Job ID = 6454462 SRX = SRX209933 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:19:39 prefetch.2.10.7: 1) Downloading 'SRR631788'... 2020-06-21T09:19:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:20:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:20:53 prefetch.2.10.7: 'SRR631788' is valid 2020-06-21T09:20:53 prefetch.2.10.7: 1) 'SRR631788' was downloaded successfully Read 8270656 spots for SRR631788/SRR631788.sra Written 8270656 spots for SRR631788/SRR631788.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: 00:01:57 8270656 reads; of these: 8270656 (100.00%) were unpaired; of these: 449491 (5.43%) aligned 0 times 6049147 (73.14%) aligned exactly 1 time 1772018 (21.43%) aligned >1 times 94.57% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 849758 / 7821165 = 0.1086 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 18:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.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 18:25:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:58: 1000000 INFO @ Sun, 21 Jun 2020 18:26:03: 2000000 INFO @ Sun, 21 Jun 2020 18:26:09: 3000000 INFO @ Sun, 21 Jun 2020 18:26:14: 4000000 INFO @ Sun, 21 Jun 2020 18:26:20: 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 18:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.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 18:26:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:26: 6000000 INFO @ Sun, 21 Jun 2020 18:26:28: 1000000 INFO @ Sun, 21 Jun 2020 18:26:32: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:26:32: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:26:32: #1 total tags in treatment: 6971407 INFO @ Sun, 21 Jun 2020 18:26:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:26:32: #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 18:26:32: #1 tags after filtering in treatment: 6971378 INFO @ Sun, 21 Jun 2020 18:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:26:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:26:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:26:32: #2 number of paired peaks: 445 WARNING @ Sun, 21 Jun 2020 18:26:32: 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 18:26:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:26:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:26:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:26:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:26:33: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 18:26:33: #2 alternative fragment length(s) may be 85,559 bps INFO @ Sun, 21 Jun 2020 18:26:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.05_model.r INFO @ Sun, 21 Jun 2020 18:26:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:26:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:26:34: 2000000 INFO @ Sun, 21 Jun 2020 18:26:40: 3000000 INFO @ Sun, 21 Jun 2020 18:26:45: 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 18:26:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:26:51: 5000000 INFO @ Sun, 21 Jun 2020 18:26:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.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 18:26:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:58: 6000000 INFO @ Sun, 21 Jun 2020 18:26:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:26:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:26:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.05_summits.bed INFO @ Sun, 21 Jun 2020 18:26:59: Done! INFO @ Sun, 21 Jun 2020 18:26:59: 1000000 pass1 - making usageList (551 chroms): 1 millis pass2 - checking and writing primary data (1742 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:27:04: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:27:04: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:27:04: #1 total tags in treatment: 6971407 INFO @ Sun, 21 Jun 2020 18:27:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:04: #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 18:27:04: #1 tags after filtering in treatment: 6971378 INFO @ Sun, 21 Jun 2020 18:27:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:05: #2 number of paired peaks: 445 WARNING @ Sun, 21 Jun 2020 18:27:05: 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 18:27:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:05: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 18:27:05: #2 alternative fragment length(s) may be 85,559 bps INFO @ Sun, 21 Jun 2020 18:27:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.10_model.r INFO @ Sun, 21 Jun 2020 18:27:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:06: 2000000 INFO @ Sun, 21 Jun 2020 18:27:12: 3000000 INFO @ Sun, 21 Jun 2020 18:27:18: 4000000 INFO @ Sun, 21 Jun 2020 18:27:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:24: 5000000 INFO @ Sun, 21 Jun 2020 18:27:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.10_summits.bed INFO @ Sun, 21 Jun 2020 18:27:30: Done! pass1 - making usageList (359 chroms): 1 millis INFO @ Sun, 21 Jun 2020 18:27:31: 6000000 pass2 - checking and writing primary data (710 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:27:37: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:27:37: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:27:37: #1 total tags in treatment: 6971407 INFO @ Sun, 21 Jun 2020 18:27:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:37: #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 18:27:38: #1 tags after filtering in treatment: 6971378 INFO @ Sun, 21 Jun 2020 18:27:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:38: #2 number of paired peaks: 445 WARNING @ Sun, 21 Jun 2020 18:27:38: 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 18:27:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:38: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 18:27:38: #2 alternative fragment length(s) may be 85,559 bps INFO @ Sun, 21 Jun 2020 18:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.20_model.r INFO @ Sun, 21 Jun 2020 18:27:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:27:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX209933/SRX209933.20_summits.bed INFO @ Sun, 21 Jun 2020 18:28:02: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 6 millis CompletedMACS2peakCalling