Job ID = 6529986 SRX = SRX5736592 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: 00:08:30 35789881 reads; of these: 35789881 (100.00%) were unpaired; of these: 807044 (2.25%) aligned 0 times 29387451 (82.11%) aligned exactly 1 time 5595386 (15.63%) aligned >1 times 97.75% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 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 16 files... [bam_rmdupse_core] 15135868 / 34982837 = 0.4327 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:10:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.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, 30 Jun 2020 03:10:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:22: 1000000 INFO @ Tue, 30 Jun 2020 03:10:28: 2000000 INFO @ Tue, 30 Jun 2020 03:10:35: 3000000 INFO @ Tue, 30 Jun 2020 03:10:41: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.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, 30 Jun 2020 03:10:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:47: 5000000 INFO @ Tue, 30 Jun 2020 03:10:53: 1000000 INFO @ Tue, 30 Jun 2020 03:10:54: 6000000 INFO @ Tue, 30 Jun 2020 03:10:59: 2000000 INFO @ Tue, 30 Jun 2020 03:11:00: 7000000 INFO @ Tue, 30 Jun 2020 03:11:05: 3000000 INFO @ Tue, 30 Jun 2020 03:11:07: 8000000 INFO @ Tue, 30 Jun 2020 03:11:12: 4000000 INFO @ Tue, 30 Jun 2020 03:11:14: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:11:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.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, 30 Jun 2020 03:11:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:18: 5000000 INFO @ Tue, 30 Jun 2020 03:11:20: 10000000 INFO @ Tue, 30 Jun 2020 03:11:22: 1000000 INFO @ Tue, 30 Jun 2020 03:11:24: 6000000 INFO @ Tue, 30 Jun 2020 03:11:27: 11000000 INFO @ Tue, 30 Jun 2020 03:11:29: 2000000 INFO @ Tue, 30 Jun 2020 03:11:31: 7000000 INFO @ Tue, 30 Jun 2020 03:11:34: 12000000 INFO @ Tue, 30 Jun 2020 03:11:35: 3000000 INFO @ Tue, 30 Jun 2020 03:11:37: 8000000 INFO @ Tue, 30 Jun 2020 03:11:40: 13000000 INFO @ Tue, 30 Jun 2020 03:11:41: 4000000 INFO @ Tue, 30 Jun 2020 03:11:43: 9000000 INFO @ Tue, 30 Jun 2020 03:11:47: 14000000 INFO @ Tue, 30 Jun 2020 03:11:48: 5000000 INFO @ Tue, 30 Jun 2020 03:11:49: 10000000 INFO @ Tue, 30 Jun 2020 03:11:54: 15000000 INFO @ Tue, 30 Jun 2020 03:11:54: 6000000 INFO @ Tue, 30 Jun 2020 03:11:56: 11000000 INFO @ Tue, 30 Jun 2020 03:12:00: 7000000 INFO @ Tue, 30 Jun 2020 03:12:00: 16000000 INFO @ Tue, 30 Jun 2020 03:12:02: 12000000 INFO @ Tue, 30 Jun 2020 03:12:06: 8000000 INFO @ Tue, 30 Jun 2020 03:12:07: 17000000 INFO @ Tue, 30 Jun 2020 03:12:08: 13000000 INFO @ Tue, 30 Jun 2020 03:12:12: 9000000 INFO @ Tue, 30 Jun 2020 03:12:14: 14000000 INFO @ Tue, 30 Jun 2020 03:12:14: 18000000 INFO @ Tue, 30 Jun 2020 03:12:18: 10000000 INFO @ Tue, 30 Jun 2020 03:12:20: 15000000 INFO @ Tue, 30 Jun 2020 03:12:21: 19000000 INFO @ Tue, 30 Jun 2020 03:12:24: 11000000 INFO @ Tue, 30 Jun 2020 03:12:26: 16000000 INFO @ Tue, 30 Jun 2020 03:12:27: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:12:27: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:12:27: #1 total tags in treatment: 19846969 INFO @ Tue, 30 Jun 2020 03:12:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:12:27: #1 tags after filtering in treatment: 19846865 INFO @ Tue, 30 Jun 2020 03:12:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:27: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:28: #2 number of paired peaks: 157 WARNING @ Tue, 30 Jun 2020 03:12:28: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:28: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:29: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:29: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:29: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:29: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 03:12:29: #2 alternative fragment length(s) may be 49,71,113,155,170,260,283,394,422,467,525,550,578,586 bps INFO @ Tue, 30 Jun 2020 03:12:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.05_model.r WARNING @ Tue, 30 Jun 2020 03:12:29: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:29: #2 You may need to consider one of the other alternative d(s): 49,71,113,155,170,260,283,394,422,467,525,550,578,586 