Job ID = 6454854 SRX = SRX2592446 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:37:55 prefetch.2.10.7: 1) Downloading 'SRR5289723'... 2020-06-21T09:37:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:56 prefetch.2.10.7: 'SRR5289723' is valid 2020-06-21T09:39:56 prefetch.2.10.7: 1) 'SRR5289723' was downloaded successfully Read 9724038 spots for SRR5289723/SRR5289723.sra Written 9724038 spots for SRR5289723/SRR5289723.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: 00:03:05 9724038 reads; of these: 9724038 (100.00%) were unpaired; of these: 1297111 (13.34%) aligned 0 times 6497792 (66.82%) aligned exactly 1 time 1929135 (19.84%) aligned >1 times 86.66% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 1954895 / 8426927 = 0.2320 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 18:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.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 18:46:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:24: 1000000 INFO @ Sun, 21 Jun 2020 18:46:29: 2000000 INFO @ Sun, 21 Jun 2020 18:46:34: 3000000 INFO @ Sun, 21 Jun 2020 18:46:39: 4000000 INFO @ Sun, 21 Jun 2020 18:46:44: 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 18:46:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.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 18:46:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:49: 6000000 INFO @ Sun, 21 Jun 2020 18:46:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:46:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:46:52: #1 total tags in treatment: 6472032 INFO @ Sun, 21 Jun 2020 18:46:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:52: #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 18:46:52: #1 tags after filtering in treatment: 6471881 INFO @ Sun, 21 Jun 2020 18:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:53: #2 number of paired peaks: 445 WARNING @ Sun, 21 Jun 2020 18:46:53: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:53: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:46:53: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:46:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.05_model.r INFO @ Sun, 21 Jun 2020 18:46:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:54: 1000000 INFO @ Sun, 21 Jun 2020 18:46:59: 2000000 INFO @ Sun, 21 Jun 2020 18:47:04: 3000000 INFO @ Sun, 21 Jun 2020 18:47:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:09: 4000000 INFO @ Sun, 21 Jun 2020 18:47:14: 5000000 INFO @ Sun, 21 Jun 2020 18:47:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.05_summits.bed INFO @ Sun, 21 Jun 2020 18:47:14: Done! pass1 - making usageList (316 chroms): 1 millis pass2 - checking and writing primary data (6252 records, 4 fields): 15 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 18:47:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.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 18:47:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:20: 6000000 INFO @ Sun, 21 Jun 2020 18:47:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:47:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:47:23: #1 total tags in treatment: 6472032 INFO @ Sun, 21 Jun 2020 18:47:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:23: #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 18:47:23: #1 tags after filtering in treatment: 6471881 INFO @ Sun, 21 Jun 2020 18:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:23: #2 number of paired peaks: 445 WARNING @ Sun, 21 Jun 2020 18:47:23: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Sun, 21 Jun 2020 18:47:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:24: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:47:24: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.10_model.r INFO @ Sun, 21 Jun 2020 18:47:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:24: 1000000 INFO @ Sun, 21 Jun 2020 18:47:29: 2000000 INFO @ Sun, 21 Jun 2020 18:47:34: 3000000 INFO @ Sun, 21 Jun 2020 18:47:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:39: 4000000 INFO @ Sun, 21 Jun 2020 18:47:45: 5000000 INFO @ Sun, 21 Jun 2020 18:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.10_summits.bed INFO @ Sun, 21 Jun 2020 18:47:46: Done! pass1 - making usageList (205 chroms): 1 millis pass2 - checking and writing primary data (3012 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:47:50: 6000000 INFO @ Sun, 21 Jun 2020 18:47:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:47:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:47:53: #1 total tags in treatment: 6472032 INFO @ Sun, 21 Jun 2020 18:47:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:53: #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 18:47:53: #1 tags after filtering in treatment: 6471881 INFO @ Sun, 21 Jun 2020 18:47:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:54: #2 number of paired peaks: 445 WARNING @ Sun, 21 Jun 2020 18:47:54: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Sun, 21 Jun 2020 18:47:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:54: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:47:54: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.20_model.r INFO @ Sun, 21 Jun 2020 18:47:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:48:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592446/SRX2592446.20_summits.bed INFO @ Sun, 21 Jun 2020 18:48:16: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (728 records, 4 fields): 7 millis CompletedMACS2peakCalling