Job ID = 14171678 SRX = SRX9986117 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: 00:04:52 18689220 reads; of these: 18689220 (100.00%) were unpaired; of these: 1502910 (8.04%) aligned 0 times 12523805 (67.01%) aligned exactly 1 time 4662505 (24.95%) aligned >1 times 91.96% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 3418210 / 17186310 = 0.1989 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:33:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.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, 11 Dec 2021 12:33:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:33:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:33:37: 1000000 INFO @ Sat, 11 Dec 2021 12:33:42: 2000000 INFO @ Sat, 11 Dec 2021 12:33:46: 3000000 INFO @ Sat, 11 Dec 2021 12:33:51: 4000000 INFO @ Sat, 11 Dec 2021 12:33:56: 5000000 INFO @ Sat, 11 Dec 2021 12:34:00: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:34:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.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, 11 Dec 2021 12:34:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:34:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:34:05: 7000000 INFO @ Sat, 11 Dec 2021 12:34:08: 1000000 INFO @ Sat, 11 Dec 2021 12:34:10: 8000000 INFO @ Sat, 11 Dec 2021 12:34:14: 2000000 INFO @ Sat, 11 Dec 2021 12:34:15: 9000000 INFO @ Sat, 11 Dec 2021 12:34:19: 3000000 INFO @ Sat, 11 Dec 2021 12:34:20: 10000000 INFO @ Sat, 11 Dec 2021 12:34:25: 4000000 INFO @ Sat, 11 Dec 2021 12:34:25: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:34:31: 12000000 INFO @ Sat, 11 Dec 2021 12:34:31: 5000000 INFO @ Sat, 11 Dec 2021 12:34:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.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, 11 Dec 2021 12:34:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:34:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:34:36: 13000000 INFO @ Sat, 11 Dec 2021 12:34:37: 6000000 INFO @ Sat, 11 Dec 2021 12:34:37: 1000000 INFO @ Sat, 11 Dec 2021 12:34:40: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:34:40: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:34:40: #1 total tags in treatment: 13768100 INFO @ Sat, 11 Dec 2021 12:34:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:34:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:34:40: #1 tags after filtering in treatment: 13768030 INFO @ Sat, 11 Dec 2021 12:34:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:34:40: #1 finished! INFO @ Sat, 11 Dec 2021 12:34:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:34:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:34:41: #2 number of paired peaks: 150 WARNING @ Sat, 11 Dec 2021 12:34:41: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 11 Dec 2021 12:34:41: start model_add_line... INFO @ Sat, 11 Dec 2021 12:34:41: start X-correlation... INFO @ Sat, 11 Dec 2021 12:34:41: end of X-cor INFO @ Sat, 11 Dec 2021 12:34:41: #2 finished! INFO @ Sat, 11 Dec 2021 12:34:41: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Dec 2021 12:34:41: #2 alternative fragment length(s) may be 0,21,38,59,117,129,551,585 bps INFO @ Sat, 11 Dec 2021 12:34:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.05_model.r WARNING @ Sat, 11 Dec 2021 12:34:41: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:34:41: #2 You may need to consider one of the other alternative d(s): 0,21,38,59,117,129,551,585 WARNING @ Sat, 11 Dec 2021 12:34:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:34:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:34:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:34:42: 7000000 INFO @ Sat, 11 Dec 2021 12:34:43: 2000000 INFO @ Sat, 11 Dec 2021 12:34:48: 3000000 INFO @ Sat, 11 Dec 2021 12:34:48: 8000000 INFO @ Sat, 11 Dec 2021 12:34:53: 4000000 INFO @ Sat, 11 Dec 2021 12:34:54: 9000000 INFO @ Sat, 11 Dec 2021 12:34:58: 5000000 INFO @ Sat, 11 Dec 2021 12:35:00: 10000000 INFO @ Sat, 11 Dec 2021 12:35:03: 6000000 INFO @ Sat, 11 Dec 2021 12:35:06: 11000000 INFO @ Sat, 11 Dec 2021 12:35:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:35:08: 7000000 INFO @ Sat, 11 Dec 2021 12:35:12: 12000000 INFO @ Sat, 11 Dec 2021 12:35:13: 8000000 INFO @ Sat, 11 Dec 2021 12:35:17: 13000000 INFO @ Sat, 11 Dec 2021 12:35:18: 9000000 INFO @ Sat, 11 Dec 2021 12:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.05_summits.bed INFO @ Sat, 11 Dec 2021 12:35:20: