Job ID = 6627517 SRX = SRX8521346 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: 00:06:12 40108613 reads; of these: 40108613 (100.00%) were unpaired; of these: 32003553 (79.79%) aligned 0 times 6340699 (15.81%) aligned exactly 1 time 1764361 (4.40%) aligned >1 times 20.21% overall alignment rate Time searching: 00:06:12 Overall time: 00:06:12 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_rmdupse_core] 1386639 / 8105060 = 0.1711 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, 14 Jul 2020 11:55:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.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, 14 Jul 2020 11:55:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:55:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:55:39: 1000000 INFO @ Tue, 14 Jul 2020 11:55:44: 2000000 INFO @ Tue, 14 Jul 2020 11:55:50: 3000000 INFO @ Tue, 14 Jul 2020 11:55:56: 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, 14 Jul 2020 11:56:01: 5000000 INFO @ Tue, 14 Jul 2020 11:56:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.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, 14 Jul 2020 11:56:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:56:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:56:08: 6000000 INFO @ Tue, 14 Jul 2020 11:56:09: 1000000 INFO @ Tue, 14 Jul 2020 11:56:13: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:56:13: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:56:13: #1 total tags in treatment: 6718421 INFO @ Tue, 14 Jul 2020 11:56:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:56:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:56:13: #1 tags after filtering in treatment: 6718226 INFO @ Tue, 14 Jul 2020 11:56:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:56:13: #1 finished! INFO @ Tue, 14 Jul 2020 11:56:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:56:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:56:14: #2 number of paired peaks: 541 WARNING @ Tue, 14 Jul 2020 11:56:14: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Tue, 14 Jul 2020 11:56:14: start model_add_line... INFO @ Tue, 14 Jul 2020 11:56:14: start X-correlation... INFO @ Tue, 14 Jul 2020 11:56:14: end of X-cor INFO @ Tue, 14 Jul 2020 11:56:14: #2 finished! INFO @ Tue, 14 Jul 2020 11:56:14: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 11:56:14: #2 alternative fragment length(s) may be 4,56,512 bps INFO @ Tue, 14 Jul 2020 11:56:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.05_model.r WARNING @ Tue, 14 Jul 2020 11:56:14: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:56:14: #2 You may need to consider one of the other alternative d(s): 4,56,512 WARNING @ Tue, 14 Jul 2020 11:56:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:56:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:56:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:56:16: 2000000 INFO @ Tue, 14 Jul 2020 11:56:22: 3000000 INFO @ Tue, 14 Jul 2020 11:56:28: 4000000 INFO @ Tue, 14 Jul 2020 11:56:28: #3 Call peaks for each chromosome... 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, 14 Jul 2020 11:56:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.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, 14 Jul 2020 11:56:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:56:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:56:34: 5000000 INFO @ Tue, 14 Jul 2020 11:56:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:56:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:56:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.05_summits.bed INFO @ Tue, 14 Jul 2020 11:56:35: Done! pass1 - making usageList (220 chroms): 1 millis pass2 - checking and writing primary data (1110 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:56:39: 1000000 INFO @ Tue, 14 Jul 2020 11:56:41: 6000000 INFO @ Tue, 14 Jul 2020 11:56:46: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:56:46: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:56:46: #1 total tags in treatment: 6718421 INFO @ Tue, 14 Jul 2020 11:56:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:56:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:56:46: 2000000 INFO @ Tue, 14 Jul 2020 11:56:46: #1 tags after filtering in treatment: 6718226 INFO @ Tue, 14 Jul 2020 11:56:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:56:46: #1 finished! INFO @ Tue, 14 Jul 2020 11:56:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:56:46: #2 number of paired peaks: 541 WARNING @ Tue, 14 Jul 2020 11:56:46: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Tue, 14 Jul 2020 11:56:46: start model_add_line... INFO @ Tue, 14 Jul 2020 11:56:47: start X-correlation... INFO @ Tue, 14 Jul 2020 11:56:47: end of X-cor INFO @ Tue, 14 Jul 2020 11:56:47: #2 finished! INFO @ Tue, 14 Jul 2020 11:56:47: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 11:56:47: #2 alternative fragment length(s) may be 4,56,512 bps INFO @ Tue, 14 Jul 2020 11:56:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.10_model.r WARNING @ Tue, 14 Jul 2020 11:56:47: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:56:47: #2 You may need to consider one of the other alternative d(s): 4,56,512 WARNING @ Tue, 14 Jul 2020 11:56:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:56:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:56:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:56:52: 3000000 INFO @ Tue, 14 Jul 2020 11:56:58: 4000000 INFO @ Tue, 14 Jul 2020 11:57:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:57:04: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:57:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:57:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:57:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.10_summits.bed INFO @ Tue, 14 Jul 2020 11:57:07: Done! pass1 - making usageList (131 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:57:11: 6000000 INFO @ Tue, 14 Jul 2020 11:57:15: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:57:15: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:57:15: #1 total tags in treatment: 6718421 INFO @ Tue, 14 Jul 2020 11:57:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:57:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:57:15: #1 tags after filtering in treatment: 6718226 INFO @ Tue, 14 Jul 2020 11:57:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:57:15: #1 finished! INFO @ Tue, 14 Jul 2020 11:57:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:57:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:57:16: #2 number of paired peaks: 541 WARNING @ Tue, 14 Jul 2020 11:57:16: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Tue, 14 Jul 2020 11:57:16: start model_add_line... INFO @ Tue, 14 Jul 2020 11:57:16: start X-correlation... INFO @ Tue, 14 Jul 2020 11:57:16: end of X-cor INFO @ Tue, 14 Jul 2020 11:57:16: #2 finished! INFO @ Tue, 14 Jul 2020 11:57:16: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 11:57:16: #2 alternative fragment length(s) may be 4,56,512 bps INFO @ Tue, 14 Jul 2020 11:57:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.20_model.r WARNING @ Tue, 14 Jul 2020 11:57:16: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:57:16: #2 You may need to consider one of the other alternative d(s): 4,56,512 WARNING @ Tue, 14 Jul 2020 11:57:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:57:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:57:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:57:30: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:57:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:57:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:57:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521346/SRX8521346.20_summits.bed INFO @ Tue, 14 Jul 2020 11:57:37: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 3 millis CompletedMACS2peakCalling