Job ID = 12265442 SRX = SRX5010752 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: 00:08:41 33393909 reads; of these: 33393909 (100.00%) were unpaired; of these: 1200980 (3.60%) aligned 0 times 25751522 (77.11%) aligned exactly 1 time 6441407 (19.29%) aligned >1 times 96.40% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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 16 files... [bam_rmdupse_core] 17844410 / 32192929 = 0.5543 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:16:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.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 @ Sat, 03 Apr 2021 07:16:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:16:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:16:50: 1000000 INFO @ Sat, 03 Apr 2021 07:16:55: 2000000 INFO @ Sat, 03 Apr 2021 07:17:01: 3000000 INFO @ Sat, 03 Apr 2021 07:17:06: 4000000 INFO @ Sat, 03 Apr 2021 07:17:11: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:17:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.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 @ Sat, 03 Apr 2021 07:17:14: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:17:14: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:17:16: 6000000 INFO @ Sat, 03 Apr 2021 07:17:20: 1000000 INFO @ Sat, 03 Apr 2021 07:17:21: 7000000 INFO @ Sat, 03 Apr 2021 07:17:26: 2000000 INFO @ Sat, 03 Apr 2021 07:17:26: 8000000 INFO @ Sat, 03 Apr 2021 07:17:32: 9000000 INFO @ Sat, 03 Apr 2021 07:17:32: 3000000 INFO @ Sat, 03 Apr 2021 07:17:37: 10000000 INFO @ Sat, 03 Apr 2021 07:17:38: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:17:43: 11000000 INFO @ Sat, 03 Apr 2021 07:17:43: 5000000 INFO @ Sat, 03 Apr 2021 07:17:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.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 @ Sat, 03 Apr 2021 07:17:44: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:17:44: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:17:48: 12000000 INFO @ Sat, 03 Apr 2021 07:17:49: 6000000 INFO @ Sat, 03 Apr 2021 07:17:50: 1000000 INFO @ Sat, 03 Apr 2021 07:17:53: 13000000 INFO @ Sat, 03 Apr 2021 07:17:55: 7000000 INFO @ Sat, 03 Apr 2021 07:17:56: 2000000 INFO @ Sat, 03 Apr 2021 07:17:59: 14000000 INFO @ Sat, 03 Apr 2021 07:18:01: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:18:01: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:18:01: #1 total tags in treatment: 14348519 INFO @ Sat, 03 Apr 2021 07:18:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:18:01: 8000000 INFO @ Sat, 03 Apr 2021 07:18:01: #1 tags after filtering in treatment: 14348443 INFO @ Sat, 03 Apr 2021 07:18:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:18:01: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:02: 3000000 INFO @ Sat, 03 Apr 2021 07:18:02: #2 number of paired peaks: 560 WARNING @ Sat, 03 Apr 2021 07:18:02: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Sat, 03 Apr 2021 07:18:02: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:03: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:03: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:03: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:03: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Apr 2021 07:18:03: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 03 Apr 2021 07:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.05_model.r WARNING @ Sat, 03 Apr 2021 07:18:03: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:03: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 03 Apr 2021 07:18:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:18:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:07: 9000000 INFO @ Sat, 03 Apr 2021 07:18:08: 4000000 INFO @ Sat, 03 Apr 2021 07:18:13: 10000000 INFO @ Sat, 03 Apr 2021 07:18:14: 5000000 INFO @ Sat, 03 Apr 2021 07:18:19: 11000000 INFO @ Sat, 03 Apr 2021 07:18:20: 6000000 INFO @ Sat, 03 Apr 2021 07:18:25: 12000000 INFO @ Sat, 03 Apr 2021 07:18:25: 7000000 INFO @ Sat, 03 Apr 2021 07:18:30: 13000000 INFO @ Sat, 03 Apr 2021 07:18:31: 8000000 INFO @ Sat, 03 Apr 2021 07:18:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:18:36: 14000000 INFO @ Sat, 03 Apr 2021 07:18:37: 9000000 INFO @ Sat, 03 Apr 2021 07:18:39: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:18:39: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:18:39: #1 total tags in treatment: 14348519 INFO @ Sat, 03 Apr 2021 07:18:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:18:39: #1 tags after filtering in treatment: 14348443 INFO @ Sat, 03 Apr 2021 07:18:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:18:39: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:40: #2 number of paired peaks: 560 WARNING @ Sat, 03 Apr 2021 07:18:40: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Sat, 03 Apr 2021 07:18:40: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:40: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:40: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:40: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:40: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Apr 2021 07:18:40: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 03 Apr 2021 07:18:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.10_model.r WARNING @ Sat, 03 Apr 2021 07:18:40: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:40: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 03 Apr 2021 07:18:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:18:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:43: 10000000 INFO @ Sat, 03 Apr 2021 07:18:49: 11000000 INFO @ Sat, 03 Apr 2021 07:18:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:18:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:18:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.05_summits.bed INFO @ Sat, 03 Apr 2021 07:18:51: Done! pass1 - making usageList (476 chroms): 3 millis pass2 - checking and writing primary data (9451 records, 4 fields): 25 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:18:55: 12000000 INFO @ Sat, 03 Apr 2021 07:19:00: 13000000 INFO @ Sat, 03 Apr 2021 07:19:06: 14000000 INFO @ Sat, 03 Apr 2021 07:19:08: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:19:08: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:19:08: #1 total tags in treatment: 14348519 INFO @ Sat, 03 Apr 2021 07:19:08: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:19:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:19:09: #1 tags after filtering in treatment: 14348443 INFO @ Sat, 03 Apr 2021 07:19:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:19:09: #1 finished! INFO @ Sat, 03 Apr 2021 07:19:09: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:19:10: #2 number of paired peaks: 560 WARNING @ Sat, 03 Apr 2021 07:19:10: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Sat, 03 Apr 2021 07:19:10: start model_add_line... INFO @ Sat, 03 Apr 2021 07:19:10: start X-correlation... INFO @ Sat, 03 Apr 2021 07:19:10: end of X-cor INFO @ Sat, 03 Apr 2021 07:19:10: #2 finished! INFO @ Sat, 03 Apr 2021 07:19:10: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Apr 2021 07:19:10: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 03 Apr 2021 07:19:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.20_model.r WARNING @ Sat, 03 Apr 2021 07:19:10: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:19:10: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 03 Apr 2021 07:19:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:19:10: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:19:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:19:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:19:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:19:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:19:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.10_summits.bed INFO @ Sat, 03 Apr 2021 07:19:26: Done! pass1 - making usageList (298 chroms): 2 millis pass2 - checking and writing primary data (3584 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:19:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:19:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:19:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:19:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010752/SRX5010752.20_summits.bed INFO @ Sat, 03 Apr 2021 07:19:56: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (778 records, 4 fields): 10 millis CompletedMACS2peakCalling