Job ID = 14171808 SRX = SRX9986155 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: 00:03:19 15642258 reads; of these: 15642258 (100.00%) were unpaired; of these: 2337934 (14.95%) aligned 0 times 11256031 (71.96%) aligned exactly 1 time 2048293 (13.09%) aligned >1 times 85.05% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 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] 3100114 / 13304324 = 0.2330 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 13:03:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.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 13:03:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:03:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:03:20: 1000000 INFO @ Sat, 11 Dec 2021 13:03:26: 2000000 INFO @ Sat, 11 Dec 2021 13:03:31: 3000000 INFO @ Sat, 11 Dec 2021 13:03:36: 4000000 INFO @ Sat, 11 Dec 2021 13:03:42: 5000000 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 13:03:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.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 13:03:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:03:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:03:47: 6000000 INFO @ Sat, 11 Dec 2021 13:03:51: 1000000 INFO @ Sat, 11 Dec 2021 13:03:53: 7000000 INFO @ Sat, 11 Dec 2021 13:03:57: 2000000 INFO @ Sat, 11 Dec 2021 13:03:59: 8000000 INFO @ Sat, 11 Dec 2021 13:04:03: 3000000 INFO @ Sat, 11 Dec 2021 13:04:05: 9000000 INFO @ Sat, 11 Dec 2021 13:04:09: 4000000 INFO @ Sat, 11 Dec 2021 13:04:10: 10000000 INFO @ Sat, 11 Dec 2021 13:04:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:04:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:04:12: #1 total tags in treatment: 10204210 INFO @ Sat, 11 Dec 2021 13:04:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:04:12: #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 13:04:12: #1 tags after filtering in treatment: 10204042 INFO @ Sat, 11 Dec 2021 13:04:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:04:12: #1 finished! INFO @ Sat, 11 Dec 2021 13:04:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:04:12: #2 looking for paired plus/minus strand peaks... 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 13:04:13: #2 number of paired peaks: 474 WARNING @ Sat, 11 Dec 2021 13:04:13: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sat, 11 Dec 2021 13:04:13: start model_add_line... INFO @ Sat, 11 Dec 2021 13:04:13: start X-correlation... INFO @ Sat, 11 Dec 2021 13:04:13: end of X-cor INFO @ Sat, 11 Dec 2021 13:04:13: #2 finished! INFO @ Sat, 11 Dec 2021 13:04:13: #2 predicted fragment length is 163 bps INFO @ Sat, 11 Dec 2021 13:04:13: #2 alternative fragment length(s) may be 0,20,163,181,249 bps INFO @ Sat, 11 Dec 2021 13:04:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.05_model.r INFO @ Sat, 11 Dec 2021 13:04:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:04:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.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 13:04:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:04:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:04:15: 5000000 INFO @ Sat, 11 Dec 2021 13:04:21: 1000000 INFO @ Sat, 11 Dec 2021 13:04:21: 6000000 INFO @ Sat, 11 Dec 2021 13:04:27: 2000000 INFO @ Sat, 11 Dec 2021 13:04:28: 7000000 INFO @ Sat, 11 Dec 2021 13:04:34: 8000000 INFO @ Sat, 11 Dec 2021 13:04:34: 3000000 INFO @ Sat, 11 Dec 2021 13:04:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:04:40: 9000000 INFO @ Sat, 11 Dec 2021 13:04:41: 4000000 INFO @ Sat, 11 Dec 2021 13:04:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:04:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:04:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.05_summits.bed INFO @ Sat, 11 Dec 2021 13:04:44: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (1302 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:04:46: 10000000 INFO @ Sat, 11 Dec 2021 13:04:47: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:04:47: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:04:47: #1 total tags in treatment: 10204210 INFO @ Sat, 11 Dec 2021 13:04:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:04:47: #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 13:04:47: 5000000 INFO @ Sat, 11 Dec 2021 13:04:48: #1 tags after filtering in treatment: 10204042 INFO @ Sat, 11 Dec 2021 13:04:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:04:48: #1 finished! INFO @ Sat, 11 Dec 2021 13:04:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:04:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:04:48: #2 number of paired peaks: 474 WARNING @ Sat, 11 Dec 2021 13:04:48: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sat, 11 Dec 2021 13:04:48: start model_add_line... INFO @ Sat, 11 Dec 2021 13:04:49: start X-correlation... INFO @ Sat, 11 Dec 2021 13:04:49: end of X-cor INFO @ Sat, 11 Dec 2021 13:04:49: #2 finished! INFO @ Sat, 11 Dec 2021 13:04:49: #2 predicted fragment length is 163 bps INFO @ Sat, 11 Dec 2021 13:04:49: #2 alternative fragment length(s) may be 0,20,163,181,249 bps INFO @ Sat, 11 Dec 2021 13:04:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.10_model.r INFO @ Sat, 11 Dec 2021 13:04:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:04:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:04:54: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:05:00: 7000000 INFO @ Sat, 11 Dec 2021 13:05:07: 8000000 INFO @ Sat, 11 Dec 2021 13:05:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:05:13: 9000000 INFO @ Sat, 11 Dec 2021 13:05:19: 10000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:05:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:05:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:05:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.10_summits.bed INFO @ Sat, 11 Dec 2021 13:05:19: Done! INFO @ Sat, 11 Dec 2021 13:05:20: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:05:20: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:05:20: #1 total tags in treatment: 10204210 INFO @ Sat, 11 Dec 2021 13:05:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:05:20: #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 13:05:21: #1 tags after filtering in treatment: 10204042 INFO @ Sat, 11 Dec 2021 13:05:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:05:21: #1 finished! INFO @ Sat, 11 Dec 2021 13:05:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:05:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:05:22: #2 number of paired peaks: 474 WARNING @ Sat, 11 Dec 2021 13:05:22: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Sat, 11 Dec 2021 13:05:22: start model_add_line... INFO @ Sat, 11 Dec 2021 13:05:22: start X-correlation... INFO @ Sat, 11 Dec 2021 13:05:22: end of X-cor INFO @ Sat, 11 Dec 2021 13:05:22: #2 finished! INFO @ Sat, 11 Dec 2021 13:05:22: #2 predicted fragment length is 163 bps INFO @ Sat, 11 Dec 2021 13:05:22: #2 alternative fragment length(s) may be 0,20,163,181,249 bps INFO @ Sat, 11 Dec 2021 13:05:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.20_model.r INFO @ Sat, 11 Dec 2021 13:05:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:05:22: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (511 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:05:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:05:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986155/SRX9986155.20_summits.bed INFO @ Sat, 11 Dec 2021 13:05:52: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 1 millis CompletedMACS2peakCalling