Job ID = 14167349 SRX = SRX7723722 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: 00:07:28 26142343 reads; of these: 26142343 (100.00%) were unpaired; of these: 5403608 (20.67%) aligned 0 times 17695597 (67.69%) aligned exactly 1 time 3043138 (11.64%) aligned >1 times 79.33% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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 12 files... [bam_rmdupse_core] 6185289 / 20738735 = 0.2982 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 @ Fri, 10 Dec 2021 12:10:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.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 @ Fri, 10 Dec 2021 12:10:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:10:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:10:15: 1000000 INFO @ Fri, 10 Dec 2021 12:10:20: 2000000 INFO @ Fri, 10 Dec 2021 12:10:26: 3000000 INFO @ Fri, 10 Dec 2021 12:10:31: 4000000 INFO @ Fri, 10 Dec 2021 12:10:36: 5000000 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 @ Fri, 10 Dec 2021 12:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.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 @ Fri, 10 Dec 2021 12:10:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:10:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:10:42: 6000000 INFO @ Fri, 10 Dec 2021 12:10:46: 1000000 INFO @ Fri, 10 Dec 2021 12:10:47: 7000000 INFO @ Fri, 10 Dec 2021 12:10:51: 2000000 INFO @ Fri, 10 Dec 2021 12:10:53: 8000000 INFO @ Fri, 10 Dec 2021 12:10:57: 3000000 INFO @ Fri, 10 Dec 2021 12:10:59: 9000000 INFO @ Fri, 10 Dec 2021 12:11:03: 4000000 INFO @ Fri, 10 Dec 2021 12:11:05: 10000000 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 @ Fri, 10 Dec 2021 12:11:09: 5000000 INFO @ Fri, 10 Dec 2021 12:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.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 @ Fri, 10 Dec 2021 12:11:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:11:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:11:10: 11000000 INFO @ Fri, 10 Dec 2021 12:11:15: 6000000 INFO @ Fri, 10 Dec 2021 12:11:17: 1000000 INFO @ Fri, 10 Dec 2021 12:11:17: 12000000 INFO @ Fri, 10 Dec 2021 12:11:21: 7000000 INFO @ Fri, 10 Dec 2021 12:11:23: 13000000 INFO @ Fri, 10 Dec 2021 12:11:23: 2000000 INFO @ Fri, 10 Dec 2021 12:11:27: 8000000 INFO @ Fri, 10 Dec 2021 12:11:29: 14000000 INFO @ Fri, 10 Dec 2021 12:11:30: 3000000 INFO @ Fri, 10 Dec 2021 12:11:33: 9000000 INFO @ Fri, 10 Dec 2021 12:11:33: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:11:33: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:11:33: #1 total tags in treatment: 14553446 INFO @ Fri, 10 Dec 2021 12:11:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:11:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:11:33: #1 tags after filtering in treatment: 14553310 INFO @ Fri, 10 Dec 2021 12:11:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:11:33: #1 finished! INFO @ Fri, 10 Dec 2021 12:11:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:11:34: #2 number of paired peaks: 309 WARNING @ Fri, 10 Dec 2021 12:11:34: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 10 Dec 2021 12:11:34: start model_add_line... INFO @ Fri, 10 Dec 2021 12:11:34: start X-correlation... INFO @ Fri, 10 Dec 2021 12:11:34: end of X-cor INFO @ Fri, 10 Dec 2021 12:11:34: #2 finished! INFO @ Fri, 10 Dec 2021 12:11:34: #2 predicted fragment length is 73 bps INFO @ Fri, 10 Dec 2021 12:11:34: #2 alternative fragment length(s) may be 4,73,574 bps INFO @ Fri, 10 Dec 2021 12:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05_model.r WARNING @ Fri, 10 Dec 2021 12:11:34: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:11:34: #2 You may need to consider one of the other alternative d(s): 4,73,574 WARNING @ Fri, 10 Dec 2021 12:11:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:11:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:11:37: 4000000 INFO @ Fri, 10 Dec 2021 12:11:39: 10000000 INFO @ Fri, 10 Dec 2021 12:11:43: 5000000 INFO @ Fri, 10 Dec 2021 12:11:45: 11000000 INFO @ Fri, 10 Dec 2021 12:11:50: 6000000 INFO @ Fri, 10 Dec 2021 12:11:52: 12000000 INFO @ Fri, 10 Dec 2021 12:11:57: 7000000 INFO @ Fri, 10 Dec 2021 12:11:58: 13000000 INFO @ Fri, 10 Dec 2021 12:12:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:12:03: 8000000 INFO @ Fri, 10 Dec 2021 12:12:04: 14000000 INFO @ Fri, 10 Dec 2021 