Job ID = 14171713 SRX = SRX9986125 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: 00:04:54 21282879 reads; of these: 21282879 (100.00%) were unpaired; of these: 1994519 (9.37%) aligned 0 times 16554056 (77.78%) aligned exactly 1 time 2734304 (12.85%) aligned >1 times 90.63% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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_sort_core] merging from 8 files... [bam_rmdupse_core] 7034702 / 19288360 = 0.3647 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.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 @ Sat, 11 Dec 2021 12:44:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:44:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:44:16: 1000000 INFO @ Sat, 11 Dec 2021 12:44:23: 2000000 INFO @ Sat, 11 Dec 2021 12:44:31: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:44:38: 4000000 INFO @ Sat, 11 Dec 2021 12:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.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 @ Sat, 11 Dec 2021 12:44:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:44:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:44:46: 5000000 INFO @ Sat, 11 Dec 2021 12:44:46: 1000000 INFO @ Sat, 11 Dec 2021 12:44:53: 6000000 INFO @ Sat, 11 Dec 2021 12:44:54: 2000000 INFO @ Sat, 11 Dec 2021 12:45:01: 7000000 INFO @ Sat, 11 Dec 2021 12:45:01: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.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 @ Sat, 11 Dec 2021 12:45:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:45:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:45:08: 8000000 INFO @ Sat, 11 Dec 2021 12:45:09: 4000000 INFO @ Sat, 11 Dec 2021 12:45:16: 9000000 INFO @ Sat, 11 Dec 2021 12:45:16: 1000000 INFO @ Sat, 11 Dec 2021 12:45:16: 5000000 INFO @ Sat, 11 Dec 2021 12:45:24: 2000000 INFO @ Sat, 11 Dec 2021 12:45:24: 6000000 INFO @ Sat, 11 Dec 2021 12:45:24: 10000000 INFO @ Sat, 11 Dec 2021 12:45:31: 3000000 INFO @ Sat, 11 Dec 2021 12:45:31: 7000000 INFO @ Sat, 11 Dec 2021 12:45:32: 11000000 INFO @ Sat, 11 Dec 2021 12:45:39: 4000000 INFO @ Sat, 11 Dec 2021 12:45:39: 8000000 INFO @ Sat, 11 Dec 2021 12:45:40: 12000000 INFO @ Sat, 11 Dec 2021 12:45:42: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:45:42: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:45:42: #1 total tags in treatment: 12253658 INFO @ Sat, 11 Dec 2021 12:45:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:45:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:45:42: #1 tags after filtering in treatment: 12253546 INFO @ Sat, 11 Dec 2021 12:45:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:45:42: #1 finished! INFO @ Sat, 11 Dec 2021 12:45:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:45:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:45:43: #2 number of paired peaks: 643 WARNING @ Sat, 11 Dec 2021 12:45:43: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sat, 11 Dec 2021 12:45:43: start model_add_line... INFO @ Sat, 11 Dec 2021 12:45:44: start X-correlation... INFO @ Sat, 11 Dec 2021 12:45:44: end of X-cor INFO @ Sat, 11 Dec 2021 12:45:44: #2 finished! INFO @ Sat, 11 Dec 2021 12:45:44: #2 predicted fragment length is 255 bps INFO @ Sat, 11 Dec 2021 12:45:44: #2 alternative fragment length(s) may be 4,255 bps INFO @ Sat, 11 Dec 2021 12:45:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.05_model.r INFO @ Sat, 11 Dec 2021 12:45:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:45:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:45:46: 5000000 INFO @ Sat, 11 Dec 2021 12:45:47: 9000000 INFO @ Sat, 11 Dec 2021 12:45:54: 6000000 INFO @ Sat, 11 Dec 2021 12:45:55: 10000000 INFO @ Sat, 11 Dec 2021 12:46:01: 7000000 INFO @ Sat, 11 Dec 2021 12:46:02: 11000000 INFO @ Sat, 11 Dec 2021 12:46:08: 8000000 INFO @ Sat, 11 Dec 2021 12:46:10: 12000000 INFO @ Sat, 11 Dec 2021 12:46:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:46:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:46:12: #1 total tags in treatment: 12253658 INFO @ Sat, 11 Dec 2021 12:46:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:46:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:46:13: #1 tags after filtering in treatment: 12253546 INFO @ Sat, 11 Dec 2021 12:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:46:13: #1 finished! INFO @ Sat, 11 Dec 2021 12:46:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:46:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:46:13: #2 number of paired peaks: 643 WARNING @ Sat, 11 Dec 2021 12:46:13: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sat, 11 Dec 2021 12:46:13: start model_add_line... INFO @ Sat, 11 Dec 2021 12:46:14: start X-correlation... INFO @ Sat, 11 Dec 2021 12:46:14: end of X-cor INFO @ Sat, 11 Dec 2021 12:46:14: #2 finished! INFO @ Sat, 11 Dec 2021 12:46:14: #2 predicted fragment length is 255 bps INFO @ Sat, 11 Dec 2021 12:46:14: #2 alternative fragment length(s) may be 4,255 bps INFO @ Sat, 11 Dec 2021 12:46:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.10_model.r INFO @ Sat, 11 Dec 2021 12:46:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:46:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:46:14: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:46:16: 9000000 INFO @ Sat, 11 Dec 2021 12:46:24: 10000000 INFO @ Sat, 11 Dec 2021 12:46:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:46:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:46:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.05_summits.bed INFO @ Sat, 11 Dec 2021 12:46:31: Done! pass1 - making usageList (87 chroms): 2 millis pass2 - checking and writing primary data (6541 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:46:32: 11000000 INFO @ Sat, 11 Dec 2021 12:46:39: 12000000 INFO @ Sat, 11 Dec 2021 12:46:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:46:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:46:41: #1 total tags in treatment: 12253658 INFO @ Sat, 11 Dec 2021 12:46:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:46:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:46:42: #1 tags after filtering in treatment: 12253546 INFO @ Sat, 11 Dec 2021 12:46:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:46:42: #1 finished! INFO @ Sat, 11 Dec 2021 12:46:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:46:43: #2 number of paired peaks: 643 WARNING @ Sat, 11 Dec 2021 12:46:43: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sat, 11 Dec 2021 12:46:43: start model_add_line... INFO @ Sat, 11 Dec 2021 12:46:43: start X-correlation... INFO @ Sat, 11 Dec 2021 12:46:43: end of X-cor INFO @ Sat, 11 Dec 2021 12:46:43: #2 finished! INFO @ Sat, 11 Dec 2021 12:46:43: #2 predicted fragment length is 255 bps INFO @ Sat, 11 Dec 2021 12:46:43: #2 alternative fragment length(s) may be 4,255 bps INFO @ Sat, 11 Dec 2021 12:46:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.20_model.r INFO @ Sat, 11 Dec 2021 12:46:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:46:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.10_summits.bed INFO @ Sat, 11 Dec 2021 12:47:00: Done! pass1 - making usageList (58 chroms): 2 millis pass2 - checking and writing primary data (2669 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:47:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:47:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:47:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:47:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986125/SRX9986125.20_summits.bed INFO @ Sat, 11 Dec 2021 12:47:29: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (710 records, 4 fields): 5 millis CompletedMACS2peakCalling