Job ID = 6455811 SRX = SRX3009518 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:27:36 prefetch.2.10.7: 1) Downloading 'SRR5832219'... 2020-06-21T10:27:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:30:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:30:03 prefetch.2.10.7: 'SRR5832219' is valid 2020-06-21T10:30:03 prefetch.2.10.7: 1) 'SRR5832219' was downloaded successfully Read 12905783 spots for SRR5832219/SRR5832219.sra Written 12905783 spots for SRR5832219/SRR5832219.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: 00:03:00 12905783 reads; of these: 12905783 (100.00%) were unpaired; of these: 4536596 (35.15%) aligned 0 times 5886022 (45.61%) aligned exactly 1 time 2483165 (19.24%) aligned >1 times 64.85% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 2230924 / 8369187 = 0.2666 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 19:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.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 19:36:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:14: 1000000 INFO @ Sun, 21 Jun 2020 19:36:20: 2000000 INFO @ Sun, 21 Jun 2020 19:36:26: 3000000 INFO @ Sun, 21 Jun 2020 19:36:32: 4000000 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 19:36:38: 5000000 INFO @ Sun, 21 Jun 2020 19:36:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.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 19:36:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:44: 6000000 INFO @ Sun, 21 Jun 2020 19:36:45: 1000000 INFO @ Sun, 21 Jun 2020 19:36:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:36:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:36:45: #1 total tags in treatment: 6138263 INFO @ Sun, 21 Jun 2020 19:36:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:45: #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 19:36:45: #1 tags after filtering in treatment: 6138084 INFO @ Sun, 21 Jun 2020 19:36:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:46: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 19:36:46: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:46: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 19:36:46: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 19:36:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.05_model.r INFO @ Sun, 21 Jun 2020 19:36:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:51: 2000000 INFO @ Sun, 21 Jun 2020 19:36:57: 3000000 INFO @ Sun, 21 Jun 2020 19:36:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:02: 4000000 INFO @ Sun, 21 Jun 2020 19:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.05_summits.bed INFO @ Sun, 21 Jun 2020 19:37:06: Done! pass1 - making usageList (557 chroms): 1 millis pass2 - checking and writing primary data (3146 records, 4 fields): 17 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 19:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.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 19:37:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:09: 5000000 INFO @ Sun, 21 Jun 2020 19:37:15: 6000000 INFO @ Sun, 21 Jun 2020 19:37:15: 1000000 INFO @ Sun, 21 Jun 2020 19:37:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:37:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:37:16: #1 total tags in treatment: 6138263 INFO @ Sun, 21 Jun 2020 19:37:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:16: #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 19:37:17: #1 tags after filtering in treatment: 6138084 INFO @ Sun, 21 Jun 2020 19:37:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:17: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:17: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 19:37:17: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 19:37:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:17: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 19:37:17: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 19:37:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.10_model.r INFO @ Sun, 21 Jun 2020 19:37:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:22: 2000000 INFO @ Sun, 21 Jun 2020 19:37:29: 3000000 INFO @ Sun, 21 Jun 2020 19:37:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:37: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.10_summits.bed INFO @ Sun, 21 Jun 2020 19:37:37: Done! pass1 - making usageList (327 chroms): 1 millis pass2 - checking and writing primary data (1184 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:44: 5000000 INFO @ Sun, 21 Jun 2020 19:37:51: 6000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:37:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:37:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:37:52: #1 total tags in treatment: 6138263 INFO @ Sun, 21 Jun 2020 19:37:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:52: #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 19:37:52: #1 tags after filtering in treatment: 6138084 INFO @ Sun, 21 Jun 2020 19:37:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:52: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 19:37:52: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 19:37:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:53: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 19:37:53: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 19:37:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.20_model.r INFO @ Sun, 21 Jun 2020 19:37:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009518/SRX3009518.20_summits.bed INFO @ Sun, 21 Jun 2020 19:38:13: Done! pass1 - making usageList (131 chroms): 1 millis pass2 - checking and writing primary data (331 records, 4 fields): 5 millis CompletedMACS2peakCalling