WARNING @ Tue, 30 Jun 2020 03:12:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:12:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:30: 12000000 INFO @ Tue, 30 Jun 2020 03:12:32: 17000000 INFO @ Tue, 30 Jun 2020 03:12:36: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:12:38: 18000000 INFO @ Tue, 30 Jun 2020 03:12:42: 14000000 INFO @ Tue, 30 Jun 2020 03:12:44: 19000000 INFO @ Tue, 30 Jun 2020 03:12:48: 15000000 INFO @ Tue, 30 Jun 2020 03:12:49: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:12:49: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:12:49: #1 total tags in treatment: 19846969 INFO @ Tue, 30 Jun 2020 03:12:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:12:49: #1 tags after filtering in treatment: 19846865 INFO @ Tue, 30 Jun 2020 03:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:49: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:51: #2 number of paired peaks: 157 WARNING @ Tue, 30 Jun 2020 03:12:51: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:51: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:51: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:51: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:51: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:51: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 03:12:51: #2 alternative fragment length(s) may be 49,71,113,155,170,260,283,394,422,467,525,550,578,586 bps INFO @ Tue, 30 Jun 2020 03:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.10_model.r WARNING @ Tue, 30 Jun 2020 03:12:51: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:51: #2 You may need to consider one of the other alternative d(s): 49,71,113,155,170,260,283,394,422,467,525,550,578,586 WARNING @ Tue, 30 Jun 2020 03:12:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:12:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:53: 16000000 INFO @ Tue, 30 Jun 2020 03:12:59: 17000000 INFO @ Tue, 30 Jun 2020 03:13:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:04: 18000000 INFO @ Tue, 30 Jun 2020 03:13:10: 19000000 INFO @ Tue, 30 Jun 2020 03:13:15: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:13:15: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:13:15: #1 total tags in treatment: 19846969 INFO @ Tue, 30 Jun 2020 03:13:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:13:15: #1 tags after filtering in treatment: 19846865 INFO @ Tue, 30 Jun 2020 03:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:15: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:16: #2 number of paired peaks: 157 WARNING @ Tue, 30 Jun 2020 03:13:16: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:16: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:16: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:16: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:16: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:16: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 03:13:16: #2 alternative fragment length(s) may be 49,71,113,155,170,260,283,394,422,467,525,550,578,586 bps INFO @ Tue, 30 Jun 2020 03:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.20_model.r WARNING @ Tue, 30 Jun 2020 03:13:16: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:13:16: #2 You may need to consider one of the other alternative d(s): 49,71,113,155,170,260,283,394,422,467,525,550,578,586 WARNING @ Tue, 30 Jun 2020 03:13:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:13:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.05_summits.bed INFO @ Tue, 30 Jun 2020 03:13:22: Done! pass1 - making usageList (141 chroms): 1 millis pass2 - checking and writing primary data (1214 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:13:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.10_summits.bed INFO @ Tue, 30 Jun 2020 03:13:42: Done! pass1 - making usageList (93 chroms): 1 millis pass2 - checking and writing primary data (368 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:13:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5736592/SRX5736592.20_summits.bed INFO @ Tue, 30 Jun 2020 03:14:14: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (106 records, 4 fields): 2 millis CompletedMACS2peakCalling