Job ID = 16439675 SRX = SRX13572052 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: 00:02:59 10683736 reads; of these: 10683736 (100.00%) were unpaired; of these: 506637 (4.74%) aligned 0 times 8674394 (81.19%) aligned exactly 1 time 1502705 (14.07%) aligned >1 times 95.26% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 882229 / 10177099 = 0.0867 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 16:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.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 16:00:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:00:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:00:53: 1000000 INFO @ Tue, 02 Aug 2022 16:01:02: 2000000 INFO @ Tue, 02 Aug 2022 16:01:10: 3000000 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 16:01:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.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 16:01:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:01:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:01:19: 4000000 INFO @ Tue, 02 Aug 2022 16:01:25: 1000000 INFO @ Tue, 02 Aug 2022 16:01:27: 5000000 INFO @ Tue, 02 Aug 2022 16:01:34: 2000000 INFO @ Tue, 02 Aug 2022 16:01:36: 6000000 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 16:01:43: 3000000 INFO @ Tue, 02 Aug 2022 16:01:45: 7000000 INFO @ Tue, 02 Aug 2022 16:01:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.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 16:01:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:01:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:01:51: 4000000 INFO @ Tue, 02 Aug 2022 16:01:55: 8000000 INFO @ Tue, 02 Aug 2022 16:01:55: 1000000 INFO @ Tue, 02 Aug 2022 16:02:00: 5000000 INFO @ Tue, 02 Aug 2022 16:02:04: 9000000 INFO @ Tue, 02 Aug 2022 16:02:04: 2000000 INFO @ Tue, 02 Aug 2022 16:02:07: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:02:07: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:02:07: #1 total tags in treatment: 9294870 INFO @ Tue, 02 Aug 2022 16:02:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:02:07: #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 16:02:07: #1 tags after filtering in treatment: 9294834 INFO @ Tue, 02 Aug 2022 16:02:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:02:07: #1 finished! INFO @ Tue, 02 Aug 2022 16:02:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:02:08: 6000000 INFO @ Tue, 02 Aug 2022 16:02:08: #2 number of paired peaks: 211 WARNING @ Tue, 02 Aug 2022 16:02:08: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 02 Aug 2022 16:02:08: start model_add_line... INFO @ Tue, 02 Aug 2022 16:02:08: start X-correlation... INFO @ Tue, 02 Aug 2022 16:02:08: end of X-cor INFO @ Tue, 02 Aug 2022 16:02:08: #2 finished! INFO @ Tue, 02 Aug 2022 16:02:08: #2 predicted fragment length is 147 bps INFO @ Tue, 02 Aug 2022 16:02:08: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 02 Aug 2022 16:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.05_model.r INFO @ Tue, 02 Aug 2022 16:02:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:02:12: 3000000 INFO @ Tue, 02 Aug 2022 16:02:16: 7000000 INFO @ Tue, 02 Aug 2022 16:02:21: 4000000 INFO @ Tue, 02 Aug 2022 16:02:25: 8000000 INFO @ Tue, 02 Aug 2022 16:02:29: 5000000 INFO @ Tue, 02 Aug 2022 16:02:33: 9000000 INFO @ Tue, 02 Aug 2022 16:02:36: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:02:36: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:02:36: #1 total tags in treatment: 9294870 INFO @ Tue, 02 Aug 2022 16:02:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:02:36: #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 16:02:36: #1 tags after filtering in treatment: 9294834 INFO @ Tue, 02 Aug 2022 16:02:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:02:36: #1 finished! INFO @ Tue, 02 Aug 2022 16:02:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:02:37: 6000000 INFO @ Tue, 02 Aug 2022 16:02:37: #2 number of paired peaks: 211 WARNING @ Tue, 02 Aug 2022 16:02:37: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 02 Aug 2022 16:02:37: start model_add_line... INFO @ Tue, 02 Aug 2022 16:02:37: start X-correlation... INFO @ Tue, 02 Aug 2022 16:02:37: end of X-cor INFO @ Tue, 02 Aug 2022 16:02:37: #2 finished! INFO @ Tue, 02 Aug 2022 16:02:37: #2 predicted fragment length is 147 bps INFO @ Tue, 02 Aug 2022 16:02:37: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 02 Aug 2022 16:02:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.10_model.r INFO @ Tue, 02 Aug 2022 16:02:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:02:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:02:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:02:46: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.05_summits.bed INFO @ Tue, 02 Aug 2022 16:02:53: Done! pass1 - making usageList (327 chroms): 2 millis pass2 - checking and writing primary data (1067 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:02:56: 8000000 INFO @ Tue, 02 Aug 2022 16:03:04: 9000000 INFO @ Tue, 02 Aug 2022 16:03:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:03:07: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:03:07: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:03:07: #1 total tags in treatment: 9294870 INFO @ Tue, 02 Aug 2022 16:03:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:03:07: #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 16:03:08: #1 tags after filtering in treatment: 9294834 INFO @ Tue, 02 Aug 2022 16:03:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:03:08: #1 finished! INFO @ Tue, 02 Aug 2022 16:03:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:03:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:03:09: #2 number of paired peaks: 211 WARNING @ Tue, 02 Aug 2022 16:03:09: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 02 Aug 2022 16:03:09: start model_add_line... INFO @ Tue, 02 Aug 2022 16:03:09: start X-correlation... INFO @ Tue, 02 Aug 2022 16:03:09: end of X-cor INFO @ Tue, 02 Aug 2022 16:03:09: #2 finished! INFO @ Tue, 02 Aug 2022 16:03:09: #2 predicted fragment length is 147 bps INFO @ Tue, 02 Aug 2022 16:03:09: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 02 Aug 2022 16:03:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.20_model.r INFO @ Tue, 02 Aug 2022 16:03:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:03:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:03:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:03:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.10_summits.bed INFO @ Tue, 02 Aug 2022 16:03:22: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (551 records, 4 fields): 30 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:03:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:03:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:03:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:03:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572052/SRX13572052.20_summits.bed INFO @ Tue, 02 Aug 2022 16:03:53: Done! pass1 - making usageList (87 chroms): 3 millis pass2 - checking and writing primary data (265 records, 4 fields): 17 millis CompletedMACS2peakCalling