Job ID = 6455921 SRX = SRX3068960 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:49:16 prefetch.2.10.7: 1) Downloading 'SRR5907436'... 2020-06-21T10:49:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:52:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:52:51 prefetch.2.10.7: 'SRR5907436' is valid 2020-06-21T10:52:51 prefetch.2.10.7: 1) 'SRR5907436' was downloaded successfully Read 11688097 spots for SRR5907436/SRR5907436.sra Written 11688097 spots for SRR5907436/SRR5907436.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: 00:01:56 11688097 reads; of these: 11688097 (100.00%) were unpaired; of these: 5000941 (42.79%) aligned 0 times 5775644 (49.41%) aligned exactly 1 time 911512 (7.80%) aligned >1 times 57.21% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 3509917 / 6687156 = 0.5249 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 19:57:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.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 19:57:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:15: 1000000 INFO @ Sun, 21 Jun 2020 19:57:21: 2000000 INFO @ Sun, 21 Jun 2020 19:57:27: 3000000 INFO @ Sun, 21 Jun 2020 19:57:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:57:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:57:28: #1 total tags in treatment: 3177239 INFO @ Sun, 21 Jun 2020 19:57:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:28: #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 19:57:28: #1 tags after filtering in treatment: 3177069 INFO @ Sun, 21 Jun 2020 19:57:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:29: #2 number of paired peaks: 1794 INFO @ Sun, 21 Jun 2020 19:57:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:29: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 19:57:29: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 19:57:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.05_model.r INFO @ Sun, 21 Jun 2020 19:57:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:36: #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 19:57:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.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 19:57:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.05_summits.bed INFO @ Sun, 21 Jun 2020 19:57:40: Done! pass1 - making usageList (461 chroms): 2 millis pass2 - checking and writing primary data (3667 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:57:46: 1000000 INFO @ Sun, 21 Jun 2020 19:57:53: 2000000 INFO @ Sun, 21 Jun 2020 19:57:59: 3000000 INFO @ Sun, 21 Jun 2020 19:58:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:58:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:58:00: #1 total tags in treatment: 3177239 INFO @ Sun, 21 Jun 2020 19:58:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:00: #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 19:58:01: #1 tags after filtering in treatment: 3177069 INFO @ Sun, 21 Jun 2020 19:58:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:01: #2 number of paired peaks: 1794 INFO @ Sun, 21 Jun 2020 19:58:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:01: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 19:58:01: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 19:58:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.10_model.r INFO @ Sun, 21 Jun 2020 19:58:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:01: #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 19:58:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.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 19:58:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.10_summits.bed INFO @ Sun, 21 Jun 2020 19:58:12: Done! pass1 - making usageList (384 chroms): 2 millis pass2 - checking and writing primary data (1897 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:58:16: 1000000 INFO @ Sun, 21 Jun 2020 19:58:22: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:58:28: 3000000 INFO @ Sun, 21 Jun 2020 19:58:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:58:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:58:29: #1 total tags in treatment: 3177239 INFO @ Sun, 21 Jun 2020 19:58:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:29: #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 19:58:29: #1 tags after filtering in treatment: 3177069 INFO @ Sun, 21 Jun 2020 19:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:30: #2 number of paired peaks: 1794 INFO @ Sun, 21 Jun 2020 19:58:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:30: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 19:58:30: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 19:58:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.20_model.r INFO @ Sun, 21 Jun 2020 19:58:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:58:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068960/SRX3068960.20_summits.bed INFO @ Sun, 21 Jun 2020 19:58:41: Done! pass1 - making usageList (195 chroms): 1 millis pass2 - checking and writing primary data (805 records, 4 fields): 7 millis CompletedMACS2peakCalling