Job ID = 6452175 SRX = ERX242713 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:31:42 prefetch.2.10.7: 1) Downloading 'ERR268488'... 2020-06-21T07:31:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:32:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:32:18 prefetch.2.10.7: 'ERR268488' is valid 2020-06-21T07:32:18 prefetch.2.10.7: 1) 'ERR268488' was downloaded successfully Read 3220885 spots for ERR268488/ERR268488.sra Written 3220885 spots for ERR268488/ERR268488.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: 00:00:41 3220885 reads; of these: 3220885 (100.00%) were unpaired; of these: 115202 (3.58%) aligned 0 times 2356624 (73.17%) aligned exactly 1 time 749059 (23.26%) aligned >1 times 96.42% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 243316 / 3105683 = 0.0783 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 16:34:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.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 16:34:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:34:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:34:27: 1000000 INFO @ Sun, 21 Jun 2020 16:34:32: 2000000 INFO @ Sun, 21 Jun 2020 16:34:37: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 16:34:37: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 16:34:37: #1 total tags in treatment: 2862367 INFO @ Sun, 21 Jun 2020 16:34:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:34:37: #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 16:34:38: #1 tags after filtering in treatment: 2862129 INFO @ Sun, 21 Jun 2020 16:34:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:34:38: #1 finished! INFO @ Sun, 21 Jun 2020 16:34:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:34:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:34:38: #2 number of paired peaks: 3003 INFO @ Sun, 21 Jun 2020 16:34:38: start model_add_line... INFO @ Sun, 21 Jun 2020 16:34:38: start X-correlation... INFO @ Sun, 21 Jun 2020 16:34:38: end of X-cor INFO @ Sun, 21 Jun 2020 16:34:38: #2 finished! INFO @ Sun, 21 Jun 2020 16:34:38: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 16:34:38: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 16:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.05_model.r INFO @ Sun, 21 Jun 2020 16:34:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:34:46: #3 Call peaks for each chromosome... 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 16:34:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:34:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:34:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.05_summits.bed INFO @ Sun, 21 Jun 2020 16:34:50: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (5326 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:34:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.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 16:34:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:34:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:34:57: 1000000 INFO @ Sun, 21 Jun 2020 16:35:02: 2000000 INFO @ Sun, 21 Jun 2020 16:35:08: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 16:35:08: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 16:35:08: #1 total tags in treatment: 2862367 INFO @ Sun, 21 Jun 2020 16:35:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:35:08: #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 16:35:08: #1 tags after filtering in treatment: 2862129 INFO @ Sun, 21 Jun 2020 16:35:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:35:08: #1 finished! INFO @ Sun, 21 Jun 2020 16:35:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:35:08: #2 number of paired peaks: 3003 INFO @ Sun, 21 Jun 2020 16:35:08: start model_add_line... INFO @ Sun, 21 Jun 2020 16:35:08: start X-correlation... INFO @ Sun, 21 Jun 2020 16:35:08: end of X-cor INFO @ Sun, 21 Jun 2020 16:35:08: #2 finished! INFO @ Sun, 21 Jun 2020 16:35:08: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 16:35:08: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 16:35:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.10_model.r INFO @ Sun, 21 Jun 2020 16:35:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:35:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:35:16: #3 Call peaks for each chromosome... 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 16:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.10_summits.bed INFO @ Sun, 21 Jun 2020 16:35:20: Done! pass1 - making usageList (155 chroms): 1 millis pass2 - checking and writing primary data (2685 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:35:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.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 16:35:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:35:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:35:27: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:35:32: 2000000 INFO @ Sun, 21 Jun 2020 16:35:38: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 16:35:38: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 16:35:38: #1 total tags in treatment: 2862367 INFO @ Sun, 21 Jun 2020 16:35:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:35:38: #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 16:35:38: #1 tags after filtering in treatment: 2862129 INFO @ Sun, 21 Jun 2020 16:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:35:38: #1 finished! INFO @ Sun, 21 Jun 2020 16:35:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:35:38: #2 number of paired peaks: 3003 INFO @ Sun, 21 Jun 2020 16:35:38: start model_add_line... INFO @ Sun, 21 Jun 2020 16:35:38: start X-correlation... INFO @ Sun, 21 Jun 2020 16:35:38: end of X-cor INFO @ Sun, 21 Jun 2020 16:35:38: #2 finished! INFO @ Sun, 21 Jun 2020 16:35:38: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 16:35:38: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 16:35:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.20_model.r INFO @ Sun, 21 Jun 2020 16:35:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:35:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:35:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:35:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:35:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:35:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX242713/ERX242713.20_summits.bed INFO @ Sun, 21 Jun 2020 16:35:50: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (982 records, 4 fields): 7 millis CompletedMACS2peakCalling