Job ID = 6458365 SRX = SRX507381 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:19:49 prefetch.2.10.7: 1) Downloading 'SRR1213168'... 2020-06-21T12:19:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:20:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:20:48 prefetch.2.10.7: 'SRR1213168' is valid 2020-06-21T12:20:48 prefetch.2.10.7: 1) 'SRR1213168' was downloaded successfully Read 5996115 spots for SRR1213168/SRR1213168.sra Written 5996115 spots for SRR1213168/SRR1213168.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: 00:01:38 5996115 reads; of these: 5996115 (100.00%) were unpaired; of these: 348203 (5.81%) aligned 0 times 3465593 (57.80%) aligned exactly 1 time 2182319 (36.40%) aligned >1 times 94.19% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 1185602 / 5647912 = 0.2099 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 21:24:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.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 21:24:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:42: 1000000 INFO @ Sun, 21 Jun 2020 21:24:48: 2000000 INFO @ Sun, 21 Jun 2020 21:24:53: 3000000 INFO @ Sun, 21 Jun 2020 21:24:59: 4000000 INFO @ Sun, 21 Jun 2020 21:25:02: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:25:02: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:25:02: #1 total tags in treatment: 4462310 INFO @ Sun, 21 Jun 2020 21:25:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:02: #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 21:25:02: #1 tags after filtering in treatment: 4462218 INFO @ Sun, 21 Jun 2020 21:25:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:02: #2 number of paired peaks: 1256 INFO @ Sun, 21 Jun 2020 21:25:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:02: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 21:25:02: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 21 Jun 2020 21:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.05_model.r WARNING @ Sun, 21 Jun 2020 21:25:02: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:02: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 21 Jun 2020 21:25:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:25:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:02: #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 21:25:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.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 21:25:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:25:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:25:11: 1000000 INFO @ Sun, 21 Jun 2020 21:25:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:25:16: 2000000 INFO @ Sun, 21 Jun 2020 21:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.05_summits.bed INFO @ Sun, 21 Jun 2020 21:25:17: Done! pass1 - making usageList (558 chroms): 2 millis pass2 - checking and writing primary data (2289 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:25:21: 3000000 INFO @ Sun, 21 Jun 2020 21:25:27: 4000000 INFO @ Sun, 21 Jun 2020 21:25:29: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:25:29: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:25:29: #1 total tags in treatment: 4462310 INFO @ Sun, 21 Jun 2020 21:25:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:29: #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 21:25:29: #1 tags after filtering in treatment: 4462218 INFO @ Sun, 21 Jun 2020 21:25:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:29: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:30: #2 number of paired peaks: 1256 INFO @ Sun, 21 Jun 2020 21:25:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:30: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 21:25:30: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 21 Jun 2020 21:25:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.10_model.r WARNING @ Sun, 21 Jun 2020 21:25:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:30: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 21 Jun 2020 21:25:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:25:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:30: #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 21:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.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 21:25:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:25:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:25:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:25:42: 1000000 INFO @ Sun, 21 Jun 2020 21:25:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.10_summits.bed INFO @ Sun, 21 Jun 2020 21:25:44: Done! pass1 - making usageList (380 chroms): 1 millis pass2 - checking and writing primary data (811 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:25:47: 2000000 INFO @ Sun, 21 Jun 2020 21:25:53: 3000000 BedGraph に変換しました。 INFO @ Sun, 21 Jun 2020 21:25:59: 4000000 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:26:01: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:26:01: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:26:01: #1 total tags in treatment: 4462310 INFO @ Sun, 21 Jun 2020 21:26:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:26:01: #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 21:26:02: #1 tags after filtering in treatment: 4462218 INFO @ Sun, 21 Jun 2020 21:26:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:26:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:26:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:26:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:26:02: #2 number of paired peaks: 1256 INFO @ Sun, 21 Jun 2020 21:26:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:26:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:26:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:26:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:26:02: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 21:26:02: #2 alternative fragment length(s) may be 4,45 bps INFO @ Sun, 21 Jun 2020 21:26:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.20_model.r WARNING @ Sun, 21 Jun 2020 21:26:02: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:26:02: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Sun, 21 Jun 2020 21:26:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:26:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:26:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:26:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:26:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507381/SRX507381.20_summits.bed INFO @ Sun, 21 Jun 2020 21:26:17: Done! pass1 - making usageList (109 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 4 millis CompletedMACS2peakCalling