Job ID = 6452647 SRX = SRX022743 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:41:36 prefetch.2.10.7: 1) Downloading 'SRR059122'... 2020-06-21T07:41:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:44:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:44:15 prefetch.2.10.7: 'SRR059122' is valid 2020-06-21T07:44:15 prefetch.2.10.7: 1) 'SRR059122' was downloaded successfully Read 10289917 spots for SRR059122/SRR059122.sra Written 10289917 spots for SRR059122/SRR059122.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: 00:02:07 10289917 reads; of these: 10289917 (100.00%) were unpaired; of these: 774907 (7.53%) aligned 0 times 7199361 (69.97%) aligned exactly 1 time 2315649 (22.50%) aligned >1 times 92.47% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 885249 / 9515010 = 0.0930 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 16:49:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.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 16:49:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:17: 1000000 INFO @ Sun, 21 Jun 2020 16:49:22: 2000000 INFO @ Sun, 21 Jun 2020 16:49:26: 3000000 INFO @ Sun, 21 Jun 2020 16:49:31: 4000000 INFO @ Sun, 21 Jun 2020 16:49:36: 5000000 INFO @ Sun, 21 Jun 2020 16:49:40: 6000000 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 16:49:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.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 16:49:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:45: 7000000 INFO @ Sun, 21 Jun 2020 16:49:49: 1000000 INFO @ Sun, 21 Jun 2020 16:49:50: 8000000 INFO @ Sun, 21 Jun 2020 16:49:53: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:49:53: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:49:53: #1 total tags in treatment: 8629761 INFO @ Sun, 21 Jun 2020 16:49:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:49:53: #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 16:49:54: #1 tags after filtering in treatment: 8629650 INFO @ Sun, 21 Jun 2020 16:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:49:54: #1 finished! INFO @ Sun, 21 Jun 2020 16:49:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:49:54: 2000000 INFO @ Sun, 21 Jun 2020 16:49:55: #2 number of paired peaks: 1393 INFO @ Sun, 21 Jun 2020 16:49:55: start model_add_line... INFO @ Sun, 21 Jun 2020 16:49:55: start X-correlation... INFO @ Sun, 21 Jun 2020 16:49:55: end of X-cor INFO @ Sun, 21 Jun 2020 16:49:55: #2 finished! INFO @ Sun, 21 Jun 2020 16:49:55: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 16:49:55: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 16:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.05_model.r INFO @ Sun, 21 Jun 2020 16:49:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:50:00: 3000000 INFO @ Sun, 21 Jun 2020 16:50:05: 4000000 INFO @ Sun, 21 Jun 2020 16:50:10: 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 16:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.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 16:50:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:50:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:50:15: 6000000 INFO @ Sun, 21 Jun 2020 16:50:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:18: 1000000 INFO @ Sun, 21 Jun 2020 16:50:20: 7000000 INFO @ Sun, 21 Jun 2020 16:50:23: 2000000 INFO @ Sun, 21 Jun 2020 16:50:26: 8000000 INFO @ Sun, 21 Jun 2020 16:50:29: 3000000 INFO @ Sun, 21 Jun 2020 16:50:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.05_summits.bed INFO @ Sun, 21 Jun 2020 16:50:29: Done! pass1 - making usageList (283 chroms): 2 millis pass2 - checking and writing primary data (5169 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:50:30: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:30: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:30: #1 total tags in treatment: 8629761 INFO @ Sun, 21 Jun 2020 16:50:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:30: #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 16:50:30: #1 tags after filtering in treatment: 8629650 INFO @ Sun, 21 Jun 2020 16:50:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:30: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:50:31: #2 number of paired peaks: 1393 INFO @ Sun, 21 Jun 2020 16:50:31: start model_add_line... INFO @ Sun, 21 Jun 2020 16:50:31: start X-correlation... INFO @ Sun, 21 Jun 2020 16:50:31: end of X-cor INFO @ Sun, 21 Jun 2020 16:50:31: #2 finished! INFO @ Sun, 21 Jun 2020 16:50:31: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 16:50:31: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 16:50:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.10_model.r INFO @ Sun, 21 Jun 2020 16:50:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:50:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:50:34: 4000000 INFO @ Sun, 21 Jun 2020 16:50:39: 5000000 INFO @ Sun, 21 Jun 2020 16:50:45: 6000000 INFO @ Sun, 21 Jun 2020 16:50:50: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:50:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:55: 8000000 INFO @ Sun, 21 Jun 2020 16:50:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:59: #1 total tags in treatment: 8629761 INFO @ Sun, 21 Jun 2020 16:50:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:59: #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 16:50:59: #1 tags after filtering in treatment: 8629650 INFO @ Sun, 21 Jun 2020 16:50:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:59: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:51:00: #2 number of paired peaks: 1393 INFO @ Sun, 21 Jun 2020 16:51:00: start model_add_line... INFO @ Sun, 21 Jun 2020 16:51:00: start X-correlation... INFO @ Sun, 21 Jun 2020 16:51:00: end of X-cor INFO @ Sun, 21 Jun 2020 16:51:00: #2 finished! INFO @ Sun, 21 Jun 2020 16:51:00: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 16:51:00: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 16:51:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.20_model.r INFO @ Sun, 21 Jun 2020 16:51:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:51:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:51:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:51:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:51:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.10_summits.bed INFO @ Sun, 21 Jun 2020 16:51:03: Done! pass1 - making usageList (213 chroms): 1 millis pass2 - checking and writing primary data (3072 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:51:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022743/SRX022743.20_summits.bed INFO @ Sun, 21 Jun 2020 16:51:32: Done! pass1 - making usageList (156 chroms): 1 millis pass2 - checking and writing primary data (1488 records, 4 fields): 8 millis CompletedMACS2peakCalling