Job ID = 6454384 SRX = SRX202127 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:09:09 prefetch.2.10.7: 1) Downloading 'SRR610273'... 2020-06-21T09:09:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:10:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:10:55 prefetch.2.10.7: 'SRR610273' is valid 2020-06-21T09:10:55 prefetch.2.10.7: 1) 'SRR610273' was downloaded successfully Read 14712177 spots for SRR610273/SRR610273.sra Written 14712177 spots for SRR610273/SRR610273.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: 00:01:50 14712177 reads; of these: 14712177 (100.00%) were unpaired; of these: 8543611 (58.07%) aligned 0 times 4662061 (31.69%) aligned exactly 1 time 1506505 (10.24%) aligned >1 times 41.93% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 3601139 / 6168566 = 0.5838 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 18:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.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 18:14:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:58: 1000000 INFO @ Sun, 21 Jun 2020 18:15:03: 2000000 INFO @ Sun, 21 Jun 2020 18:15:07: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:15:07: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:15:07: #1 total tags in treatment: 2567427 INFO @ Sun, 21 Jun 2020 18:15:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:07: #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 18:15:07: #1 tags after filtering in treatment: 2567222 INFO @ Sun, 21 Jun 2020 18:15:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:07: #2 number of paired peaks: 3416 INFO @ Sun, 21 Jun 2020 18:15:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:07: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:15:07: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:15:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.05_model.r INFO @ Sun, 21 Jun 2020 18:15:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.05_summits.bed INFO @ Sun, 21 Jun 2020 18:15:17: Done! pass1 - making usageList (433 chroms): 2 millis pass2 - checking and writing primary data (4362 records, 4 fields): 15 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 18:15:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.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 18:15:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:30: 1000000 INFO @ Sun, 21 Jun 2020 18:15:36: 2000000 INFO @ Sun, 21 Jun 2020 18:15:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:15:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:15:40: #1 total tags in treatment: 2567427 INFO @ Sun, 21 Jun 2020 18:15:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:40: #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 18:15:40: #1 tags after filtering in treatment: 2567222 INFO @ Sun, 21 Jun 2020 18:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:40: #2 number of paired peaks: 3416 INFO @ Sun, 21 Jun 2020 18:15:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:40: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:15:40: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.10_model.r INFO @ Sun, 21 Jun 2020 18:15:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.10_summits.bed INFO @ Sun, 21 Jun 2020 18:15:50: Done! pass1 - making usageList (174 chroms): 1 millis pass2 - checking and writing primary data (2593 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 18:15:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.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 18:15:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:58: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:16:03: 2000000 INFO @ Sun, 21 Jun 2020 18:16:07: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:16:07: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:16:07: #1 total tags in treatment: 2567427 INFO @ Sun, 21 Jun 2020 18:16:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:07: #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 18:16:07: #1 tags after filtering in treatment: 2567222 INFO @ Sun, 21 Jun 2020 18:16:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:07: #2 number of paired peaks: 3416 INFO @ Sun, 21 Jun 2020 18:16:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:07: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:16:07: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:16:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.20_model.r INFO @ Sun, 21 Jun 2020 18:16:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:16:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202127/SRX202127.20_summits.bed INFO @ Sun, 21 Jun 2020 18:16:16: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (1725 records, 4 fields): 6 millis CompletedMACS2peakCalling