Job ID = 6454550 SRX = SRX231875 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:13:39 prefetch.2.10.7: 1) Downloading 'SRR696749'... 2020-06-21T09:13:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:15:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:15:21 prefetch.2.10.7: 'SRR696749' is valid 2020-06-21T09:15:21 prefetch.2.10.7: 1) 'SRR696749' was downloaded successfully Read 7361270 spots for SRR696749/SRR696749.sra Written 7361270 spots for SRR696749/SRR696749.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: 00:00:01 Multiseed full-index search: 00:00:51 7361270 reads; of these: 7361270 (100.00%) were unpaired; of these: 4370892 (59.38%) aligned 0 times 2279016 (30.96%) aligned exactly 1 time 711362 (9.66%) aligned >1 times 40.62% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 203098 / 2990378 = 0.0679 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 18:17:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.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 18:17:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:05: 1000000 INFO @ Sun, 21 Jun 2020 18:18:13: 2000000 INFO @ Sun, 21 Jun 2020 18:18:19: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:18:19: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:18:19: #1 total tags in treatment: 2787280 INFO @ Sun, 21 Jun 2020 18:18:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:19: #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 18:18:20: #1 tags after filtering in treatment: 2787226 INFO @ Sun, 21 Jun 2020 18:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:20: #2 number of paired peaks: 459 WARNING @ Sun, 21 Jun 2020 18:18:20: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sun, 21 Jun 2020 18:18:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:20: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:18:20: #2 alternative fragment length(s) may be 72,549 bps INFO @ Sun, 21 Jun 2020 18:18:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.05_model.r INFO @ Sun, 21 Jun 2020 18:18:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:20: #3 Pre-compute pvalue-qvalue table... 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 18:18:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.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 18:18:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.05_summits.bed INFO @ Sun, 21 Jun 2020 18:18:30: Done! pass1 - making usageList (146 chroms): 2 millis pass2 - checking and writing primary data (2784 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:18:35: 1000000 INFO @ Sun, 21 Jun 2020 18:18:42: 2000000 INFO @ Sun, 21 Jun 2020 18:18:49: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:18:49: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:18:49: #1 total tags in treatment: 2787280 INFO @ Sun, 21 Jun 2020 18:18:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:49: #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 18:18:49: #1 tags after filtering in treatment: 2787226 INFO @ Sun, 21 Jun 2020 18:18:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:49: #2 number of paired peaks: 459 WARNING @ Sun, 21 Jun 2020 18:18:49: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sun, 21 Jun 2020 18:18:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:49: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:18:49: #2 alternative fragment length(s) may be 72,549 bps INFO @ Sun, 21 Jun 2020 18:18:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.10_model.r INFO @ Sun, 21 Jun 2020 18:18:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:49: #3 Pre-compute pvalue-qvalue table... 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 18:18:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.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 18:18:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.10_summits.bed INFO @ Sun, 21 Jun 2020 18:18:59: Done! pass1 - making usageList (93 chroms): 2 millis pass2 - checking and writing primary data (767 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:19:04: 1000000 INFO @ Sun, 21 Jun 2020 18:19:10: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:19:17: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:19:17: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:19:17: #1 total tags in treatment: 2787280 INFO @ Sun, 21 Jun 2020 18:19:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:17: #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 18:19:17: #1 tags after filtering in treatment: 2787226 INFO @ Sun, 21 Jun 2020 18:19:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:17: #2 number of paired peaks: 459 WARNING @ Sun, 21 Jun 2020 18:19:17: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sun, 21 Jun 2020 18:19:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:17: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:19:17: #2 alternative fragment length(s) may be 72,549 bps INFO @ Sun, 21 Jun 2020 18:19:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.20_model.r INFO @ Sun, 21 Jun 2020 18:19:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:19:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231875/SRX231875.20_summits.bed INFO @ Sun, 21 Jun 2020 18:19:27: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 4 millis CompletedMACS2peakCalling