Job ID = 16439181 SRX = SRX15206450 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: 00:00:01 Multiseed full-index search: 00:05:03 23843646 reads; of these: 23843646 (100.00%) were unpaired; of these: 735455 (3.08%) aligned 0 times 19773572 (82.93%) aligned exactly 1 time 3334619 (13.99%) aligned >1 times 96.92% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 1980792 / 23108191 = 0.0857 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 14:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.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 14:52:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:52:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:52:49: 1000000 INFO @ Tue, 02 Aug 2022 14:52:55: 2000000 INFO @ Tue, 02 Aug 2022 14:53:00: 3000000 INFO @ Tue, 02 Aug 2022 14:53:06: 4000000 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 14:53:12: 5000000 INFO @ Tue, 02 Aug 2022 14:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.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 14:53:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:53:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:53:18: 6000000 INFO @ Tue, 02 Aug 2022 14:53:20: 1000000 INFO @ Tue, 02 Aug 2022 14:53:24: 7000000 INFO @ Tue, 02 Aug 2022 14:53:26: 2000000 INFO @ Tue, 02 Aug 2022 14:53:30: 8000000 INFO @ Tue, 02 Aug 2022 14:53:32: 3000000 INFO @ Tue, 02 Aug 2022 14:53:36: 9000000 INFO @ Tue, 02 Aug 2022 14:53:38: 4000000 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 14:53:43: 10000000 INFO @ Tue, 02 Aug 2022 14:53:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.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 14:53:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:53:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:53:44: 5000000 INFO @ Tue, 02 Aug 2022 14:53:49: 11000000 INFO @ Tue, 02 Aug 2022 14:53:50: 1000000 INFO @ Tue, 02 Aug 2022 14:53:51: 6000000 INFO @ Tue, 02 Aug 2022 14:53:55: 12000000 INFO @ Tue, 02 Aug 2022 14:53:56: 2000000 INFO @ Tue, 02 Aug 2022 14:53:57: 7000000 INFO @ Tue, 02 Aug 2022 14:54:01: 13000000 INFO @ Tue, 02 Aug 2022 14:54:02: 3000000 INFO @ Tue, 02 Aug 2022 14:54:03: 8000000 INFO @ Tue, 02 Aug 2022 14:54:07: 14000000 INFO @ Tue, 02 Aug 2022 14:54:09: 4000000 INFO @ Tue, 02 Aug 2022 14:54:10: 9000000 INFO @ Tue, 02 Aug 2022 14:54:14: 15000000 INFO @ Tue, 02 Aug 2022 14:54:15: 5000000 INFO @ Tue, 02 Aug 2022 14:54:16: 10000000 INFO @ Tue, 02 Aug 2022 14:54:20: 16000000 INFO @ Tue, 02 Aug 2022 14:54:21: 6000000 INFO @ Tue, 02 Aug 2022 14:54:22: 11000000 INFO @ Tue, 02 Aug 2022 14:54:26: 17000000 INFO @ Tue, 02 Aug 2022 14:54:27: 7000000 INFO @ Tue, 02 Aug 2022 14:54:28: 12000000 INFO @ Tue, 02 Aug 2022 14:54:33: 18000000 INFO @ Tue, 02 Aug 2022 14:54:34: 8000000 INFO @ Tue, 02 Aug 2022 14:54:35: 13000000 INFO @ Tue, 02 Aug 2022 14:54:39: 19000000 INFO @ Tue, 02 Aug 2022 14:54:40: 9000000 INFO @ Tue, 02 Aug 2022 14:54:41: 14000000 INFO @ Tue, 02 Aug 2022 14:54:45: 20000000 INFO @ Tue, 02 Aug 2022 14:54:46: 10000000 INFO @ Tue, 02 Aug 2022 14:54:47: 15000000 INFO @ Tue, 02 Aug 2022 14:54:52: 21000000 INFO @ Tue, 02 Aug 2022 14:54:53: 11000000 INFO @ Tue, 02 Aug 2022 14:54:53: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:54:53: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:54:53: #1 total tags in treatment: 21127399 INFO @ Tue, 02 Aug 2022 14:54:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:54:53: #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 14:54:53: #1 tags after filtering in treatment: 21127309 INFO @ Tue, 02 Aug 2022 14:54:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:54:53: #1 finished! INFO @ Tue, 02 Aug 2022 14:54:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:54:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:54:54: 16000000 INFO @ Tue, 02 Aug 2022 14:54:55: #2 number of paired peaks: 174 WARNING @ Tue, 02 Aug 2022 14:54:55: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 02 Aug 2022 14:54:55: start model_add_line... INFO @ Tue, 02 Aug 2022 14:54:55: start X-correlation... INFO @ Tue, 02 Aug 2022 14:54:55: end of X-cor INFO @ Tue, 02 Aug 2022 14:54:55: #2 finished! INFO @ Tue, 02 Aug 2022 14:54:55: #2 predicted fragment length is 51 bps INFO @ Tue, 02 Aug 2022 14:54:55: #2 alternative fragment length(s) may be 2,51,583,585,592,595 bps INFO @ Tue, 02 Aug 2022 14:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.05_model.r WARNING @ Tue, 02 Aug 2022 14:54:55: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:54:55: #2 You may need to consider one of the other alternative d(s): 2,51,583,585,592,595 WARNING @ Tue, 02 Aug 2022 14:54:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:54:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:54:59: 12000000 INFO @ Tue, 