12:12:07: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:12:07: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:12:07: #1 total tags in treatment: 14553446 INFO @ Fri, 10 Dec 2021 12:12:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:12:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:12:08: #1 tags after filtering in treatment: 14553310 INFO @ Fri, 10 Dec 2021 12:12:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:12:08: #1 finished! INFO @ Fri, 10 Dec 2021 12:12:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:12:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:12:09: #2 number of paired peaks: 309 WARNING @ Fri, 10 Dec 2021 12:12:09: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 10 Dec 2021 12:12:09: start model_add_line... INFO @ Fri, 10 Dec 2021 12:12:09: start X-correlation... INFO @ Fri, 10 Dec 2021 12:12:09: end of X-cor INFO @ Fri, 10 Dec 2021 12:12:09: #2 finished! INFO @ Fri, 10 Dec 2021 12:12:09: #2 predicted fragment length is 73 bps INFO @ Fri, 10 Dec 2021 12:12:09: #2 alternative fragment length(s) may be 4,73,574 bps INFO @ Fri, 10 Dec 2021 12:12:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10_model.r WARNING @ Fri, 10 Dec 2021 12:12:09: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:12:09: #2 You may need to consider one of the other alternative d(s): 4,73,574 WARNING @ Fri, 10 Dec 2021 12:12:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:12:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:12:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:12:10: 9000000 INFO @ Fri, 10 Dec 2021 12:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05_summits.bed INFO @ Fri, 10 Dec 2021 12:12:15: Done! INFO @ Fri, 10 Dec 2021 12:12:16: 10000000 BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (441 chroms): 2 millis pass2 - checking and writing primary data (1552 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:12:23: 11000000 INFO @ Fri, 10 Dec 2021 12:12:30: 12000000 INFO @ Fri, 10 Dec 2021 12:12:36: 13000000 INFO @ Fri, 10 Dec 2021 12:12:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:12:42: 14000000 INFO @ Fri, 10 Dec 2021 12:12:46: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:12:46: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:12:46: #1 total tags in treatment: 14553446 INFO @ Fri, 10 Dec 2021 12:12:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:12:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:12:47: #1 tags after filtering in treatment: 14553310 INFO @ Fri, 10 Dec 2021 12:12:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:12:47: #1 finished! INFO @ Fri, 10 Dec 2021 12:12:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:12:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:12:48: #2 number of paired peaks: 309 WARNING @ Fri, 10 Dec 2021 12:12:48: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 10 Dec 2021 12:12:48: start model_add_line... INFO @ Fri, 10 Dec 2021 12:12:48: start X-correlation... INFO @ Fri, 10 Dec 2021 12:12:48: end of X-cor INFO @ Fri, 10 Dec 2021 12:12:48: #2 finished! INFO @ Fri, 10 Dec 2021 12:12:48: #2 predicted fragment length is 73 bps INFO @ Fri, 10 Dec 2021 12:12:48: #2 alternative fragment length(s) may be 4,73,574 bps INFO @ Fri, 10 Dec 2021 12:12:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20_model.r WARNING @ Fri, 10 Dec 2021 12:12:48: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:12:48: #2 You may need to consider one of the other alternative d(s): 4,73,574 WARNING @ Fri, 10 Dec 2021 12:12:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:12:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:12:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:12:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:12:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:12:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10_summits.bed INFO @ Fri, 10 Dec 2021 12:12:50: Done! pass1 - making usageList (307 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:13:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:13:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:13:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:13:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20_summits.bed INFO @ Fri, 10 Dec 2021 12:13:28: Done! pass1 - making usageList (128 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 9 millis CompletedMACS2peakCalling