Job ID = 6627567 SRX = SRX8521370 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: 00:05:15 37140720 reads; of these: 37140720 (100.00%) were unpaired; of these: 32243041 (86.81%) aligned 0 times 3633472 (9.78%) aligned exactly 1 time 1264207 (3.40%) aligned >1 times 13.19% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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] 670889 / 4897679 = 0.1370 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 12:08:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.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 12:08:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:08:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:08:43: 1000000 INFO @ Tue, 14 Jul 2020 12:08:49: 2000000 INFO @ Tue, 14 Jul 2020 12:08:55: 3000000 INFO @ Tue, 14 Jul 2020 12:09:01: 4000000 INFO @ Tue, 14 Jul 2020 12:09:02: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:09:02: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:09:02: #1 total tags in treatment: 4226790 INFO @ Tue, 14 Jul 2020 12:09:02: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:09:02: #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 12:09:03: #1 tags after filtering in treatment: 4226559 INFO @ Tue, 14 Jul 2020 12:09:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:09:03: #1 finished! INFO @ Tue, 14 Jul 2020 12:09:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:09:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:09:03: #2 number of paired peaks: 758 WARNING @ Tue, 14 Jul 2020 12:09:03: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 14 Jul 2020 12:09:03: start model_add_line... INFO @ Tue, 14 Jul 2020 12:09:03: start X-correlation... INFO @ Tue, 14 Jul 2020 12:09:03: end of X-cor INFO @ Tue, 14 Jul 2020 12:09:03: #2 finished! INFO @ Tue, 14 Jul 2020 12:09:03: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 12:09:03: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 12:09:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.05_model.r WARNING @ Tue, 14 Jul 2020 12:09:03: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:09:03: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 12:09:03: #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 12:09:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:09:03: #3 Pre-compute pvalue-qvalue table... 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 12:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.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 12:09:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:09:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:09:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:09:13: 1000000 INFO @ Tue, 14 Jul 2020 12:09:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:09:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:09:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.05_summits.bed INFO @ Tue, 14 Jul 2020 12:09:17: Done! pass1 - making usageList (214 chroms): 1 millis pass2 - checking and writing primary data (960 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:09:19: 2000000 INFO @ Tue, 14 Jul 2020 12:09:25: 3000000 INFO @ Tue, 14 Jul 2020 12:09:30: 4000000 INFO @ Tue, 14 Jul 2020 12:09:32: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:09:32: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:09:32: #1 total tags in treatment: 4226790 INFO @ Tue, 14 Jul 2020 12:09:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:09:32: #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 12:09:32: #1 tags after filtering in treatment: 4226559 INFO @ Tue, 14 Jul 2020 12:09:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:09:32: #1 finished! INFO @ Tue, 14 Jul 2020 12:09:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:09:33: #2 number of paired peaks: 758 WARNING @ Tue, 14 Jul 2020 12:09:33: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 14 Jul 2020 12:09:33: start model_add_line... INFO @ Tue, 14 Jul 2020 12:09:33: start X-correlation... INFO @ Tue, 14 Jul 2020 12:09:33: end of X-cor INFO @ Tue, 14 Jul 2020 12:09:33: #2 finished! INFO @ Tue, 14 Jul 2020 12:09:33: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 12:09:33: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 12:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.10_model.r WARNING @ Tue, 14 Jul 2020 12:09:33: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:09:33: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 12:09:33: #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 12:09:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:09:33: #3 Pre-compute pvalue-qvalue table... 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 12:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.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 12:09:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:09:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:09:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:09:43: 1000000 INFO @ Tue, 14 Jul 2020 12:09:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:09:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:09:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.10_summits.bed INFO @ Tue, 14 Jul 2020 12:09:47: Done! pass1 - making usageList (136 chroms): 1 millis pass2 - checking and writing primary data (408 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:09:49: 2000000 INFO @ Tue, 14 Jul 2020 12:09:55: 3000000 INFO @ Tue, 14 Jul 2020 12:10:01: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:10:02: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:10:02: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:10:02: #1 total tags in treatment: 4226790 INFO @ Tue, 14 Jul 2020 12:10:02: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:10:02: #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 12:10:03: #1 tags after filtering in treatment: 4226559 INFO @ Tue, 14 Jul 2020 12:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:10:03: #1 finished! INFO @ Tue, 14 Jul 2020 12:10:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:10:03: #2 number of paired peaks: 758 WARNING @ Tue, 14 Jul 2020 12:10:03: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 14 Jul 2020 12:10:03: start model_add_line... INFO @ Tue, 14 Jul 2020 12:10:03: start X-correlation... INFO @ Tue, 14 Jul 2020 12:10:03: end of X-cor INFO @ Tue, 14 Jul 2020 12:10:03: #2 finished! INFO @ Tue, 14 Jul 2020 12:10:03: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 12:10:03: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 12:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.20_model.r WARNING @ Tue, 14 Jul 2020 12:10:03: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:10:03: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 12:10:03: #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 12:10:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:10:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:10:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:10:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:10:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:10:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521370/SRX8521370.20_summits.bed INFO @ Tue, 14 Jul 2020 12:10:17: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 4 millis CompletedMACS2peakCalling