Job ID = 6452689 SRX = SRX025489 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:48:15 prefetch.2.10.7: 1) Downloading 'SRR063893'... 2020-06-21T07:48:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:50:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:50:12 prefetch.2.10.7: 'SRR063893' is valid 2020-06-21T07:50:12 prefetch.2.10.7: 1) 'SRR063893' was downloaded successfully Read 4744819 spots for SRR063893/SRR063893.sra Written 4744819 spots for SRR063893/SRR063893.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: 00:00:49 4744819 reads; of these: 4744819 (100.00%) were unpaired; of these: 687989 (14.50%) aligned 0 times 3289143 (69.32%) aligned exactly 1 time 767687 (16.18%) aligned >1 times 85.50% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 2156027 / 4056830 = 0.5315 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 16:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.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 16:52:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:34: 1000000 INFO @ Sun, 21 Jun 2020 16:52:38: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:52:38: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:52:38: #1 total tags in treatment: 1900803 INFO @ Sun, 21 Jun 2020 16:52:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:52:38: #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 16:52:39: #1 tags after filtering in treatment: 1900544 INFO @ Sun, 21 Jun 2020 16:52:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:52:39: #1 finished! INFO @ Sun, 21 Jun 2020 16:52:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:52:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:52:39: #2 number of paired peaks: 4214 INFO @ Sun, 21 Jun 2020 16:52:39: start model_add_line... INFO @ Sun, 21 Jun 2020 16:52:39: start X-correlation... INFO @ Sun, 21 Jun 2020 16:52:39: end of X-cor INFO @ Sun, 21 Jun 2020 16:52:39: #2 finished! INFO @ Sun, 21 Jun 2020 16:52:39: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 16:52:39: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 21 Jun 2020 16:52:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.05_model.r INFO @ Sun, 21 Jun 2020 16:52:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:52:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:52:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:52:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:52:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.05_summits.bed INFO @ Sun, 21 Jun 2020 16:52:46: Done! pass1 - making usageList (264 chroms): 2 millis pass2 - checking and writing primary data (4881 records, 4 fields): 12 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 16:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.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 16:52:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:04: 1000000 INFO @ Sun, 21 Jun 2020 16:53:09: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:53:09: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:53:09: #1 total tags in treatment: 1900803 INFO @ Sun, 21 Jun 2020 16:53:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:53:09: #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 16:53:09: #1 tags after filtering in treatment: 1900544 INFO @ Sun, 21 Jun 2020 16:53:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:53:09: #1 finished! INFO @ Sun, 21 Jun 2020 16:53:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:53:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:53:10: #2 number of paired peaks: 4214 INFO @ Sun, 21 Jun 2020 16:53:10: start model_add_line... INFO @ Sun, 21 Jun 2020 16:53:10: start X-correlation... INFO @ Sun, 21 Jun 2020 16:53:10: end of X-cor INFO @ Sun, 21 Jun 2020 16:53:10: #2 finished! INFO @ Sun, 21 Jun 2020 16:53:10: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 16:53:10: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 21 Jun 2020 16:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.10_model.r INFO @ Sun, 21 Jun 2020 16:53:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:53:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:53:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.10_summits.bed INFO @ Sun, 21 Jun 2020 16:53:17: Done! pass1 - making usageList (180 chroms): 1 millis pass2 - checking and writing primary data (3771 records, 4 fields): 8 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 16:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.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 16:53:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:34: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:53:39: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:53:39: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:53:39: #1 total tags in treatment: 1900803 INFO @ Sun, 21 Jun 2020 16:53:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:53:39: #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 16:53:40: #1 tags after filtering in treatment: 1900544 INFO @ Sun, 21 Jun 2020 16:53:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:53:40: #1 finished! INFO @ Sun, 21 Jun 2020 16:53:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:53:40: #2 number of paired peaks: 4214 INFO @ Sun, 21 Jun 2020 16:53:40: start model_add_line... INFO @ Sun, 21 Jun 2020 16:53:40: start X-correlation... INFO @ Sun, 21 Jun 2020 16:53:40: end of X-cor INFO @ Sun, 21 Jun 2020 16:53:40: #2 finished! INFO @ Sun, 21 Jun 2020 16:53:40: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 16:53:40: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 21 Jun 2020 16:53:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.20_model.r INFO @ Sun, 21 Jun 2020 16:53:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:53:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:53:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025489/SRX025489.20_summits.bed INFO @ Sun, 21 Jun 2020 16:53:47: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (2717 records, 4 fields): 7 millis CompletedMACS2peakCalling