Job ID = 16439682 SRX = SRX13572056 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: 00:04:05 15741169 reads; of these: 15741169 (100.00%) were unpaired; of these: 794657 (5.05%) aligned 0 times 12757354 (81.04%) aligned exactly 1 time 2189158 (13.91%) aligned >1 times 94.95% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 1287788 / 14946512 = 0.0862 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 16:03:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.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 16:03:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:03:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:03:42: 1000000 INFO @ Tue, 02 Aug 2022 16:03:49: 2000000 INFO @ Tue, 02 Aug 2022 16:03:56: 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 16:04:03: 4000000 INFO @ Tue, 02 Aug 2022 16:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.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 16:04:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:04:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:04:10: 5000000 INFO @ Tue, 02 Aug 2022 16:04:12: 1000000 INFO @ Tue, 02 Aug 2022 16:04:17: 6000000 INFO @ Tue, 02 Aug 2022 16:04:20: 2000000 INFO @ Tue, 02 Aug 2022 16:04:25: 7000000 INFO @ Tue, 02 Aug 2022 16:04:28: 3000000 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 16:04:33: 8000000 INFO @ Tue, 02 Aug 2022 16:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.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 16:04:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:04:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:04:36: 4000000 INFO @ Tue, 02 Aug 2022 16:04:40: 9000000 INFO @ Tue, 02 Aug 2022 16:04:42: 1000000 INFO @ Tue, 02 Aug 2022 16:04:44: 5000000 INFO @ Tue, 02 Aug 2022 16:04:47: 10000000 INFO @ Tue, 02 Aug 2022 16:04:49: 2000000 INFO @ Tue, 02 Aug 2022 16:04:52: 6000000 INFO @ Tue, 02 Aug 2022 16:04:55: 11000000 INFO @ Tue, 02 Aug 2022 16:04:57: 3000000 INFO @ Tue, 02 Aug 2022 16:05:00: 7000000 INFO @ Tue, 02 Aug 2022 16:05:03: 12000000 INFO @ Tue, 02 Aug 2022 16:05:04: 4000000 INFO @ Tue, 02 Aug 2022 16:05:09: 8000000 INFO @ Tue, 02 Aug 2022 16:05:11: 13000000 INFO @ Tue, 02 Aug 2022 16:05:12: 5000000 INFO @ Tue, 02 Aug 2022 16:05:16: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:05:16: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:05:16: #1 total tags in treatment: 13658724 INFO @ Tue, 02 Aug 2022 16:05:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:05:16: #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 16:05:17: #1 tags after filtering in treatment: 13658694 INFO @ Tue, 02 Aug 2022 16:05:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:05:17: #1 finished! INFO @ Tue, 02 Aug 2022 16:05:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:05:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:05:17: 9000000 INFO @ Tue, 02 Aug 2022 16:05:18: #2 number of paired peaks: 172 WARNING @ Tue, 02 Aug 2022 16:05:18: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Tue, 02 Aug 2022 16:05:18: start model_add_line... INFO @ Tue, 02 Aug 2022 16:05:18: start X-correlation... INFO @ Tue, 02 Aug 2022 16:05:18: end of X-cor INFO @ Tue, 02 Aug 2022 16:05:18: #2 finished! INFO @ Tue, 02 Aug 2022 16:05:18: #2 predicted fragment length is 136 bps INFO @ Tue, 02 Aug 2022 16:05:18: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 02 Aug 2022 16:05:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.05_model.r INFO @ Tue, 02 Aug 2022 16:05:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:05:19: 6000000 INFO @ Tue, 02 Aug 2022 16:05:25: 10000000 INFO @ Tue, 02 Aug 2022 16:05:27: 7000000 INFO @ Tue, 02 Aug 2022 16:05:33: 11000000 INFO @ Tue, 02 Aug 2022 16:05:35: 8000000 INFO @ Tue, 02 Aug 2022 16:05:42: 9000000 INFO @ Tue, 02 Aug 2022 16:05:42: 12000000 INFO @ Tue, 02 Aug 2022 16:05:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:05:49: 10000000 INFO @ Tue, 02 Aug 2022 16:05:50: 13000000 INFO @ Tue, 02 Aug 2022 16:05:56: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:05:56: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:05:56: #1 total tags in treatment: 13658724 INFO @ Tue, 02 Aug 2022 16:05:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:05:56: #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 16:05:57: 11000000 INFO @ Tue, 02 Aug 2022 16:05:57: #1 tags after filtering in treatment: 13658694 INFO @ Tue, 02 Aug 2022 16:05:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:05:57: #1 finished! INFO @ Tue, 02 Aug 2022 16:05:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:05:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:05:58: #2 number of paired peaks: 172 WARNING @ Tue, 02 Aug 2022 16:05:58: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Tue, 02 Aug 2022 16:05:58: start model_add_line... INFO @ Tue, 02 Aug 2022 16:05:58: start X-correlation... INFO @ Tue, 02 Aug 2022 16:05:58: end of X-cor INFO @ Tue, 02 Aug 2022 16:05:58: #2 finished! INFO @ Tue, 02 Aug 2022 16:05:58: #2 predicted fragment length is 136 bps INFO @ Tue, 02 Aug 2022 16:05:58: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 02 Aug 2022 16:05:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.10_model.r INFO @ Tue, 02 Aug 2022 16:05:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:05:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.05_summits.bed INFO @ Tue, 02 Aug 2022 16:05:59: Done! pass1 - making usageList (373 chroms): 1 millis pass2 - checking and writing primary data (1296 records, 4 fields): 107 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:06:05: 12000000 INFO @ Tue, 02 Aug 2022 16:06:12: 13000000 INFO @ Tue, 02 Aug 2022 16:06:17: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:06:17: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:06:17: #1 total tags in treatment: 13658724 INFO @ Tue, 02 Aug 2022 16:06:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:06:17: #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 16:06:18: #1 tags after filtering in treatment: 13658694 INFO @ Tue, 02 Aug 2022 16:06:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:06:18: #1 finished! INFO @ Tue, 02 Aug 2022 16:06:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:06:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:06:19: #2 number of paired peaks: 172 WARNING @ Tue, 02 Aug 2022 16:06:19: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Tue, 02 Aug 2022 16:06:19: start model_add_line... INFO @ Tue, 02 Aug 2022 16:06:19: start X-correlation... INFO @ Tue, 02 Aug 2022 16:06:19: end of X-cor INFO @ Tue, 02 Aug 2022 16:06:19: #2 finished! INFO @ Tue, 02 Aug 2022 16:06:19: #2 predicted fragment length is 136 bps INFO @ Tue, 02 Aug 2022 16:06:19: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 02 Aug 2022 16:06:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.20_model.r INFO @ Tue, 02 Aug 2022 16:06:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:06:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:06:24: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:06:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:06:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:06:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.10_summits.bed INFO @ Tue, 02 Aug 2022 16:06:38: Done! pass1 - making usageList (240 chroms): 1 millis pass2 - checking and writing primary data (691 records, 4 fields): 81 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:06:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:07:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:07:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:07:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572056/SRX13572056.20_summits.bed INFO @ Tue, 02 Aug 2022 16:07:00: Done! pass1 - making usageList (99 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。