02 Aug 2022 14:55:00: 17000000 INFO @ Tue, 02 Aug 2022 14:55:05: 13000000 INFO @ Tue, 02 Aug 2022 14:55:06: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:55:11: 14000000 INFO @ Tue, 02 Aug 2022 14:55:13: 19000000 INFO @ Tue, 02 Aug 2022 14:55:18: 15000000 INFO @ Tue, 02 Aug 2022 14:55:19: 20000000 INFO @ Tue, 02 Aug 2022 14:55:24: 16000000 INFO @ Tue, 02 Aug 2022 14:55:25: 21000000 INFO @ Tue, 02 Aug 2022 14:55:26: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:55:26: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:55:26: #1 total tags in treatment: 21127399 INFO @ Tue, 02 Aug 2022 14:55:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:55:26: #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 14:55:27: #1 tags after filtering in treatment: 21127309 INFO @ Tue, 02 Aug 2022 14:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:55:27: #1 finished! INFO @ Tue, 02 Aug 2022 14:55:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:55:28: #2 number of paired peaks: 174 WARNING @ Tue, 02 Aug 2022 14:55:28: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 02 Aug 2022 14:55:28: start model_add_line... INFO @ Tue, 02 Aug 2022 14:55:28: start X-correlation... INFO @ Tue, 02 Aug 2022 14:55:28: end of X-cor INFO @ Tue, 02 Aug 2022 14:55:28: #2 finished! INFO @ Tue, 02 Aug 2022 14:55:28: #2 predicted fragment length is 51 bps INFO @ Tue, 02 Aug 2022 14:55:28: #2 alternative fragment length(s) may be 2,51,583,585,592,595 bps INFO @ Tue, 02 Aug 2022 14:55:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.10_model.r WARNING @ Tue, 02 Aug 2022 14:55:28: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:55:28: #2 You may need to consider one of the other alternative d(s): 2,51,583,585,592,595 WARNING @ Tue, 02 Aug 2022 14:55:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:55:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:55:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:55:30: 17000000 INFO @ Tue, 02 Aug 2022 14:55:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:55:36: 18000000 INFO @ Tue, 02 Aug 2022 14:55:42: 19000000 INFO @ Tue, 02 Aug 2022 14:55:48: 20000000 INFO @ Tue, 02 Aug 2022 14:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.05_summits.bed INFO @ Tue, 02 Aug 2022 14:55:51: Done! pass1 - making usageList (148 chroms): 1 millis pass2 - checking and writing primary data (491 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:55:54: 21000000 INFO @ Tue, 02 Aug 2022 14:55:55: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:55:55: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:55:55: #1 total tags in treatment: 21127399 INFO @ Tue, 02 Aug 2022 14:55:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:55:55: #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 14:55:55: #1 tags after filtering in treatment: 21127309 INFO @ Tue, 02 Aug 2022 14:55:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:55:55: #1 finished! INFO @ Tue, 02 Aug 2022 14:55:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:55:56: #2 number of paired peaks: 174 WARNING @ Tue, 02 Aug 2022 14:55:56: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 02 Aug 2022 14:55:56: start model_add_line... INFO @ Tue, 02 Aug 2022 14:55:57: start X-correlation... INFO @ Tue, 02 Aug 2022 14:55:57: end of X-cor INFO @ Tue, 02 Aug 2022 14:55:57: #2 finished! INFO @ Tue, 02 Aug 2022 14:55:57: #2 predicted fragment length is 51 bps INFO @ Tue, 02 Aug 2022 14:55:57: #2 alternative fragment length(s) may be 2,51,583,585,592,595 bps INFO @ Tue, 02 Aug 2022 14:55:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.20_model.r WARNING @ Tue, 02 Aug 2022 14:55:57: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:55:57: #2 You may need to consider one of the other alternative d(s): 2,51,583,585,592,595 WARNING @ Tue, 02 Aug 2022 14:55:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:55:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:55:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:56:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:56:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:56:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:56:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.10_summits.bed INFO @ Tue, 02 Aug 2022 14:56:24: Done! pass1 - making usageList (111 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:56:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:56:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:56:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:56:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206450/SRX15206450.20_summits.bed INFO @ Tue, 02 Aug 2022 14:56:51: Done! pass1 - making usageList (85 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 10 millis CompletedMACS2peakCalling