Job ID = 6627640 SRX = SRX8521379 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: 00:08:31 54372229 reads; of these: 54372229 (100.00%) were unpaired; of these: 45855764 (84.34%) aligned 0 times 6470459 (11.90%) aligned exactly 1 time 2046006 (3.76%) aligned >1 times 15.66% overall alignment rate Time searching: 00:08:31 Overall time: 00:08:31 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] 1715200 / 8516465 = 0.2014 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 12:35:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.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 12:35:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:35:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:35:14: 1000000 INFO @ Tue, 14 Jul 2020 12:35:20: 2000000 INFO @ Tue, 14 Jul 2020 12:35:27: 3000000 INFO @ Tue, 14 Jul 2020 12:35:34: 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 12:35:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.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 12:35:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:35:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:35:41: 5000000 INFO @ Tue, 14 Jul 2020 12:35:45: 1000000 INFO @ Tue, 14 Jul 2020 12:35:48: 6000000 INFO @ Tue, 14 Jul 2020 12:35:52: 2000000 INFO @ Tue, 14 Jul 2020 12:35:54: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 12:35:54: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 12:35:54: #1 total tags in treatment: 6801265 INFO @ Tue, 14 Jul 2020 12:35:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:35:54: #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 12:35:54: #1 tags after filtering in treatment: 6801081 INFO @ Tue, 14 Jul 2020 12:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:35:54: #1 finished! INFO @ Tue, 14 Jul 2020 12:35:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:35:55: #2 number of paired peaks: 612 WARNING @ Tue, 14 Jul 2020 12:35:55: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 14 Jul 2020 12:35:55: start model_add_line... INFO @ Tue, 14 Jul 2020 12:35:55: start X-correlation... INFO @ Tue, 14 Jul 2020 12:35:55: end of X-cor INFO @ Tue, 14 Jul 2020 12:35:55: #2 finished! INFO @ Tue, 14 Jul 2020 12:35:55: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 12:35:55: #2 alternative fragment length(s) may be 61,523,557 bps INFO @ Tue, 14 Jul 2020 12:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.05_model.r WARNING @ Tue, 14 Jul 2020 12:35:55: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:35:55: #2 You may need to consider one of the other alternative d(s): 61,523,557 WARNING @ Tue, 14 Jul 2020 12:35:55: #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 12:35:55: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:35:59: 3000000 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 12:36:06: 4000000 INFO @ Tue, 14 Jul 2020 12:36:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.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 12:36:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:36:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:36:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:36:13: 5000000 INFO @ Tue, 14 Jul 2020 12:36:14: 1000000 INFO @ Tue, 14 Jul 2020 12:36:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:36:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:36:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.05_summits.bed INFO @ Tue, 14 Jul 2020 12:36:17: Done! pass1 - making usageList (264 chroms): 1 millis pass2 - checking and writing primary data (1164 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:36:20: 2000000 INFO @ Tue, 14 Jul 2020 12:36:20: 6000000 INFO @ Tue, 14 Jul 2020 12:36:26: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 12:36:26: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 12:36:26: #1 total tags in treatment: 6801265 INFO @ Tue, 14 Jul 2020 12:36:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:36:26: #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 12:36:26: 3000000 INFO @ Tue, 14 Jul 2020 12:36:27: #1 tags after filtering in treatment: 6801081 INFO @ Tue, 14 Jul 2020 12:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:36:27: #1 finished! INFO @ Tue, 14 Jul 2020 12:36:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:36:27: #2 number of paired peaks: 612 WARNING @ Tue, 14 Jul 2020 12:36:27: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 14 Jul 2020 12:36:27: start model_add_line... INFO @ Tue, 14 Jul 2020 12:36:27: start X-correlation... INFO @ Tue, 14 Jul 2020 12:36:27: end of X-cor INFO @ Tue, 14 Jul 2020 12:36:27: #2 finished! INFO @ Tue, 14 Jul 2020 12:36:27: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 12:36:27: #2 alternative fragment length(s) may be 61,523,557 bps INFO @ Tue, 14 Jul 2020 12:36:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.10_model.r WARNING @ Tue, 14 Jul 2020 12:36:27: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:36:27: #2 You may need to consider one of the other alternative d(s): 61,523,557 WARNING @ Tue, 14 Jul 2020 12:36:27: #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 12:36:27: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:36:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:36:32: 4000000 INFO @ Tue, 14 Jul 2020 12:36:38: 5000000 INFO @ Tue, 14 Jul 2020 12:36:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:36:44: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.10_summits.bed INFO @ Tue, 14 Jul 2020 12:36:48: Done! pass1 - making usageList (147 chroms): 0 millis pass2 - checking and writing primary data (456 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:36:49: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 12:36:49: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 12:36:49: #1 total tags in treatment: 6801265 INFO @ Tue, 14 Jul 2020 12:36:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:36:49: #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 12:36:49: #1 tags after filtering in treatment: 6801081 INFO @ Tue, 14 Jul 2020 12:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:36:49: #1 finished! INFO @ Tue, 14 Jul 2020 12:36:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:36:50: #2 number of paired peaks: 612 WARNING @ Tue, 14 Jul 2020 12:36:50: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 14 Jul 2020 12:36:50: start model_add_line... INFO @ Tue, 14 Jul 2020 12:36:50: start X-correlation... INFO @ Tue, 14 Jul 2020 12:36:50: end of X-cor INFO @ Tue, 14 Jul 2020 12:36:50: #2 finished! INFO @ Tue, 14 Jul 2020 12:36:50: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 12:36:50: #2 alternative fragment length(s) may be 61,523,557 bps INFO @ Tue, 14 Jul 2020 12:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.20_model.r WARNING @ Tue, 14 Jul 2020 12:36:50: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:36:50: #2 You may need to consider one of the other alternative d(s): 61,523,557 WARNING @ Tue, 14 Jul 2020 12:36:50: #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 12:36:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:36:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:37:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:37:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:37:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:37:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521379/SRX8521379.20_summits.bed INFO @ Tue, 14 Jul 2020 12:37:11: Done! pass1 - making usageList (89 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 3 millis CompletedMACS2peakCalling