Job ID = 6452511 SRX = SRX013111 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:51:15 prefetch.2.10.7: 1) Downloading 'SRR030377'... 2020-06-21T07:51:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:51:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:51:30 prefetch.2.10.7: 'SRR030377' is valid 2020-06-21T07:51:30 prefetch.2.10.7: 1) 'SRR030377' was downloaded successfully Read 469851 spots for SRR030377/SRR030377.sra Written 469851 spots for SRR030377/SRR030377.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: 00:00:05 469851 reads; of these: 469851 (100.00%) were unpaired; of these: 43250 (9.21%) aligned 0 times 361434 (76.93%) aligned exactly 1 time 65167 (13.87%) aligned >1 times 90.79% overall alignment rate Time searching: 00:00:05 Overall time: 00:00:05 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] 39324 / 426601 = 0.0922 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 16:52:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.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 16:52:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:16: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:52:16: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:52:16: #1 total tags in treatment: 387277 INFO @ Sun, 21 Jun 2020 16:52:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:52:16: #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 16:52:16: #1 tags after filtering in treatment: 386584 INFO @ Sun, 21 Jun 2020 16:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:52:16: #1 finished! INFO @ Sun, 21 Jun 2020 16:52:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:52:16: #2 number of paired peaks: 2451 INFO @ Sun, 21 Jun 2020 16:52:16: start model_add_line... INFO @ Sun, 21 Jun 2020 16:52:16: start X-correlation... INFO @ Sun, 21 Jun 2020 16:52:16: end of X-cor INFO @ Sun, 21 Jun 2020 16:52:16: #2 finished! INFO @ Sun, 21 Jun 2020 16:52:16: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 16:52:16: #2 alternative fragment length(s) may be 165,189 bps INFO @ Sun, 21 Jun 2020 16:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.05_model.r INFO @ Sun, 21 Jun 2020 16:52:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:52:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:52:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:52:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:52:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.05_summits.bed INFO @ Sun, 21 Jun 2020 16:52:18: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 1 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 16:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.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 16:52:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:47: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:52:47: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:52:47: #1 total tags in treatment: 387277 INFO @ Sun, 21 Jun 2020 16:52:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:52:47: #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 16:52:47: #1 tags after filtering in treatment: 386584 INFO @ Sun, 21 Jun 2020 16:52:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:52:47: #1 finished! INFO @ Sun, 21 Jun 2020 16:52:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:52:47: #2 number of paired peaks: 2451 INFO @ Sun, 21 Jun 2020 16:52:47: start model_add_line... INFO @ Sun, 21 Jun 2020 16:52:47: start X-correlation... INFO @ Sun, 21 Jun 2020 16:52:47: end of X-cor INFO @ Sun, 21 Jun 2020 16:52:47: #2 finished! INFO @ Sun, 21 Jun 2020 16:52:47: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 16:52:47: #2 alternative fragment length(s) may be 165,189 bps INFO @ Sun, 21 Jun 2020 16:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.10_model.r INFO @ Sun, 21 Jun 2020 16:52:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:52:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:52:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:52:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:52:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.10_summits.bed INFO @ Sun, 21 Jun 2020 16:52:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 0 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 16:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.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 16:53:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:14: #1 read treatment tags... 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 16:53:16: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:53:16: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:53:16: #1 total tags in treatment: 387277 INFO @ Sun, 21 Jun 2020 16:53:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:53:16: #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 16:53:16: #1 tags after filtering in treatment: 386584 INFO @ Sun, 21 Jun 2020 16:53:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:53:16: #1 finished! INFO @ Sun, 21 Jun 2020 16:53:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:53:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:53:16: #2 number of paired peaks: 2451 INFO @ Sun, 21 Jun 2020 16:53:16: start model_add_line... INFO @ Sun, 21 Jun 2020 16:53:16: start X-correlation... INFO @ Sun, 21 Jun 2020 16:53:16: end of X-cor INFO @ Sun, 21 Jun 2020 16:53:16: #2 finished! INFO @ Sun, 21 Jun 2020 16:53:16: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 16:53:16: #2 alternative fragment length(s) may be 165,189 bps INFO @ Sun, 21 Jun 2020 16:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.20_model.r INFO @ Sun, 21 Jun 2020 16:53:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:53:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013111/SRX013111.20_summits.bed INFO @ Sun, 21 Jun 2020 16:53:18: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling