Job ID = 6529848 SRX = SRX5243666 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: 00:02:21 8023210 reads; of these: 8023210 (100.00%) were unpaired; of these: 507678 (6.33%) aligned 0 times 5736466 (71.50%) aligned exactly 1 time 1779066 (22.17%) aligned >1 times 93.67% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 1536176 / 7515532 = 0.2044 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 03:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.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 03:07:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:07:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:07:45: 1000000 INFO @ Tue, 30 Jun 2020 03:07:50: 2000000 INFO @ Tue, 30 Jun 2020 03:07:56: 3000000 INFO @ Tue, 30 Jun 2020 03:08:02: 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 03:08:08: 5000000 INFO @ Tue, 30 Jun 2020 03:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.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 03:08:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:08:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:08:13: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:08:13: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:08:13: #1 total tags in treatment: 5979356 INFO @ Tue, 30 Jun 2020 03:08:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:08:13: #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 03:08:14: #1 tags after filtering in treatment: 5979199 INFO @ Tue, 30 Jun 2020 03:08:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:08:14: #1 finished! INFO @ Tue, 30 Jun 2020 03:08:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:08:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:08:14: #2 number of paired peaks: 462 WARNING @ Tue, 30 Jun 2020 03:08:14: Fewer paired peaks (462) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 462 pairs to build model! INFO @ Tue, 30 Jun 2020 03:08:14: start model_add_line... INFO @ Tue, 30 Jun 2020 03:08:14: start X-correlation... INFO @ Tue, 30 Jun 2020 03:08:14: end of X-cor INFO @ Tue, 30 Jun 2020 03:08:14: #2 finished! INFO @ Tue, 30 Jun 2020 03:08:14: #2 predicted fragment length is 127 bps INFO @ Tue, 30 Jun 2020 03:08:14: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 30 Jun 2020 03:08:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.05_model.r INFO @ Tue, 30 Jun 2020 03:08:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:08:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:08:15: 1000000 INFO @ Tue, 30 Jun 2020 03:08:22: 2000000 INFO @ Tue, 30 Jun 2020 03:08:28: 3000000 INFO @ Tue, 30 Jun 2020 03:08:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:08:34: 4000000 INFO @ Tue, 30 Jun 2020 03:08:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:08:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:08:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.05_summits.bed INFO @ Tue, 30 Jun 2020 03:08:36: Done! pass1 - making usageList (363 chroms): 1 millis pass2 - checking and writing primary data (1388 records, 4 fields): 13 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 @ Tue, 30 Jun 2020 03:08:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.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 03:08:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:08:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:08:41: 5000000 INFO @ Tue, 30 Jun 2020 03:08:46: 1000000 INFO @ Tue, 30 Jun 2020 03:08:47: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:08:47: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:08:47: #1 total tags in treatment: 5979356 INFO @ Tue, 30 Jun 2020 03:08:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:08:47: #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 03:08:48: #1 tags after filtering in treatment: 5979199 INFO @ Tue, 30 Jun 2020 03:08:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:08:48: #1 finished! INFO @ Tue, 30 Jun 2020 03:08:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:08:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:08:48: #2 number of paired peaks: 462 WARNING @ Tue, 30 Jun 2020 03:08:48: Fewer paired peaks (462) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 462 pairs to build model! INFO @ Tue, 30 Jun 2020 03:08:48: start model_add_line... INFO @ Tue, 30 Jun 2020 03:08:48: start X-correlation... INFO @ Tue, 30 Jun 2020 03:08:48: end of X-cor INFO @ Tue, 30 Jun 2020 03:08:48: #2 finished! INFO @ Tue, 30 Jun 2020 03:08:48: #2 predicted fragment length is 127 bps INFO @ Tue, 30 Jun 2020 03:08:48: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 30 Jun 2020 03:08:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.10_model.r INFO @ Tue, 30 Jun 2020 03:08:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:08:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:08:52: 2000000 INFO @ Tue, 30 Jun 2020 03:08:58: 3000000 INFO @ Tue, 30 Jun 2020 03:09:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:09:04: 4000000 INFO @ Tue, 30 Jun 2020 03:09:10: 5000000 INFO @ Tue, 30 Jun 2020 03:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.10_summits.bed INFO @ Tue, 30 Jun 2020 03:09:11: Done! pass1 - making usageList (246 chroms): 1 millis pass2 - checking and writing primary data (509 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:09:16: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:09:16: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:09:16: #1 total tags in treatment: 5979356 INFO @ Tue, 30 Jun 2020 03:09:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:09:16: #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 03:09:16: #1 tags after filtering in treatment: 5979199 INFO @ Tue, 30 Jun 2020 03:09:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:09:16: #1 finished! INFO @ Tue, 30 Jun 2020 03:09:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:09:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:09:17: #2 number of paired peaks: 462 WARNING @ Tue, 30 Jun 2020 03:09:17: Fewer paired peaks (462) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 462 pairs to build model! INFO @ Tue, 30 Jun 2020 03:09:17: start model_add_line... INFO @ Tue, 30 Jun 2020 03:09:17: start X-correlation... INFO @ Tue, 30 Jun 2020 03:09:17: end of X-cor INFO @ Tue, 30 Jun 2020 03:09:17: #2 finished! INFO @ Tue, 30 Jun 2020 03:09:17: #2 predicted fragment length is 127 bps INFO @ Tue, 30 Jun 2020 03:09:17: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 30 Jun 2020 03:09:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.20_model.r INFO @ Tue, 30 Jun 2020 03:09:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:09:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:09:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:09:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:09:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243666/SRX5243666.20_summits.bed INFO @ Tue, 30 Jun 2020 03:09:40: Done! pass1 - making usageList (105 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 8 millis CompletedMACS2peakCalling