Job ID = 6529710 SRX = SRX3989972 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: 00:04:53 19091508 reads; of these: 19091508 (100.00%) were unpaired; of these: 863888 (4.52%) aligned 0 times 14922452 (78.16%) aligned exactly 1 time 3305168 (17.31%) aligned >1 times 95.48% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 4463659 / 18227620 = 0.2449 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 02:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.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 02:39:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:39:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:39:37: 1000000 INFO @ Tue, 30 Jun 2020 02:39:43: 2000000 INFO @ Tue, 30 Jun 2020 02:39:48: 3000000 INFO @ Tue, 30 Jun 2020 02:39:54: 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 02:40:00: 5000000 INFO @ Tue, 30 Jun 2020 02:40:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.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 02:40:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:06: 6000000 INFO @ Tue, 30 Jun 2020 02:40:06: 1000000 INFO @ Tue, 30 Jun 2020 02:40:12: 7000000 INFO @ Tue, 30 Jun 2020 02:40:12: 2000000 INFO @ Tue, 30 Jun 2020 02:40:17: 3000000 INFO @ Tue, 30 Jun 2020 02:40:17: 8000000 INFO @ Tue, 30 Jun 2020 02:40:22: 4000000 INFO @ Tue, 30 Jun 2020 02:40:23: 9000000 INFO @ Tue, 30 Jun 2020 02:40:27: 5000000 INFO @ Tue, 30 Jun 2020 02:40:29: 10000000 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 02:40:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.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 02:40:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:33: 6000000 INFO @ Tue, 30 Jun 2020 02:40:35: 11000000 INFO @ Tue, 30 Jun 2020 02:40:37: 1000000 INFO @ Tue, 30 Jun 2020 02:40:38: 7000000 INFO @ Tue, 30 Jun 2020 02:40:41: 12000000 INFO @ Tue, 30 Jun 2020 02:40:42: 2000000 INFO @ Tue, 30 Jun 2020 02:40:44: 8000000 INFO @ Tue, 30 Jun 2020 02:40:47: 13000000 INFO @ Tue, 30 Jun 2020 02:40:48: 3000000 INFO @ Tue, 30 Jun 2020 02:40:49: 9000000 INFO @ Tue, 30 Jun 2020 02:40:52: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:40:52: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:40:52: #1 total tags in treatment: 13763961 INFO @ Tue, 30 Jun 2020 02:40:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:40:52: #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 02:40:52: #1 tags after filtering in treatment: 13763960 INFO @ Tue, 30 Jun 2020 02:40:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:40:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:40:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:40:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:40:53: #2 number of paired peaks: 104 WARNING @ Tue, 30 Jun 2020 02:40:53: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 30 Jun 2020 02:40:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:40:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:40:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:40:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:40:53: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:40:53: #2 alternative fragment length(s) may be 4,55,100,443,474,489,510,536,540,550 bps INFO @ Tue, 30 Jun 2020 02:40:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.05_model.r WARNING @ Tue, 30 Jun 2020 02:40:53: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:40:53: #2 You may need to consider one of the other alternative d(s): 4,55,100,443,474,489,510,536,540,550 WARNING @ Tue, 30 Jun 2020 02:40:53: #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 02:40:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:40:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:40:53: 4000000 INFO @ Tue, 30 Jun 2020 02:40:54: 10000000 INFO @ Tue, 30 Jun 2020 02:40:59: 5000000 INFO @ Tue, 30 Jun 2020 02:40:59: 11000000 INFO @ Tue, 30 Jun 2020 02:41:05: 6000000 INFO @ Tue, 30 Jun 2020 02:41:05: 12000000 INFO @ Tue, 30 Jun 2020 02:41:10: 7000000 INFO @ Tue, 30 Jun 2020 02:41:10: 13000000 INFO @ Tue, 30 Jun 2020 02:41:15: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:41:15: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:41:15: #1 total tags in treatment: 13763961 INFO @ Tue, 30 Jun 2020 02:41:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:15: #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 02:41:15: #1 tags after filtering in treatment: 13763960 INFO @ Tue, 30 Jun 2020 02:41:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:15: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:16: 8000000 INFO @ Tue, 30 Jun 2020 02:41:16: #2 number of paired peaks: 104 WARNING @ Tue, 30 Jun 2020 02:41:16: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:16: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:16: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:16: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:41:16: #2 alternative fragment length(s) may be 4,55,100,443,474,489,510,536,540,550 bps INFO @ Tue, 30 Jun 2020 02:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.10_model.r WARNING @ Tue, 30 Jun 2020 02:41:16: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:16: #2 You may need to consider one of the other alternative d(s): 4,55,100,443,474,489,510,536,540,550 WARNING @ Tue, 30 Jun 2020 02:41:16: #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 02:41:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:41:21: 9000000 INFO @ Tue, 30 Jun 2020 02:41:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:41:26: 10000000 INFO @ Tue, 30 Jun 2020 02:41:31: 11000000 INFO @ Tue, 30 Jun 2020 02:41:37: 12000000 INFO @ Tue, 30 Jun 2020 02:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:41:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.05_summits.bed INFO @ Tue, 30 Jun 2020 02:41:37: Done! pass1 - making usageList (183 chroms): 1 millis pass2 - checking and writing primary data (1369 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:41:42: 13000000 INFO @ Tue, 30 Jun 2020 02:41:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:41:46: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:41:46: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:41:46: #1 total tags in treatment: 13763961 INFO @ Tue, 30 Jun 2020 02:41:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:46: #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 02:41:47: #1 tags after filtering in treatment: 13763960 INFO @ Tue, 30 Jun 2020 02:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:47: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:48: #2 number of paired peaks: 104 WARNING @ Tue, 30 Jun 2020 02:41:48: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:48: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:48: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:48: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:48: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:48: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:41:48: #2 alternative fragment length(s) may be 4,55,100,443,474,489,510,536,540,550 bps INFO @ Tue, 30 Jun 2020 02:41:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.20_model.r WARNING @ Tue, 30 Jun 2020 02:41:48: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:48: #2 You may need to consider one of the other alternative d(s): 4,55,100,443,474,489,510,536,540,550 WARNING @ Tue, 30 Jun 2020 02:41:48: #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 02:41:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:41:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:41:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:41:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.10_summits.bed INFO @ Tue, 30 Jun 2020 02:41:59: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:42:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:42:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:42:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:42:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3989972/SRX3989972.20_summits.bed INFO @ Tue, 30 Jun 2020 02:42:30: Done! pass1 - making usageList (59 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 2 millis CompletedMACS2peakCalling