Job ID = 14172610 SRX = SRX9891435 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: 00:05:02 18811805 reads; of these: 18811805 (100.00%) were unpaired; of these: 2722211 (14.47%) aligned 0 times 13900742 (73.89%) aligned exactly 1 time 2188852 (11.64%) aligned >1 times 85.53% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 2082568 / 16089594 = 0.1294 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 16:20:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.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 16:20:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:20:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:20:06: 1000000 INFO @ Sat, 11 Dec 2021 16:20:11: 2000000 INFO @ Sat, 11 Dec 2021 16:20:16: 3000000 INFO @ Sat, 11 Dec 2021 16:20:21: 4000000 INFO @ Sat, 11 Dec 2021 16:20:27: 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 16:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.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 16:20:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:20:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:20:32: 6000000 INFO @ Sat, 11 Dec 2021 16:20:36: 1000000 INFO @ Sat, 11 Dec 2021 16:20:38: 7000000 INFO @ Sat, 11 Dec 2021 16:20:42: 2000000 INFO @ Sat, 11 Dec 2021 16:20:43: 8000000 INFO @ Sat, 11 Dec 2021 16:20:47: 3000000 INFO @ Sat, 11 Dec 2021 16:20:49: 9000000 INFO @ Sat, 11 Dec 2021 16:20:53: 4000000 INFO @ Sat, 11 Dec 2021 16:20:55: 10000000 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 16:20:59: 5000000 INFO @ Sat, 11 Dec 2021 16:21:00: 11000000 INFO @ Sat, 11 Dec 2021 16:21:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.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 16:21:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:21:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:21:04: 6000000 INFO @ Sat, 11 Dec 2021 16:21:06: 1000000 INFO @ Sat, 11 Dec 2021 16:21:06: 12000000 INFO @ Sat, 11 Dec 2021 16:21:10: 7000000 INFO @ Sat, 11 Dec 2021 16:21:12: 2000000 INFO @ Sat, 11 Dec 2021 16:21:12: 13000000 INFO @ Sat, 11 Dec 2021 16:21:16: 8000000 INFO @ Sat, 11 Dec 2021 16:21:18: 3000000 INFO @ Sat, 11 Dec 2021 16:21:18: 14000000 INFO @ Sat, 11 Dec 2021 16:21:18: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 16:21:18: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 16:21:18: #1 total tags in treatment: 14007026 INFO @ Sat, 11 Dec 2021 16:21:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:21:18: #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 16:21:19: #1 tags after filtering in treatment: 14007003 INFO @ Sat, 11 Dec 2021 16:21:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:21:19: #1 finished! INFO @ Sat, 11 Dec 2021 16:21:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:21:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:21:20: #2 number of paired peaks: 389 WARNING @ Sat, 11 Dec 2021 16:21:20: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Sat, 11 Dec 2021 16:21:20: start model_add_line... INFO @ Sat, 11 Dec 2021 16:21:20: start X-correlation... INFO @ Sat, 11 Dec 2021 16:21:20: end of X-cor INFO @ Sat, 11 Dec 2021 16:21:20: #2 finished! INFO @ Sat, 11 Dec 2021 16:21:20: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 16:21:20: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 11 Dec 2021 16:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.05_model.r INFO @ Sat, 11 Dec 2021 16:21:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:21:22: 9000000 INFO @ Sat, 11 Dec 2021 16:21:23: 4000000 INFO @ Sat, 11 Dec 2021 16:21:27: 10000000 INFO @ Sat, 11 Dec 2021 16:21:29: 5000000 INFO @ Sat, 11 Dec 2021 16:21:33: 11000000 INFO @ Sat, 11 Dec 2021 16:21:35: 6000000 INFO @ Sat, 11 Dec 2021 16:21:39: 12000000 INFO @ Sat, 11 Dec 2021 16:21:40: 7000000 INFO @ Sat, 11 Dec 2021 16:21:45: 13000000 INFO @ Sat, 11 Dec 2021 16:21:46: 8000000 INFO @ Sat, 11 Dec 2021 16:21:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:21:51: 14000000 INFO @ Sat, 11 Dec 2021 16:21:51: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 16:21:51: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 16:21:51: #1 total tags in treatment: 14007026 INFO @ Sat, 11 Dec 2021 16:21:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:21:51: #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 16:21:52: #1 tags after filtering in treatment: 14007003 INFO @ Sat, 11 Dec 2021 16:21:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:21:52: #1 finished! INFO @ Sat, 11 Dec 2021 16:21:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:21:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:21:52: 9000000 INFO @ Sat, 11 Dec 2021 16:21:53: #2 number of paired peaks: 389 WARNING @ Sat, 11 Dec 2021 16:21:53: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Sat, 11 Dec 2021 16:21:53: start model_add_line... INFO @ Sat, 11 Dec 2021 16:21:53: start X-correlation... INFO @ Sat, 11 Dec 2021 16:21:53: end of X-cor INFO @ Sat, 11 Dec 2021 16:21:53: #2 finished! INFO @ Sat, 11 Dec 2021 16:21:53: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 16:21:53: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 11 Dec 2021 16:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.10_model.r INFO @ Sat, 11 Dec 2021 16:21:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:21:57: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:22:03: 11000000 INFO @ Sat, 11 Dec 2021 16:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.05_summits.bed INFO @ Sat, 11 Dec 2021 16:22:05: Done! pass1 - making usageList (364 chroms): 2 millis pass2 - checking and writing primary data (8067 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:22:08: 12000000 INFO @ Sat, 11 Dec 2021 16:22:14: 13000000 INFO @ Sat, 11 Dec 2021 16:22:19: 14000000 INFO @ Sat, 11 Dec 2021 16:22:19: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 16:22:19: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 16:22:19: #1 total tags in treatment: 14007026 INFO @ Sat, 11 Dec 2021 16:22:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:22:19: #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 16:22:20: #1 tags after filtering in treatment: 14007003 INFO @ Sat, 11 Dec 2021 16:22:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:22:20: #1 finished! INFO @ Sat, 11 Dec 2021 16:22:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:22:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:22:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:22:21: #2 number of paired peaks: 389 WARNING @ Sat, 11 Dec 2021 16:22:21: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Sat, 11 Dec 2021 16:22:21: start model_add_line... INFO @ Sat, 11 Dec 2021 16:22:21: start X-correlation... INFO @ Sat, 11 Dec 2021 16:22:21: end of X-cor INFO @ Sat, 11 Dec 2021 16:22:21: #2 finished! INFO @ Sat, 11 Dec 2021 16:22:21: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 16:22:21: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 11 Dec 2021 16:22:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.20_model.r INFO @ Sat, 11 Dec 2021 16:22:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:22:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:22:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:22:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:22:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.10_summits.bed INFO @ Sat, 11 Dec 2021 16:22:34: Done! pass1 - making usageList (260 chroms): 1 millis pass2 - checking and writing primary data (2850 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:22:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:23:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:23:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:23:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9891435/SRX9891435.20_summits.bed INFO @ Sat, 11 Dec 2021 16:23:03: Done! pass1 - making usageList (130 chroms): 1 millis pass2 - checking and writing primary data (1044 records, 4 fields): 7 millis CompletedMACS2peakCalling