Job ID = 6454050 SRX = SRX1794234 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:01:49 prefetch.2.10.7: 1) Downloading 'SRR3575274'... 2020-06-21T09:01:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:03:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:03:22 prefetch.2.10.7: 'SRR3575274' is valid 2020-06-21T09:03:22 prefetch.2.10.7: 1) 'SRR3575274' was downloaded successfully Read 10581836 spots for SRR3575274/SRR3575274.sra Written 10581836 spots for SRR3575274/SRR3575274.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: 00:02:34 10581836 reads; of these: 10581836 (100.00%) were unpaired; of these: 878614 (8.30%) aligned 0 times 7865876 (74.33%) aligned exactly 1 time 1837346 (17.36%) aligned >1 times 91.70% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 1409896 / 9703222 = 0.1453 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 18:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.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 18:09:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:37: 1000000 INFO @ Sun, 21 Jun 2020 18:09:43: 2000000 INFO @ Sun, 21 Jun 2020 18:09:48: 3000000 INFO @ Sun, 21 Jun 2020 18:09:54: 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 18:10:00: 5000000 INFO @ Sun, 21 Jun 2020 18:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.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 18:10:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:06: 6000000 INFO @ Sun, 21 Jun 2020 18:10:08: 1000000 INFO @ Sun, 21 Jun 2020 18:10:12: 7000000 INFO @ Sun, 21 Jun 2020 18:10:14: 2000000 INFO @ Sun, 21 Jun 2020 18:10:18: 8000000 INFO @ Sun, 21 Jun 2020 18:10:20: 3000000 INFO @ Sun, 21 Jun 2020 18:10:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:10:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:10:20: #1 total tags in treatment: 8293326 INFO @ Sun, 21 Jun 2020 18:10:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:20: #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 18:10:21: #1 tags after filtering in treatment: 8293155 INFO @ Sun, 21 Jun 2020 18:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:22: #2 number of paired peaks: 4045 INFO @ Sun, 21 Jun 2020 18:10:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:22: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:10:22: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:10:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.05_model.r INFO @ Sun, 21 Jun 2020 18:10:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:10:26: 4000000 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 18:10:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.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 18:10:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:32: 5000000 INFO @ Sun, 21 Jun 2020 18:10:38: 6000000 INFO @ Sun, 21 Jun 2020 18:10:38: 1000000 INFO @ Sun, 21 Jun 2020 18:10:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:44: 2000000 INFO @ Sun, 21 Jun 2020 18:10:44: 7000000 INFO @ Sun, 21 Jun 2020 18:10:50: 3000000 INFO @ Sun, 21 Jun 2020 18:10:50: 8000000 INFO @ Sun, 21 Jun 2020 18:10:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:10:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:10:52: #1 total tags in treatment: 8293326 INFO @ Sun, 21 Jun 2020 18:10:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:52: #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 18:10:52: #1 tags after filtering in treatment: 8293155 INFO @ Sun, 21 Jun 2020 18:10:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:53: #2 number of paired peaks: 4045 INFO @ Sun, 21 Jun 2020 18:10:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:53: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:10:53: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:10:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.10_model.r INFO @ Sun, 21 Jun 2020 18:10:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:10:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.05_summits.bed INFO @ Sun, 21 Jun 2020 18:10:55: Done! pass1 - making usageList (403 chroms): 2 millis pass2 - checking and writing primary data (8932 records, 4 fields): 22 millis INFO @ Sun, 21 Jun 2020 18:10:56: 4000000 CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:11:02: 5000000 INFO @ Sun, 21 Jun 2020 18:11:07: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:11:13: 7000000 INFO @ Sun, 21 Jun 2020 18:11:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:11:19: 8000000 INFO @ Sun, 21 Jun 2020 18:11:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:11:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:11:21: #1 total tags in treatment: 8293326 INFO @ Sun, 21 Jun 2020 18:11:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:21: #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 18:11:21: #1 tags after filtering in treatment: 8293155 INFO @ Sun, 21 Jun 2020 18:11:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:11:22: #2 number of paired peaks: 4045 INFO @ Sun, 21 Jun 2020 18:11:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:22: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:11:22: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.20_model.r INFO @ Sun, 21 Jun 2020 18:11:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:11:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:11:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:11:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.10_summits.bed INFO @ Sun, 21 Jun 2020 18:11:28: Done! pass1 - making usageList (227 chroms): 2 millis pass2 - checking and writing primary data (6514 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:11:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:11:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:11:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:11:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794234/SRX1794234.20_summits.bed INFO @ Sun, 21 Jun 2020 18:11:54: Done! pass1 - making usageList (146 chroms): 2 millis pass2 - checking and writing primary data (4529 records, 4 fields): 11 millis CompletedMACS2peakCalling