Done! pass1 - making usageList (471 chroms): 1 millis pass2 - checking and writing primary data (1682 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:35:22: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:35:22: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:35:22: #1 total tags in treatment: 13768100 INFO @ Sat, 11 Dec 2021 12:35:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:35:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:35:22: #1 tags after filtering in treatment: 13768030 INFO @ Sat, 11 Dec 2021 12:35:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:35:22: #1 finished! INFO @ Sat, 11 Dec 2021 12:35:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:35:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:35:23: #2 number of paired peaks: 150 WARNING @ Sat, 11 Dec 2021 12:35:23: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 11 Dec 2021 12:35:23: start model_add_line... INFO @ Sat, 11 Dec 2021 12:35:23: 10000000 INFO @ Sat, 11 Dec 2021 12:35:23: start X-correlation... INFO @ Sat, 11 Dec 2021 12:35:23: end of X-cor INFO @ Sat, 11 Dec 2021 12:35:23: #2 finished! INFO @ Sat, 11 Dec 2021 12:35:23: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Dec 2021 12:35:23: #2 alternative fragment length(s) may be 0,21,38,59,117,129,551,585 bps INFO @ Sat, 11 Dec 2021 12:35:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.10_model.r WARNING @ Sat, 11 Dec 2021 12:35:23: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:35:23: #2 You may need to consider one of the other alternative d(s): 0,21,38,59,117,129,551,585 WARNING @ Sat, 11 Dec 2021 12:35:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:35:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:35:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:35:28: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:35:33: 12000000 INFO @ Sat, 11 Dec 2021 12:35:38: 13000000 INFO @ Sat, 11 Dec 2021 12:35:42: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:35:42: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:35:42: #1 total tags in treatment: 13768100 INFO @ Sat, 11 Dec 2021 12:35:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:35:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:35:42: #1 tags after filtering in treatment: 13768030 INFO @ Sat, 11 Dec 2021 12:35:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:35:42: #1 finished! INFO @ Sat, 11 Dec 2021 12:35:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:35:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:35:43: #2 number of paired peaks: 150 WARNING @ Sat, 11 Dec 2021 12:35:43: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 11 Dec 2021 12:35:43: start model_add_line... INFO @ Sat, 11 Dec 2021 12:35:43: start X-correlation... INFO @ Sat, 11 Dec 2021 12:35:43: end of X-cor INFO @ Sat, 11 Dec 2021 12:35:43: #2 finished! INFO @ Sat, 11 Dec 2021 12:35:43: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Dec 2021 12:35:43: #2 alternative fragment length(s) may be 0,21,38,59,117,129,551,585 bps INFO @ Sat, 11 Dec 2021 12:35:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.20_model.r WARNING @ Sat, 11 Dec 2021 12:35:43: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:35:43: #2 You may need to consider one of the other alternative d(s): 0,21,38,59,117,129,551,585 WARNING @ Sat, 11 Dec 2021 12:35:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:35:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:35:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:35:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:36:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:36:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:36:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.10_summits.bed INFO @ Sat, 11 Dec 2021 12:36:02: Done! pass1 - making usageList (252 chroms): 1 millis pass2 - checking and writing primary data (531 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:36:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:36:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:36:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:36:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986117/SRX9986117.20_summits.bed INFO @ Sat, 11 Dec 2021 12:36:21: Done! pass1 - making usageList (82 chroms): 0 millis pass2 - checking and writing primary data (146 records, 4 fields): 5 millis CompletedMACS2peakCalling