Job ID = 6452702 SRX = SRX026743 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:06:09 prefetch.2.10.7: 1) Downloading 'SRR065629'... 2020-06-21T08:06:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:08:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:08:41 prefetch.2.10.7: 'SRR065629' is valid 2020-06-21T08:08:41 prefetch.2.10.7: 1) 'SRR065629' was downloaded successfully Read 8558831 spots for SRR065629/SRR065629.sra Written 8558831 spots for SRR065629/SRR065629.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: 00:01:32 8558831 reads; of these: 8558831 (100.00%) were unpaired; of these: 1467302 (17.14%) aligned 0 times 6156969 (71.94%) aligned exactly 1 time 934560 (10.92%) aligned >1 times 82.86% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 1355005 / 7091529 = 0.1911 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 17:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.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 17:12:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:12:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:12:45: 1000000 INFO @ Sun, 21 Jun 2020 17:12:51: 2000000 INFO @ Sun, 21 Jun 2020 17:12:56: 3000000 INFO @ Sun, 21 Jun 2020 17:13:02: 4000000 INFO @ Sun, 21 Jun 2020 17:13:07: 5000000 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 17:13:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.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 17:13:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:13:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:13:11: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:13:11: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:13:11: #1 total tags in treatment: 5736524 INFO @ Sun, 21 Jun 2020 17:13:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:13:11: #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 17:13:12: #1 tags after filtering in treatment: 5736273 INFO @ Sun, 21 Jun 2020 17:13:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:13:12: #1 finished! INFO @ Sun, 21 Jun 2020 17:13:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:13:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:13:12: #2 number of paired peaks: 2848 INFO @ Sun, 21 Jun 2020 17:13:12: start model_add_line... INFO @ Sun, 21 Jun 2020 17:13:12: start X-correlation... INFO @ Sun, 21 Jun 2020 17:13:12: end of X-cor INFO @ Sun, 21 Jun 2020 17:13:12: #2 finished! INFO @ Sun, 21 Jun 2020 17:13:12: #2 predicted fragment length is 304 bps INFO @ Sun, 21 Jun 2020 17:13:12: #2 alternative fragment length(s) may be 304 bps INFO @ Sun, 21 Jun 2020 17:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.05_model.r INFO @ Sun, 21 Jun 2020 17:13:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:13:16: 1000000 INFO @ Sun, 21 Jun 2020 17:13:21: 2000000 INFO @ Sun, 21 Jun 2020 17:13:27: 3000000 INFO @ Sun, 21 Jun 2020 17:13:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:13:33: 4000000 INFO @ Sun, 21 Jun 2020 17:13:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:13:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:13:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.05_summits.bed INFO @ Sun, 21 Jun 2020 17:13:36: Done! pass1 - making usageList (290 chroms): 2 millis pass2 - checking and writing primary data (7976 records, 4 fields): 17 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 17:13:39: 5000000 INFO @ Sun, 21 Jun 2020 17:13:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.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 17:13:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:13:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:13:43: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:13:43: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:13:43: #1 total tags in treatment: 5736524 INFO @ Sun, 21 Jun 2020 17:13:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:13:43: #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 17:13:43: #1 tags after filtering in treatment: 5736273 INFO @ Sun, 21 Jun 2020 17:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:13:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:13:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:13:44: #2 number of paired peaks: 2848 INFO @ Sun, 21 Jun 2020 17:13:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:13:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:13:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:13:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:13:44: #2 predicted fragment length is 304 bps INFO @ Sun, 21 Jun 2020 17:13:44: #2 alternative fragment length(s) may be 304 bps INFO @ Sun, 21 Jun 2020 17:13:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.10_model.r INFO @ Sun, 21 Jun 2020 17:13:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:13:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:13:46: 1000000 INFO @ Sun, 21 Jun 2020 17:13:52: 2000000 INFO @ Sun, 21 Jun 2020 17:13:57: 3000000 INFO @ Sun, 21 Jun 2020 17:14:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:14:03: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:14:09: 5000000 INFO @ Sun, 21 Jun 2020 17:14:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:14:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:14:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.10_summits.bed INFO @ Sun, 21 Jun 2020 17:14:10: Done! pass1 - making usageList (233 chroms): 2 millis pass2 - checking and writing primary data (3934 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:14:13: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:14:13: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:14:13: #1 total tags in treatment: 5736524 INFO @ Sun, 21 Jun 2020 17:14:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:14:13: #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 17:14:13: #1 tags after filtering in treatment: 5736273 INFO @ Sun, 21 Jun 2020 17:14:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:14:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:14:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:14:14: #2 number of paired peaks: 2848 INFO @ Sun, 21 Jun 2020 17:14:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:14:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:14:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:14:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:14:14: #2 predicted fragment length is 304 bps INFO @ Sun, 21 Jun 2020 17:14:14: #2 alternative fragment length(s) may be 304 bps INFO @ Sun, 21 Jun 2020 17:14:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.20_model.r INFO @ Sun, 21 Jun 2020 17:14:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:14:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:14:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:14:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:14:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:14:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026743/SRX026743.20_summits.bed INFO @ Sun, 21 Jun 2020 17:14:39: Done! pass1 - making usageList (146 chroms): 1 millis pass2 - checking and writing primary data (1789 records, 4 fields): 6 millis CompletedMACS2peakCalling