Job ID = 16436821 SRX = SRX11638459 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:06 27919588 reads; of these: 27919588 (100.00%) were unpaired; of these: 2907634 (10.41%) aligned 0 times 22173487 (79.42%) aligned exactly 1 time 2838467 (10.17%) aligned >1 times 89.59% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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 12 files... [bam_rmdupse_core] 5546608 / 25011954 = 0.2218 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 12:11:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.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 12:11:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:11:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:11:33: 1000000 INFO @ Tue, 02 Aug 2022 12:11:41: 2000000 INFO @ Tue, 02 Aug 2022 12:11:50: 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 12:11:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.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 12:11:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:11:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:11:58: 4000000 INFO @ Tue, 02 Aug 2022 12:12:04: 1000000 INFO @ Tue, 02 Aug 2022 12:12:08: 5000000 INFO @ Tue, 02 Aug 2022 12:12:14: 2000000 INFO @ Tue, 02 Aug 2022 12:12:16: 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 12:12:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.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 12:12:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:12:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:12:24: 3000000 INFO @ Tue, 02 Aug 2022 12:12:25: 7000000 INFO @ Tue, 02 Aug 2022 12:12:33: 1000000 INFO @ Tue, 02 Aug 2022 12:12:34: 4000000 INFO @ Tue, 02 Aug 2022 12:12:35: 8000000 INFO @ Tue, 02 Aug 2022 12:12:44: 2000000 INFO @ Tue, 02 Aug 2022 12:12:44: 9000000 INFO @ Tue, 02 Aug 2022 12:12:44: 5000000 INFO @ Tue, 02 Aug 2022 12:12:53: 10000000 INFO @ Tue, 02 Aug 2022 12:12:53: 3000000 INFO @ Tue, 02 Aug 2022 12:12:54: 6000000 INFO @ Tue, 02 Aug 2022 12:13:02: 11000000 INFO @ Tue, 02 Aug 2022 12:13:04: 7000000 INFO @ Tue, 02 Aug 2022 12:13:04: 4000000 INFO @ Tue, 02 Aug 2022 12:13:11: 12000000 INFO @ Tue, 02 Aug 2022 12:13:14: 5000000 INFO @ Tue, 02 Aug 2022 12:13:14: 8000000 INFO @ Tue, 02 Aug 2022 12:13:20: 13000000 INFO @ Tue, 02 Aug 2022 12:13:24: 6000000 INFO @ Tue, 02 Aug 2022 12:13:24: 9000000 INFO @ Tue, 02 Aug 2022 12:13:29: 14000000 INFO @ Tue, 02 Aug 2022 12:13:34: 7000000 INFO @ Tue, 02 Aug 2022 12:13:34: 10000000 INFO @ Tue, 02 Aug 2022 12:13:39: 15000000 INFO @ Tue, 02 Aug 2022 12:13:44: 8000000 INFO @ Tue, 02 Aug 2022 12:13:44: 11000000 INFO @ Tue, 02 Aug 2022 12:13:48: 16000000 INFO @ Tue, 02 Aug 2022 12:13:54: 12000000 INFO @ Tue, 02 Aug 2022 12:13:54: 9000000 INFO @ Tue, 02 Aug 2022 12:13:58: 17000000 INFO @ Tue, 02 Aug 2022 12:14:04: 13000000 INFO @ Tue, 02 Aug 2022 12:14:05: 10000000 INFO @ Tue, 02 Aug 2022 12:14:07: 18000000 INFO @ Tue, 02 Aug 2022 12:14:15: 11000000 INFO @ Tue, 02 Aug 2022 12:14:15: 14000000 INFO @ Tue, 02 Aug 2022 12:14:16: 19000000 INFO @ Tue, 02 Aug 2022 12:14:21: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:14:21: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:14:21: #1 total tags in treatment: 19465346 INFO @ Tue, 02 Aug 2022 12:14:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:14:21: #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 12:14:22: #1 tags after filtering in treatment: 19465335 INFO @ Tue, 02 Aug 2022 12:14:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:14:22: #1 finished! INFO @ Tue, 02 Aug 2022 12:14:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:14:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:14:23: #2 number of paired peaks: 992 WARNING @ Tue, 02 Aug 2022 12:14:23: Fewer paired peaks (992) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 992 pairs to build model! INFO @ Tue, 02 Aug 2022 12:14:23: start model_add_line... INFO @ Tue, 02 Aug 2022 12:14:24: start X-correlation... INFO @ Tue, 02 Aug 2022 12:14:24: end of X-cor INFO @ Tue, 02 Aug 2022 12:14:24: #2 finished! INFO @ Tue, 02 Aug 2022 12:14:24: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 12:14:24: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 12:14:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.05_model.r