Job ID = 6529831 SRX = SRX495239 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: 00:05:41 20194013 reads; of these: 20194013 (100.00%) were unpaired; of these: 986126 (4.88%) aligned 0 times 13987308 (69.26%) aligned exactly 1 time 5220579 (25.85%) aligned >1 times 95.12% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 5381469 / 19207887 = 0.2802 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 03:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.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 03:11:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:06: 1000000 INFO @ Tue, 30 Jun 2020 03:11:11: 2000000 INFO @ Tue, 30 Jun 2020 03:11:17: 3000000 INFO @ Tue, 30 Jun 2020 03:11:22: 4000000 INFO @ Tue, 30 Jun 2020 03:11:27: 5000000 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 03:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.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 03:11:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:33: 6000000 INFO @ Tue, 30 Jun 2020 03:11:36: 1000000 INFO @ Tue, 30 Jun 2020 03:11:39: 7000000 INFO @ Tue, 30 Jun 2020 03:11:42: 2000000 INFO @ Tue, 30 Jun 2020 03:11:44: 8000000 INFO @ Tue, 30 Jun 2020 03:11:47: 3000000 INFO @ Tue, 30 Jun 2020 03:11:50: 9000000 INFO @ Tue, 30 Jun 2020 03:11:53: 4000000 INFO @ Tue, 30 Jun 2020 03:11:56: 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 03:11:59: 5000000 INFO @ Tue, 30 Jun 2020 03:12:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.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 03:12:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:02: 11000000 INFO @ Tue, 30 Jun 2020 03:12:05: 6000000 INFO @ Tue, 30 Jun 2020 03:12:06: 1000000 INFO @ Tue, 30 Jun 2020 03:12:08: 12000000 INFO @ Tue, 30 Jun 2020 03:12:10: 7000000 INFO @ Tue, 30 Jun 2020 03:12:12: 2000000 INFO @ Tue, 30 Jun 2020 03:12:13: 13000000 INFO @ Tue, 30 Jun 2020 03:12:16: 8000000 INFO @ Tue, 30 Jun 2020 03:12:18: 3000000 INFO @ Tue, 30 Jun 2020 03:12:18: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:12:18: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:12:18: #1 total tags in treatment: 13826418 INFO @ Tue, 30 Jun 2020 03:12:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:18: #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 03:12:19: #1 tags after filtering in treatment: 13826413 INFO @ Tue, 30 Jun 2020 03:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:19: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:20: #2 number of paired peaks: 181 WARNING @ Tue, 30 Jun 2020 03:12:20: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:20: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:20: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:20: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:20: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:20: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 03:12:20: #2 alternative fragment length(s) may be 4,11,46,70,451,490,563,587 bps INFO @ Tue, 30 Jun 2020 03:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.05_model.r WARNING @ Tue, 30 Jun 2020 03:12:20: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:20: #2 You may need to consider one of the other alternative d(s): 4,11,46,70,451,490,563,587 WARNING @ Tue, 30 Jun 2020 03:12:20: #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 03:12:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:22: 9000000 INFO @ Tue, 30 Jun 2020 03:12:23: 4000000 INFO @ Tue, 30 Jun 2020 03:12:28: 10000000 INFO @ Tue, 30 Jun 2020 03:12:29: 5000000 INFO @ Tue, 30 Jun 2020 03:12:33: 11000000 INFO @ Tue, 30 Jun 2020 03:12:35: 6000000 INFO @ Tue, 30 Jun 2020 03:12:39: 12000000 INFO @ Tue, 30 Jun 2020 03:12:41: 7000000 INFO @ Tue, 30 Jun 2020 03:12:45: 13000000 INFO @ Tue, 30 Jun 2020 03:12:47: 8000000 INFO @ Tue, 30 Jun 2020 03:12:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:50: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:12:50: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:12:50: #1 total tags in treatment: 13826418 INFO @ Tue, 30 Jun 2020 03:12:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:50: #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 03:12:51: #1 tags after filtering in treatment: 13826413 INFO @ Tue, 30 Jun 2020 03:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:51: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:52: #2 number of paired peaks: 181 WARNING @ Tue, 30 Jun 2020 03:12:52: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:52: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:52: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:52: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:52: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:52: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 03:12:52: #2 alternative fragment length(s) may be 4,11,46,70,451,490,563,587 bps INFO @ Tue, 30 Jun 2020 03:12:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.10_model.r WARNING @ Tue, 30 Jun 2020 03:12:52: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:52: #2 You may need to consider one of the other alternative d(s): 4,11,46,70,451,490,563,587 WARNING @ Tue, 30 Jun 2020 03:12:52: #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 03:12:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:53: 9000000 INFO @ Tue, 30 Jun 2020 03:12:58: 10000000 INFO @ Tue, 30 Jun 2020 03:13:04: 11000000 INFO @ Tue, 30 Jun 2020 03:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.05_summits.bed INFO @ Tue, 30 Jun 2020 03:13:04: Done! pass1 - making usageList (462 chroms): 1 millis pass2 - checking and writing primary data (2014 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:13:09: 12000000 INFO @ Tue, 30 Jun 2020 03:13:15: 13000000 INFO @ Tue, 30 Jun 2020 03:13:20: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:13:20: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:13:20: #1 total tags in treatment: 13826418 INFO @ Tue, 30 Jun 2020 03:13:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:20: #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 03:13:20: #1 tags after filtering in treatment: 13826413 INFO @ Tue, 30 Jun 2020 03:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:20: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:21: #2 number of paired peaks: 181 WARNING @ Tue, 30 Jun 2020 03:13:21: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:21: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:21: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:21: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:21: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:21: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 03:13:21: #2 alternative fragment length(s) may be 4,11,46,70,451,490,563,587 bps INFO @ Tue, 30 Jun 2020 03:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.20_model.r WARNING @ Tue, 30 Jun 2020 03:13:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:13:21: #2 You may need to consider one of the other alternative d(s): 4,11,46,70,451,490,563,587 WARNING @ Tue, 30 Jun 2020 03:13:21: #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 03:13:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.10_summits.bed INFO @ Tue, 30 Jun 2020 03:13:35: Done! pass1 - making usageList (381 chroms): 1 millis pass2 - checking and writing primary data (1299 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:13:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495239/SRX495239.20_summits.bed INFO @ Tue, 30 Jun 2020 03:14:04: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (141 records, 4 fields): 4 millis CompletedMACS2peakCalling