Job ID = 6454839 SRX = SRX2592435 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:34:41 prefetch.2.10.7: 1) Downloading 'SRR5289712'... 2020-06-21T09:34:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:36:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:36:50 prefetch.2.10.7: 'SRR5289712' is valid 2020-06-21T09:36:50 prefetch.2.10.7: 1) 'SRR5289712' was downloaded successfully Read 9383872 spots for SRR5289712/SRR5289712.sra Written 9383872 spots for SRR5289712/SRR5289712.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: 00:02:30 9383872 reads; of these: 9383872 (100.00%) were unpaired; of these: 922959 (9.84%) aligned 0 times 7404079 (78.90%) aligned exactly 1 time 1056834 (11.26%) aligned >1 times 90.16% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 2657100 / 8460913 = 0.3140 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 18:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.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 18:42:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:47: 1000000 INFO @ Sun, 21 Jun 2020 18:42:54: 2000000 INFO @ Sun, 21 Jun 2020 18:43:02: 3000000 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 18:43:09: 4000000 INFO @ Sun, 21 Jun 2020 18:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.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 18:43:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:18: 1000000 INFO @ Sun, 21 Jun 2020 18:43:18: 5000000 INFO @ Sun, 21 Jun 2020 18:43:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:43:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:43:24: #1 total tags in treatment: 5803813 INFO @ Sun, 21 Jun 2020 18:43:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:24: #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 18:43:25: #1 tags after filtering in treatment: 5803517 INFO @ Sun, 21 Jun 2020 18:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:26: #2 number of paired peaks: 384 WARNING @ Sun, 21 Jun 2020 18:43:26: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Sun, 21 Jun 2020 18:43:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:26: 2000000 INFO @ Sun, 21 Jun 2020 18:43:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:26: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 18:43:26: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 18:43:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.05_model.r INFO @ Sun, 21 Jun 2020 18:43:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:43:33: 3000000 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 18:43:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.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 18:43:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:41: 4000000 INFO @ Sun, 21 Jun 2020 18:43:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:48: 1000000 INFO @ Sun, 21 Jun 2020 18:43:49: 5000000 INFO @ Sun, 21 Jun 2020 18:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.05_summits.bed INFO @ Sun, 21 Jun 2020 18:43:52: Done! pass1 - making usageList (219 chroms): 2 millis pass2 - checking and writing primary data (12259 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:43:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:43:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:43:55: #1 total tags in treatment: 5803813 INFO @ Sun, 21 Jun 2020 18:43:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:55: #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 18:43:56: #1 tags after filtering in treatment: 5803517 INFO @ Sun, 21 Jun 2020 18:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:56: 2000000 INFO @ Sun, 21 Jun 2020 18:43:57: #2 number of paired peaks: 384 WARNING @ Sun, 21 Jun 2020 18:43:57: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Sun, 21 Jun 2020 18:43:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:57: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 18:43:57: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 18:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.10_model.r INFO @ Sun, 21 Jun 2020 18:43:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:04: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:44:12: 4000000 INFO @ Sun, 21 Jun 2020 18:44:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:20: 5000000 INFO @ Sun, 21 Jun 2020 18:44:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.10_summits.bed INFO @ Sun, 21 Jun 2020 18:44:21: Done! pass1 - making usageList (147 chroms): 2 millis pass2 - checking and writing primary data (8916 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:44:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:44:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:44:26: #1 total tags in treatment: 5803813 INFO @ Sun, 21 Jun 2020 18:44:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:26: #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 18:44:26: #1 tags after filtering in treatment: 5803517 INFO @ Sun, 21 Jun 2020 18:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:27: #2 number of paired peaks: 384 WARNING @ Sun, 21 Jun 2020 18:44:27: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Sun, 21 Jun 2020 18:44:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:27: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 18:44:27: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 18:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.20_model.r INFO @ Sun, 21 Jun 2020 18:44:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592435/SRX2592435.20_summits.bed INFO @ Sun, 21 Jun 2020 18:44:53: Done! pass1 - making usageList (96 chroms): 2 millis pass2 - checking and writing primary data (5935 records, 4 fields): 11 millis CompletedMACS2peakCalling