INFO @ Tue, 02 Aug 2022 12:14:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:14:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:14:25: 12000000 INFO @ Tue, 02 Aug 2022 12:14:26: 15000000 INFO @ Tue, 02 Aug 2022 12:14:35: 13000000 INFO @ Tue, 02 Aug 2022 12:14:36: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:14:45: 14000000 INFO @ Tue, 02 Aug 2022 12:14:47: 17000000 INFO @ Tue, 02 Aug 2022 12:14:55: 15000000 INFO @ Tue, 02 Aug 2022 12:14:56: 18000000 INFO @ Tue, 02 Aug 2022 12:15:05: 16000000 INFO @ Tue, 02 Aug 2022 12:15:06: 19000000 INFO @ Tue, 02 Aug 2022 12:15:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:15:11: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:15:11: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:15:11: #1 total tags in treatment: 19465346 INFO @ Tue, 02 Aug 2022 12:15:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:15:11: #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 12:15:12: #1 tags after filtering in treatment: 19465335 INFO @ Tue, 02 Aug 2022 12:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:15:12: #1 finished! INFO @ Tue, 02 Aug 2022 12:15:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:15:14: #2 number of paired peaks: 992 WARNING @ Tue, 02 Aug 2022 12:15:14: Fewer paired peaks (992) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 992 pairs to build model! INFO @ Tue, 02 Aug 2022 12:15:14: start model_add_line... INFO @ Tue, 02 Aug 2022 12:15:14: start X-correlation... INFO @ Tue, 02 Aug 2022 12:15:14: end of X-cor INFO @ Tue, 02 Aug 2022 12:15:14: #2 finished! INFO @ Tue, 02 Aug 2022 12:15:14: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 12:15:14: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 12:15:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.10_model.r INFO @ Tue, 02 Aug 2022 12:15:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:15:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:15:16: 17000000 INFO @ Tue, 02 Aug 2022 12:15:25: 18000000 INFO @ Tue, 02 Aug 2022 12:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:15:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.05_summits.bed INFO @ Tue, 02 Aug 2022 12:15:28: Done! pass1 - making usageList (196 chroms): 3 millis pass2 - checking and writing primary data (11487 records, 4 fields): 81 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:15:35: 19000000 INFO @ Tue, 02 Aug 2022 12:15:40: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:15:40: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:15:40: #1 total tags in treatment: 19465346 INFO @ Tue, 02 Aug 2022 12:15:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:15:40: #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 12:15:41: #1 tags after filtering in treatment: 19465335 INFO @ Tue, 02 Aug 2022 12:15:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:15:41: #1 finished! INFO @ Tue, 02 Aug 2022 12:15:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:15:43: #2 number of paired peaks: 992 WARNING @ Tue, 02 Aug 2022 12:15:43: Fewer paired peaks (992) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 992 pairs to build model! INFO @ Tue, 02 Aug 2022 12:15:43: start model_add_line... INFO @ Tue, 02 Aug 2022 12:15:43: start X-correlation... INFO @ Tue, 02 Aug 2022 12:15:43: end of X-cor INFO @ Tue, 02 Aug 2022 12:15:43: #2 finished! INFO @ Tue, 02 Aug 2022 12:15:43: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 12:15:43: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 12:15:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.20_model.r INFO @ Tue, 02 Aug 2022 12:15:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:15:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:15:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.10_summits.bed INFO @ Tue, 02 Aug 2022 12:16:19: Done! pass1 - making usageList (120 chroms): 3 millis pass2 - checking and writing primary data (7654 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:16:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX11638459/SRX11638459.20_summits.bed INFO @ Tue, 02 Aug 2022 12:16:47: Done! pass1 - making usageList (80 chroms): 2 millis pass2 - checking and writing primary data (4250 records, 4 fields): 101 millis CompletedMACS2peakCalling