Job ID = 14171706 SRX = SRX9986128 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: 00:03:14 17030863 reads; of these: 17030863 (100.00%) were unpaired; of these: 1513979 (8.89%) aligned 0 times 13255619 (77.83%) aligned exactly 1 time 2261265 (13.28%) aligned >1 times 91.11% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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] 4609188 / 15516884 = 0.2970 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 12:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.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 12:39:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:39:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:39:13: 1000000 INFO @ Sat, 11 Dec 2021 12:39:19: 2000000 INFO @ Sat, 11 Dec 2021 12:39:26: 3000000 INFO @ Sat, 11 Dec 2021 12:39:32: 4000000 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 12:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.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 12:39:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:39:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:39:38: 5000000 INFO @ Sat, 11 Dec 2021 12:39:44: 6000000 INFO @ Sat, 11 Dec 2021 12:39:44: 1000000 INFO @ Sat, 11 Dec 2021 12:39:49: 7000000 INFO @ Sat, 11 Dec 2021 12:39:50: 2000000 INFO @ Sat, 11 Dec 2021 12:39:55: 8000000 INFO @ Sat, 11 Dec 2021 12:39:56: 3000000 INFO @ Sat, 11 Dec 2021 12:40:01: 9000000 INFO @ Sat, 11 Dec 2021 12:40:03: 4000000 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 12:40:06: 10000000 INFO @ Sat, 11 Dec 2021 12:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.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 12:40:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:40:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:40:09: 5000000 INFO @ Sat, 11 Dec 2021 12:40:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:40:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:40:12: #1 total tags in treatment: 10907696 INFO @ Sat, 11 Dec 2021 12:40:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:40:12: #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 12:40:12: #1 tags after filtering in treatment: 10907541 INFO @ Sat, 11 Dec 2021 12:40:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:40:12: #1 finished! INFO @ Sat, 11 Dec 2021 12:40:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:40:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:40:13: 1000000 INFO @ Sat, 11 Dec 2021 12:40:13: #2 number of paired peaks: 484 WARNING @ Sat, 11 Dec 2021 12:40:13: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Sat, 11 Dec 2021 12:40:13: start model_add_line... INFO @ Sat, 11 Dec 2021 12:40:13: start X-correlation... INFO @ Sat, 11 Dec 2021 12:40:13: end of X-cor INFO @ Sat, 11 Dec 2021 12:40:13: #2 finished! INFO @ Sat, 11 Dec 2021 12:40:13: #2 predicted fragment length is 193 bps INFO @ Sat, 11 Dec 2021 12:40:13: #2 alternative fragment length(s) may be 2,153,170,193,228 bps INFO @ Sat, 11 Dec 2021 12:40:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.05_model.r INFO @ Sat, 11 Dec 2021 12:40:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:40:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:40:15: 6000000 INFO @ Sat, 11 Dec 2021 12:40:19: 2000000 INFO @ Sat, 11 Dec 2021 12:40:22: 7000000 INFO @ Sat, 11 Dec 2021 12:40:24: 3000000 INFO @ Sat, 11 Dec 2021 12:40:28: 8000000 INFO @ Sat, 11 Dec 2021 12:40:30: 4000000 INFO @ Sat, 11 Dec 2021 12:40:35: 9000000 INFO @ Sat, 11 Dec 2021 12:40:35: 5000000 INFO @ Sat, 11 Dec 2021 12:40:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:40:41: 10000000 INFO @ Sat, 11 Dec 2021 12:40:41: 6000000 INFO @ Sat, 11 Dec 2021 12:40:47: 7000000 INFO @ Sat, 11 Dec 2021 12:40:47: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:40:47: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:40:47: #1 total tags in treatment: 10907696 INFO @ Sat, 11 Dec 2021 12:40:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:40:47: #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 12:40:47: #1 tags after filtering in treatment: 10907541 INFO @ Sat, 11 Dec 2021 12:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:40:47: #1 finished! INFO @ Sat, 11 Dec 2021 12:40:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:40:48: #2 number of paired peaks: 484 WARNING @ Sat, 11 Dec 2021 12:40:48: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Sat, 11 Dec 2021 12:40:48: start model_add_line... INFO @ Sat, 11 Dec 2021 12:40:48: start X-correlation... INFO @ Sat, 11 Dec 2021 12:40:48: end of X-cor INFO @ Sat, 11 Dec 2021 12:40:48: #2 finished! INFO @ Sat, 11 Dec 2021 12:40:48: #2 predicted fragment length is 193 bps INFO @ Sat, 11 Dec 2021 12:40:48: #2 alternative fragment length(s) may be 2,153,170,193,228 bps INFO @ Sat, 11 Dec 2021 12:40:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.10_model.r INFO @ Sat, 11 Dec 2021 12:40:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:40:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:40:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:40:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:40:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.05_summits.bed INFO @ Sat, 11 Dec 2021 12:40:50: Done! pass1 - making usageList (86 chroms): 2 millis pass2 - checking and writing primary data (4811 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:40:52: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:40:58: 9000000 INFO @ Sat, 11 Dec 2021 12:41:02: 10000000 INFO @ Sat, 11 Dec 2021 12:41:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:41:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:41:07: #1 total tags in treatment: 10907696 INFO @ Sat, 11 Dec 2021 12:41:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:41:07: #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 12:41:07: #1 tags after filtering in treatment: 10907541 INFO @ Sat, 11 Dec 2021 12:41:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:41:07: #1 finished! INFO @ Sat, 11 Dec 2021 12:41:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:41:08: #2 number of paired peaks: 484 WARNING @ Sat, 11 Dec 2021 12:41:08: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Sat, 11 Dec 2021 12:41:08: start model_add_line... INFO @ Sat, 11 Dec 2021 12:41:08: start X-correlation... INFO @ Sat, 11 Dec 2021 12:41:08: end of X-cor INFO @ Sat, 11 Dec 2021 12:41:08: #2 finished! INFO @ Sat, 11 Dec 2021 12:41:08: #2 predicted fragment length is 193 bps INFO @ Sat, 11 Dec 2021 12:41:08: #2 alternative fragment length(s) may be 2,153,170,193,228 bps INFO @ Sat, 11 Dec 2021 12:41:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.20_model.r INFO @ Sat, 11 Dec 2021 12:41:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:41:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:41:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:41:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:41:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:41:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.10_summits.bed INFO @ Sat, 11 Dec 2021 12:41:26: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (1373 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:41:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986128/SRX9986128.20_summits.bed INFO @ Sat, 11 Dec 2021 12:41:44: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 2 millis CompletedMACS2peakCalling