Job ID = 6454541 SRX = SRX229429 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:22:29 prefetch.2.10.7: 1) Downloading 'SRR688261'... 2020-06-21T09:22:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:24:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:24:12 prefetch.2.10.7: 'SRR688261' is valid 2020-06-21T09:24:12 prefetch.2.10.7: 1) 'SRR688261' was downloaded successfully Read 8394583 spots for SRR688261/SRR688261.sra Written 8394583 spots for SRR688261/SRR688261.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: 00:00:59 8394583 reads; of these: 8394583 (100.00%) were unpaired; of these: 4938544 (58.83%) aligned 0 times 2889572 (34.42%) aligned exactly 1 time 566467 (6.75%) aligned >1 times 41.17% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 272628 / 3456039 = 0.0789 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 18:26:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.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 18:26:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:00: 1000000 INFO @ Sun, 21 Jun 2020 18:27:06: 2000000 INFO @ Sun, 21 Jun 2020 18:27:12: 3000000 INFO @ Sun, 21 Jun 2020 18:27:14: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:27:14: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:27:14: #1 total tags in treatment: 3183411 INFO @ Sun, 21 Jun 2020 18:27:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:14: #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 18:27:14: #1 tags after filtering in treatment: 3183310 INFO @ Sun, 21 Jun 2020 18:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:14: #2 number of paired peaks: 557 WARNING @ Sun, 21 Jun 2020 18:27:14: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Sun, 21 Jun 2020 18:27:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:14: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 18:27:14: #2 alternative fragment length(s) may be 77 bps INFO @ Sun, 21 Jun 2020 18:27:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.05_model.r INFO @ Sun, 21 Jun 2020 18:27:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:22: #3 Call peaks for each chromosome... 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 18:27:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.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 18:27:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.05_summits.bed INFO @ Sun, 21 Jun 2020 18:27:26: Done! pass1 - making usageList (136 chroms): 1 millis pass2 - checking and writing primary data (4199 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:27:30: 1000000 INFO @ Sun, 21 Jun 2020 18:27:36: 2000000 INFO @ Sun, 21 Jun 2020 18:27:43: 3000000 INFO @ Sun, 21 Jun 2020 18:27:44: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:27:44: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:27:44: #1 total tags in treatment: 3183411 INFO @ Sun, 21 Jun 2020 18:27:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:44: #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 18:27:45: #1 tags after filtering in treatment: 3183310 INFO @ Sun, 21 Jun 2020 18:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:45: #2 number of paired peaks: 557 WARNING @ Sun, 21 Jun 2020 18:27:45: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Sun, 21 Jun 2020 18:27:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:45: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:45: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:45: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:45: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 18:27:45: #2 alternative fragment length(s) may be 77 bps INFO @ Sun, 21 Jun 2020 18:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.10_model.r INFO @ Sun, 21 Jun 2020 18:27:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:52: #3 Call peaks for each chromosome... 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 18:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.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 18:27:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.10_summits.bed INFO @ Sun, 21 Jun 2020 18:27:56: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (1193 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:28:01: 1000000 INFO @ Sun, 21 Jun 2020 18:28:06: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:28:13: 3000000 INFO @ Sun, 21 Jun 2020 18:28:14: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:28:14: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:28:14: #1 total tags in treatment: 3183411 INFO @ Sun, 21 Jun 2020 18:28:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:14: #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 18:28:14: #1 tags after filtering in treatment: 3183310 INFO @ Sun, 21 Jun 2020 18:28:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:15: #2 number of paired peaks: 557 WARNING @ Sun, 21 Jun 2020 18:28:15: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Sun, 21 Jun 2020 18:28:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:15: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 18:28:15: #2 alternative fragment length(s) may be 77 bps INFO @ Sun, 21 Jun 2020 18:28:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.20_model.r INFO @ Sun, 21 Jun 2020 18:28:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:28:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX229429/SRX229429.20_summits.bed INFO @ Sun, 21 Jun 2020 18:28:26: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 5 millis CompletedMACS2peakCalling