Job ID = 6453791 SRX = SRX1490783 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:42:02 prefetch.2.10.7: 1) Downloading 'SRR3031650'... 2020-06-21T08:42:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:49 prefetch.2.10.7: 'SRR3031650' is valid 2020-06-21T08:43:49 prefetch.2.10.7: 1) 'SRR3031650' was downloaded successfully Read 11684197 spots for SRR3031650/SRR3031650.sra Written 11684197 spots for SRR3031650/SRR3031650.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: 00:02:37 11684197 reads; of these: 11684197 (100.00%) were unpaired; of these: 1307941 (11.19%) aligned 0 times 9374932 (80.24%) aligned exactly 1 time 1001324 (8.57%) aligned >1 times 88.81% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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_sort_core] merging from 8 files... [bam_rmdupse_core] 7218877 / 10376256 = 0.6957 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 17:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.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 17:49:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:13: 1000000 INFO @ Sun, 21 Jun 2020 17:49:20: 2000000 INFO @ Sun, 21 Jun 2020 17:49:26: 3000000 INFO @ Sun, 21 Jun 2020 17:49:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:49:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:49:27: #1 total tags in treatment: 3157379 INFO @ Sun, 21 Jun 2020 17:49:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:27: #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 17:49:28: #1 tags after filtering in treatment: 3157235 INFO @ Sun, 21 Jun 2020 17:49:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:28: #2 number of paired peaks: 6254 INFO @ Sun, 21 Jun 2020 17:49:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:28: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 17:49:28: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 17:49:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.05_model.r INFO @ Sun, 21 Jun 2020 17:49:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:28: #3 Pre-compute pvalue-qvalue table... 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 17:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.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 17:49:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:42: 1000000 INFO @ Sun, 21 Jun 2020 17:49:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:44: Done! pass1 - making usageList (152 chroms): 1 millis pass2 - checking and writing primary data (1579 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:48: 2000000 INFO @ Sun, 21 Jun 2020 17:49:54: 3000000 INFO @ Sun, 21 Jun 2020 17:49:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:49:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:49:55: #1 total tags in treatment: 3157379 INFO @ Sun, 21 Jun 2020 17:49:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:55: #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 17:49:56: #1 tags after filtering in treatment: 3157235 INFO @ Sun, 21 Jun 2020 17:49:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:56: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:56: #2 number of paired peaks: 6254 INFO @ Sun, 21 Jun 2020 17:49:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:56: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 17:49:56: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 17:49:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.10_model.r INFO @ Sun, 21 Jun 2020 17:49:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:56: #3 Pre-compute pvalue-qvalue table... 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 17:50:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.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 17:50:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.10_summits.bed INFO @ Sun, 21 Jun 2020 17:50:11: Done! pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (1042 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:50:14: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:50:19: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:50:25: 3000000 INFO @ Sun, 21 Jun 2020 17:50:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:26: #1 total tags in treatment: 3157379 INFO @ Sun, 21 Jun 2020 17:50:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:26: #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 17:50:26: #1 tags after filtering in treatment: 3157235 INFO @ Sun, 21 Jun 2020 17:50:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:27: #2 number of paired peaks: 6254 INFO @ Sun, 21 Jun 2020 17:50:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:27: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 17:50:27: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 17:50:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.20_model.r INFO @ Sun, 21 Jun 2020 17:50:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1490783/SRX1490783.20_summits.bed INFO @ Sun, 21 Jun 2020 17:50:41: Done! pass1 - making usageList (109 chroms): 0 millis pass2 - checking and writing primary data (696 records, 4 fields): 5 millis CompletedMACS2peakCalling