Job ID = 6530044 SRX = SRX647916 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: 00:03:44 12882872 reads; of these: 12882872 (100.00%) were unpaired; of these: 905339 (7.03%) aligned 0 times 9419112 (73.11%) aligned exactly 1 time 2558421 (19.86%) aligned >1 times 92.97% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 1044836 / 11977533 = 0.0872 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 03:17:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.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 03:17:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:17:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:17:15: 1000000 INFO @ Tue, 30 Jun 2020 03:17:23: 2000000 INFO @ Tue, 30 Jun 2020 03:17:31: 3000000 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 03:17:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.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 03:17:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:17:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:17:39: 4000000 INFO @ Tue, 30 Jun 2020 03:17:45: 1000000 INFO @ Tue, 30 Jun 2020 03:17:47: 5000000 INFO @ Tue, 30 Jun 2020 03:17:53: 2000000 INFO @ Tue, 30 Jun 2020 03:17:56: 6000000 INFO @ Tue, 30 Jun 2020 03:18:02: 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, 30 Jun 2020 03:18:05: 7000000 INFO @ Tue, 30 Jun 2020 03:18:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.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 03:18:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:18:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:18:11: 4000000 INFO @ Tue, 30 Jun 2020 03:18:14: 8000000 INFO @ Tue, 30 Jun 2020 03:18:15: 1000000 INFO @ Tue, 30 Jun 2020 03:18:19: 5000000 INFO @ Tue, 30 Jun 2020 03:18:23: 9000000 INFO @ Tue, 30 Jun 2020 03:18:24: 2000000 INFO @ Tue, 30 Jun 2020 03:18:28: 6000000 INFO @ Tue, 30 Jun 2020 03:18:32: 10000000 INFO @ Tue, 30 Jun 2020 03:18:33: 3000000 INFO @ Tue, 30 Jun 2020 03:18:37: 7000000 INFO @ Tue, 30 Jun 2020 03:18:41: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:18:41: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:18:41: #1 total tags in treatment: 10932697 INFO @ Tue, 30 Jun 2020 03:18:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:18:41: #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 03:18:41: #1 tags after filtering in treatment: 10932696 INFO @ Tue, 30 Jun 2020 03:18:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:18:41: #1 finished! INFO @ Tue, 30 Jun 2020 03:18:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:18:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:18:42: 4000000 INFO @ Tue, 30 Jun 2020 03:18:42: #2 number of paired peaks: 342 WARNING @ Tue, 30 Jun 2020 03:18:42: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 30 Jun 2020 03:18:42: start model_add_line... INFO @ Tue, 30 Jun 2020 03:18:42: start X-correlation... INFO @ Tue, 30 Jun 2020 03:18:42: end of X-cor INFO @ Tue, 30 Jun 2020 03:18:42: #2 finished! INFO @ Tue, 30 Jun 2020 03:18:42: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:18:42: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 03:18:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.05_model.r WARNING @ Tue, 30 Jun 2020 03:18:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:18:42: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 03:18:42: #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 03:18:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:18:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:18:45: 8000000 INFO @ Tue, 30 Jun 2020 03:18:51: 5000000 INFO @ Tue, 30 Jun 2020 03:18:55: 9000000 INFO @ Tue, 30 Jun 2020 03:19:00: 6000000 INFO @ Tue, 30 Jun 2020 03:19:03: 10000000 INFO @ Tue, 30 Jun 2020 03:19:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:19:08: 7000000 INFO @ Tue, 30 Jun 2020 03:19:11: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:19:11: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:19:11: #1 total tags in treatment: 10932697 INFO @ Tue, 30 Jun 2020 03:19:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:19:11: #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 03:19:12: #1 tags after filtering in treatment: 10932696 INFO @ Tue, 30 Jun 2020 03:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:19:12: #1 finished! INFO @ Tue, 30 Jun 2020 03:19:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:19:12: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:19:13: #2 number of paired peaks: 342 WARNING @ Tue, 30 Jun 2020 03:19:13: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 30 Jun 2020 03:19:13: start model_add_line... INFO @ Tue, 30 Jun 2020 03:19:13: start X-correlation... INFO @ Tue, 30 Jun 2020 03:19:13: end of X-cor INFO @ Tue, 30 Jun 2020 03:19:13: #2 finished! INFO @ Tue, 30 Jun 2020 03:19:13: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:19:13: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 03:19:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.10_model.r WARNING @ Tue, 30 Jun 2020 03:19:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:19:13: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 03:19:13: #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 03:19:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:19:17: 8000000 INFO @ Tue, 30 Jun 2020 03:19:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:19:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:19:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.05_summits.bed INFO @ Tue, 30 Jun 2020 03:19:18: Done! pass1 - making usageList (529 chroms): 1 millis pass2 - checking and writing primary data (1938 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:19:25: 9000000 INFO @ Tue, 30 Jun 2020 03:19:33: 10000000 INFO @ Tue, 30 Jun 2020 03:19:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:19:40: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:19:40: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:19:40: #1 total tags in treatment: 10932697 INFO @ Tue, 30 Jun 2020 03:19:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:19:40: #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 03:19:41: #1 tags after filtering in treatment: 10932696 INFO @ Tue, 30 Jun 2020 03:19:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:19:41: #1 finished! INFO @ Tue, 30 Jun 2020 03:19:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:19:42: #2 number of paired peaks: 342 WARNING @ Tue, 30 Jun 2020 03:19:42: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 30 Jun 2020 03:19:42: start model_add_line... INFO @ Tue, 30 Jun 2020 03:19:42: start X-correlation... INFO @ Tue, 30 Jun 2020 03:19:42: end of X-cor INFO @ Tue, 30 Jun 2020 03:19:42: #2 finished! INFO @ Tue, 30 Jun 2020 03:19:42: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:19:42: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 03:19:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.20_model.r WARNING @ Tue, 30 Jun 2020 03:19:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:19:42: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 03:19:42: #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 03:19:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:19:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:19:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:19:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.10_summits.bed INFO @ Tue, 30 Jun 2020 03:19:47: Done! pass1 - making usageList (374 chroms): 2 millis pass2 - checking and writing primary data (948 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:20:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:20:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:20:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:20:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647916/SRX647916.20_summits.bed INFO @ Tue, 30 Jun 2020 03:20:16: Done! pass1 - making usageList (178 chroms): 1 millis pass2 - checking and writing primary data (339 records, 4 fields): 7 millis CompletedMACS2peakCalling