Job ID = 16439290 SRX = SRX15206452 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:09 12830987 reads; of these: 12830987 (100.00%) were unpaired; of these: 225119 (1.75%) aligned 0 times 11346396 (88.43%) aligned exactly 1 time 1259472 (9.82%) aligned >1 times 98.25% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 842350 / 12605868 = 0.0668 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.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, 02 Aug 2022 15:00:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:00:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:00:55: 1000000 INFO @ Tue, 02 Aug 2022 15:01:04: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:01:14: 3000000 INFO @ Tue, 02 Aug 2022 15:01:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.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, 02 Aug 2022 15:01:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:01:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:01:23: 4000000 INFO @ Tue, 02 Aug 2022 15:01:25: 1000000 INFO @ Tue, 02 Aug 2022 15:01:33: 5000000 INFO @ Tue, 02 Aug 2022 15:01:35: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:01:43: 6000000 INFO @ Tue, 02 Aug 2022 15:01:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.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, 02 Aug 2022 15:01:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:01:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:01:46: 3000000 INFO @ Tue, 02 Aug 2022 15:01:54: 7000000 INFO @ Tue, 02 Aug 2022 15:01:55: 1000000 INFO @ Tue, 02 Aug 2022 15:01:56: 4000000 INFO @ Tue, 02 Aug 2022 15:02:04: 8000000 INFO @ Tue, 02 Aug 2022 15:02:05: 2000000 INFO @ Tue, 02 Aug 2022 15:02:06: 5000000 INFO @ Tue, 02 Aug 2022 15:02:14: 9000000 INFO @ Tue, 02 Aug 2022 15:02:15: 3000000 INFO @ Tue, 02 Aug 2022 15:02:16: 6000000 INFO @ Tue, 02 Aug 2022 15:02:25: 4000000 INFO @ Tue, 02 Aug 2022 15:02:25: 10000000 INFO @ Tue, 02 Aug 2022 15:02:27: 7000000 INFO @ Tue, 02 Aug 2022 15:02:34: 5000000 INFO @ Tue, 02 Aug 2022 15:02:36: 11000000 INFO @ Tue, 02 Aug 2022 15:02:38: 8000000 INFO @ Tue, 02 Aug 2022 15:02:44: 6000000 INFO @ Tue, 02 Aug 2022 15:02:45: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:02:45: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:02:45: #1 total tags in treatment: 11763518 INFO @ Tue, 02 Aug 2022 15:02:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:02:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:02:45: #1 tags after filtering in treatment: 11763323 INFO @ Tue, 02 Aug 2022 15:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:02:45: #1 finished! INFO @ Tue, 02 Aug 2022 15:02:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:02:46: #2 number of paired peaks: 222 WARNING @ Tue, 02 Aug 2022 15:02:46: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 02 Aug 2022 15:02:46: start model_add_line... INFO @ Tue, 02 Aug 2022 15:02:46: start X-correlation... INFO @ Tue, 02 Aug 2022 15:02:47: end of X-cor INFO @ Tue, 02 Aug 2022 15:02:47: #2 finished! INFO @ Tue, 02 Aug 2022 15:02:47: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 15:02:47: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 02 Aug 2022 15:02:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.05_model.r INFO @ Tue, 02 Aug 2022 15:02:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:02:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:02:48: 9000000 INFO @ Tue, 02 Aug 2022 15:02:54: 7000000 INFO @ Tue, 02 Aug 2022 15:02:58: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:03:03: 8000000 INFO @ Tue, 02 Aug 2022 15:03:08: 11000000 INFO @ Tue, 02 Aug 2022 15:03:13: 9000000 INFO @ Tue, 02 Aug 2022 15:03:16: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:03:16: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:03:16: #1 total tags in treatment: 11763518 INFO @ Tue, 02 Aug 2022 15:03:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:03:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:03:17: #1 tags after filtering in treatment: 11763323 INFO @ Tue, 02 Aug 2022 15:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:03:17: #1 finished! INFO @ Tue, 02 Aug 2022 15:03:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:03:18: #2 number of paired peaks: 222 WARNING @ Tue, 02 Aug 2022 15:03:18: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 02 Aug 2022 15:03:18: start model_add_line... INFO @ Tue, 02 Aug 2022 15:03:18: start X-correlation... INFO @ Tue, 02 Aug 2022 15:03:18: end of X-cor INFO @ Tue, 02 Aug 2022 15:03:18: #2 finished! INFO @ Tue, 02 Aug 2022 15:03:18: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 15:03:18: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 02 Aug 2022 15:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.10_model.r INFO @ Tue, 02 Aug 2022 15:03:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:03:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:03:23: 10000000 INFO @ Tue, 02 Aug 2022 15:03:32: 11000000 INFO @ Tue, 02 Aug 2022 15:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:03:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:03:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:03:40: #1 total tags in treatment: 11763518 INFO @ Tue, 02 Aug 2022 15:03:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:03:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.05_summits.bed INFO @ Tue, 02 Aug 2022 15:03:40: Done! pass1 - making usageList (91 chroms): 2 millis pass2 - checking and writing primary data (630 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:03:40: #1 tags after filtering in treatment: 11763323 INFO @ Tue, 02 Aug 2022 15:03:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:03:40: #1 finished! INFO @ Tue, 02 Aug 2022 15:03:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:03:40: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:03:41: #2 number of paired peaks: 222 WARNING @ Tue, 02 Aug 2022 15:03:41: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 02 Aug 2022 15:03:41: start model_add_line... INFO @ Tue, 02 Aug 2022 15:03:41: start X-correlation... INFO @ Tue, 02 Aug 2022 15:03:41: end of X-cor INFO @ Tue, 02 Aug 2022 15:03:41: #2 finished! INFO @ Tue, 02 Aug 2022 15:03:41: #2 predicted fragment length is 183 bps INFO @ Tue, 02 Aug 2022 15:03:41: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 02 Aug 2022 15:03:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.20_model.r INFO @ Tue, 02 Aug 2022 15:03:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:03:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:03:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:04:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.10_summits.bed INFO @ Tue, 02 Aug 2022 15:04:10: Done! pass1 - making usageList (70 chroms): 2 millis pass2 - checking and writing primary data (197 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:04:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:04:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206452/SRX15206452.20_summits.bed INFO @ Tue, 02 Aug 2022 15:04:34: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (109 records, 4 fields): 42 millis CompletedMACS2peakCalling