treatment: 1168027 INFO @ Sun, 21 Jun 2020 22:59:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:05: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:05: #2 number of paired peaks: 1144 INFO @ Sun, 21 Jun 2020 22:59:05: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:05: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:05: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:05: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:05: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 22:59:05: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 22:59:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.20_model.r INFO @ Sun, 21 Jun 2020 22:59:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:59:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:59:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:59:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914962/SRX914962.20_summits.bed INFO @ Sun, 21 Jun 2020 22:59:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 1 millis CompletedMACS2peakCalling