Job ID = 6453426 SRX = SRX1134701 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:23:32 prefetch.2.10.7: 1) Downloading 'SRR2147082'... 2020-06-21T08:23:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:28:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:28:08 prefetch.2.10.7: 1) 'SRR2147082' was downloaded successfully 2020-06-21T08:28:08 prefetch.2.10.7: 'SRR2147082' has 0 unresolved dependencies Read 20759096 spots for SRR2147082/SRR2147082.sra Written 20759096 spots for SRR2147082/SRR2147082.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: 00:04:13 20759096 reads; of these: 20759096 (100.00%) were unpaired; of these: 1834162 (8.84%) aligned 0 times 16195052 (78.01%) aligned exactly 1 time 2729882 (13.15%) aligned >1 times 91.16% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 10216955 / 18924934 = 0.5399 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 17:37:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.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 17:37:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:45: 1000000 INFO @ Sun, 21 Jun 2020 17:37:50: 2000000 INFO @ Sun, 21 Jun 2020 17:37:56: 3000000 INFO @ Sun, 21 Jun 2020 17:38:02: 4000000 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 17:38:08: 5000000 INFO @ Sun, 21 Jun 2020 17:38:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.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 17:38:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:14: 1000000 INFO @ Sun, 21 Jun 2020 17:38:15: 6000000 INFO @ Sun, 21 Jun 2020 17:38:20: 2000000 INFO @ Sun, 21 Jun 2020 17:38:22: 7000000 INFO @ Sun, 21 Jun 2020 17:38:25: 3000000 INFO @ Sun, 21 Jun 2020 17:38:28: 8000000 INFO @ Sun, 21 Jun 2020 17:38:31: 4000000 INFO @ Sun, 21 Jun 2020 17:38:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:38:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:38:33: #1 total tags in treatment: 8707979 INFO @ Sun, 21 Jun 2020 17:38:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:33: #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 17:38:33: #1 tags after filtering in treatment: 8707839 INFO @ Sun, 21 Jun 2020 17:38:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:33: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:34: #2 number of paired peaks: 3704 INFO @ Sun, 21 Jun 2020 17:38:34: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:34: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:34: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:34: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:34: #2 predicted fragment length is 199 bps INFO @ Sun, 21 Jun 2020 17:38:34: #2 alternative fragment length(s) may be 199 bps INFO @ Sun, 21 Jun 2020 17:38:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.05_model.r INFO @ Sun, 21 Jun 2020 17:38:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:38:36: 5000000 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 17:38:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.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 17:38:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:42: 6000000 INFO @ Sun, 21 Jun 2020 17:38:45: 1000000 INFO @ Sun, 21 Jun 2020 17:38:48: 7000000 INFO @ Sun, 21 Jun 2020 17:38:51: 2000000 INFO @ Sun, 21 Jun 2020 17:38:53: 8000000 INFO @ Sun, 21 Jun 2020 17:38:57: 3000000 INFO @ Sun, 21 Jun 2020 17:38:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:38:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:38:58: #1 total tags in treatment: 8707979 INFO @ Sun, 21 Jun 2020 17:38:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:58: #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 17:38:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:58: #1 tags after filtering in treatment: 8707839 INFO @ Sun, 21 Jun 2020 17:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:59: #2 number of paired peaks: 3704 INFO @ Sun, 21 Jun 2020 17:38:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:59: #2 predicted fragment length is 199 bps INFO @ Sun, 21 Jun 2020 17:38:59: #2 alternative fragment length(s) may be 199 bps INFO @ Sun, 21 Jun 2020 17:38:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.10_model.r INFO @ Sun, 21 Jun 2020 17:38:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:03: 4000000 INFO @ Sun, 21 Jun 2020 17:39:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.05_summits.bed INFO @ Sun, 21 Jun 2020 17:39:09: Done! INFO @ Sun, 21 Jun 2020 17:39:09: 5000000 pass1 - making usageList (242 chroms): 2 millis pass2 - checking and writing primary data (6952 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:39:15: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:39:21: 7000000 INFO @ Sun, 21 Jun 2020 17:39:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:27: 8000000 INFO @ Sun, 21 Jun 2020 17:39:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:39:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:39:31: #1 total tags in treatment: 8707979 INFO @ Sun, 21 Jun 2020 17:39:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:31: #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 17:39:32: #1 tags after filtering in treatment: 8707839 INFO @ Sun, 21 Jun 2020 17:39:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:32: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:33: #2 number of paired peaks: 3704 INFO @ Sun, 21 Jun 2020 17:39:33: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:33: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:33: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:33: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:33: #2 predicted fragment length is 199 bps INFO @ Sun, 21 Jun 2020 17:39:33: #2 alternative fragment length(s) may be 199 bps INFO @ Sun, 21 Jun 2020 17:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.20_model.r INFO @ Sun, 21 Jun 2020 17:39:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.10_summits.bed INFO @ Sun, 21 Jun 2020 17:39:35: Done! BigWig に変換しました。 pass1 - making usageList (152 chroms): 1 millis pass2 - checking and writing primary data (5114 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:39:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:40:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134701/SRX1134701.20_summits.bed INFO @ Sun, 21 Jun 2020 17:40:09: Done! pass1 - making usageList (96 chroms): 2 millis pass2 - checking and writing primary data (3447 records, 4 fields): 7 millis CompletedMACS2peakCalling