Job ID = 6529849 SRX = SRX5243667 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:38 10049435 reads; of these: 10049435 (100.00%) were unpaired; of these: 669839 (6.67%) aligned 0 times 7297965 (72.62%) aligned exactly 1 time 2081631 (20.71%) aligned >1 times 93.33% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 1951713 / 9379596 = 0.2081 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 @ Tue, 30 Jun 2020 03:08:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.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 @ Tue, 30 Jun 2020 03:08:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:08:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:08:42: 1000000 INFO @ Tue, 30 Jun 2020 03:08:49: 2000000 INFO @ Tue, 30 Jun 2020 03:08:55: 3000000 INFO @ Tue, 30 Jun 2020 03:09:02: 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 @ Tue, 30 Jun 2020 03:09:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.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 @ Tue, 30 Jun 2020 03:09:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:09: 5000000 INFO @ Tue, 30 Jun 2020 03:09:13: 1000000 INFO @ Tue, 30 Jun 2020 03:09:16: 6000000 INFO @ Tue, 30 Jun 2020 03:09:20: 2000000 INFO @ Tue, 30 Jun 2020 03:09:24: 7000000 INFO @ Tue, 30 Jun 2020 03:09:27: 3000000 INFO @ Tue, 30 Jun 2020 03:09:28: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:09:28: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:09:28: #1 total tags in treatment: 7427883 INFO @ Tue, 30 Jun 2020 03:09:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:09:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:09:28: #1 tags after filtering in treatment: 7427754 INFO @ Tue, 30 Jun 2020 03:09:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:09:28: #1 finished! INFO @ Tue, 30 Jun 2020 03:09:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:09:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:09:29: #2 number of paired peaks: 351 WARNING @ Tue, 30 Jun 2020 03:09:29: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 30 Jun 2020 03:09:29: start model_add_line... INFO @ Tue, 30 Jun 2020 03:09:29: start X-correlation... INFO @ Tue, 30 Jun 2020 03:09:29: end of X-cor INFO @ Tue, 30 Jun 2020 03:09:29: #2 finished! INFO @ Tue, 30 Jun 2020 03:09:29: #2 predicted fragment length is 185 bps INFO @ Tue, 30 Jun 2020 03:09:29: #2 alternative fragment length(s) may be 4,163,185 bps INFO @ Tue, 30 Jun 2020 03:09:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.05_model.r INFO @ Tue, 30 Jun 2020 03:09:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:09:29: #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 @ Tue, 30 Jun 2020 03:09:34: 4000000 INFO @ Tue, 30 Jun 2020 03:09:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.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 @ Tue, 30 Jun 2020 03:09:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:41: 5000000 INFO @ Tue, 30 Jun 2020 03:09:43: 1000000 INFO @ Tue, 30 Jun 2020 03:09:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:09:49: 6000000 INFO @ Tue, 30 Jun 2020 03:09:50: 2000000 INFO @ Tue, 30 Jun 2020 03:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.05_summits.bed INFO @ Tue, 30 Jun 2020 03:09:54: Done! pass1 - making usageList (386 chroms): 2 millis pass2 - checking and writing primary data (1798 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:09:57: 7000000 INFO @ Tue, 30 Jun 2020 03:09:58: 3000000 INFO @ Tue, 30 Jun 2020 03:10:00: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:10:00: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:10:00: #1 total tags in treatment: 7427883 INFO @ Tue, 30 Jun 2020 03:10:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:10:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:10:01: #1 tags after filtering in treatment: 7427754 INFO @ Tue, 30 Jun 2020 03:10:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:10:01: #1 finished! INFO @ Tue, 30 Jun 2020 03:10:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:10:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:10:01: #2 number of paired peaks: 351 WARNING @ Tue, 30 Jun 2020 03:10:01: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 30 Jun 2020 03:10:01: start model_add_line... INFO @ Tue, 30 Jun 2020 03:10:01: start X-correlation... INFO @ Tue, 30 Jun 2020 03:10:02: end of X-cor INFO @ Tue, 30 Jun 2020 03:10:02: #2 finished! INFO @ Tue, 30 Jun 2020 03:10:02: #2 predicted fragment length is 185 bps INFO @ Tue, 30 Jun 2020 03:10:02: #2 alternative fragment length(s) may be 4,163,185 bps INFO @ Tue, 30 Jun 2020 03:10:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.10_model.r INFO @ Tue, 30 Jun 2020 03:10:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:10:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:10:05: 4000000 INFO @ Tue, 30 Jun 2020 03:10:13: 5000000 INFO @ Tue, 30 Jun 2020 03:10:17: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:10:20: 6000000 INFO @ Tue, 30 Jun 2020 03:10:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:10:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:10:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.10_summits.bed INFO @ Tue, 30 Jun 2020 03:10:26: Done! pass1 - making usageList (271 chroms): 2 millis pass2 - checking and writing primary data (615 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:10:28: 7000000 INFO @ Tue, 30 Jun 2020 03:10:32: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:10:32: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:10:32: #1 total tags in treatment: 7427883 INFO @ Tue, 30 Jun 2020 03:10:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:10:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:10:33: #1 tags after filtering in treatment: 7427754 INFO @ Tue, 30 Jun 2020 03:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:10:33: #1 finished! INFO @ Tue, 30 Jun 2020 03:10:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:10:33: #2 number of paired peaks: 351 WARNING @ Tue, 30 Jun 2020 03:10:33: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 30 Jun 2020 03:10:33: start model_add_line... INFO @ Tue, 30 Jun 2020 03:10:33: start X-correlation... INFO @ Tue, 30 Jun 2020 03:10:33: end of X-cor INFO @ Tue, 30 Jun 2020 03:10:33: #2 finished! INFO @ Tue, 30 Jun 2020 03:10:33: #2 predicted fragment length is 185 bps INFO @ Tue, 30 Jun 2020 03:10:33: #2 alternative fragment length(s) may be 4,163,185 bps INFO @ Tue, 30 Jun 2020 03:10:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.20_model.r INFO @ Tue, 30 Jun 2020 03:10:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:10:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:10:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:10:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:10:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:10:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243667/SRX5243667.20_summits.bed INFO @ Tue, 30 Jun 2020 03:10:58: Done! pass1 - making usageList (146 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 9 millis CompletedMACS2peakCalling