Job ID = 14167655 SRX = SRX4712965 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: 00:05:56 20379348 reads; of these: 20379348 (100.00%) were unpaired; of these: 588011 (2.89%) aligned 0 times 15357327 (75.36%) aligned exactly 1 time 4434010 (21.76%) aligned >1 times 97.11% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 2101392 / 19791337 = 0.1062 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 13:12:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.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 13:12:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:12:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:12:36: 1000000 INFO @ Fri, 10 Dec 2021 13:12:44: 2000000 INFO @ Fri, 10 Dec 2021 13:12:52: 3000000 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 13:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.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 13:12:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:12:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:13:00: 4000000 INFO @ Fri, 10 Dec 2021 13:13:06: 1000000 INFO @ Fri, 10 Dec 2021 13:13:08: 5000000 INFO @ Fri, 10 Dec 2021 13:13:14: 2000000 INFO @ Fri, 10 Dec 2021 13:13:15: 6000000 INFO @ Fri, 10 Dec 2021 13:13:22: 3000000 INFO @ Fri, 10 Dec 2021 13:13:22: 7000000 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 13:13:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.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 13:13:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:13:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:13:30: 8000000 INFO @ Fri, 10 Dec 2021 13:13:30: 4000000 INFO @ Fri, 10 Dec 2021 13:13:37: 1000000 INFO @ Fri, 10 Dec 2021 13:13:37: 9000000 INFO @ Fri, 10 Dec 2021 13:13:38: 5000000 INFO @ Fri, 10 Dec 2021 13:13:45: 10000000 INFO @ Fri, 10 Dec 2021 13:13:45: 2000000 INFO @ Fri, 10 Dec 2021 13:13:46: 6000000 INFO @ Fri, 10 Dec 2021 13:13:52: 11000000 INFO @ Fri, 10 Dec 2021 13:13:54: 7000000 INFO @ Fri, 10 Dec 2021 13:13:54: 3000000 INFO @ Fri, 10 Dec 2021 13:13:59: 12000000 INFO @ Fri, 10 Dec 2021 13:14:01: 8000000 INFO @ Fri, 10 Dec 2021 13:14:03: 4000000 INFO @ Fri, 10 Dec 2021 13:14:07: 13000000 INFO @ Fri, 10 Dec 2021 13:14:09: 9000000 INFO @ Fri, 10 Dec 2021 13:14:12: 5000000 INFO @ Fri, 10 Dec 2021 13:14:14: 14000000 INFO @ Fri, 10 Dec 2021 13:14:17: 10000000 INFO @ Fri, 10 Dec 2021 13:14:21: 6000000 INFO @ Fri, 10 Dec 2021 13:14:22: 15000000 INFO @ Fri, 10 Dec 2021 13:14:25: 11000000 INFO @ Fri, 10 Dec 2021 13:14:29: 7000000 INFO @ Fri, 10 Dec 2021 13:14:29: 16000000 INFO @ Fri, 10 Dec 2021 13:14:33: 12000000 INFO @ Fri, 10 Dec 2021 13:14:37: 17000000 INFO @ Fri, 10 Dec 2021 13:14:38: 8000000 INFO @ Fri, 10 Dec 2021 13:14:40: 13000000 INFO @ Fri, 10 Dec 2021 13:14:42: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:14:42: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:14:42: #1 total tags in treatment: 17689945 INFO @ Fri, 10 Dec 2021 13:14:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:14:42: #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 13:14:43: #1 tags after filtering in treatment: 17689940 INFO @ Fri, 10 Dec 2021 13:14:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:14:43: #1 finished! INFO @ Fri, 10 Dec 2021 13:14:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:14:44: #2 number of paired peaks: 337 WARNING @ Fri, 10 Dec 2021 13:14:44: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Fri, 10 Dec 2021 13:14:44: start model_add_line... INFO @ Fri, 10 Dec 2021 13:14:45: start X-correlation... INFO @ Fri, 10 Dec 2021 13:14:45: end of X-cor INFO @ Fri, 10 Dec 2021 13:14:45: #2 finished! INFO @ Fri, 10 Dec 2021 13:14:45: #2 predicted fragment length is 56 bps INFO @ Fri, 10 Dec 2021 13:14:45: #2 alternative fragment length(s) may be 4,56 bps INFO @ Fri, 10 Dec 2021 13:14:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.05_model.r WARNING @ Fri, 10 Dec 2021 13:14:45: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:14:45: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Fri, 10 Dec 2021 13:14:45: #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 13:14:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:14:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:14:46: 9000000 INFO @ Fri, 10 Dec 2021 13:14:48: 14000000 INFO @ Fri, 10 Dec 2021 13:14:55: 10000000 INFO @ Fri, 10 Dec 2021 13:14:56: 15000000 INFO @ Fri, 10 Dec 2021 13:15:03: 16000000 INFO @ Fri, 10 Dec 2021 13:15:03: 11000000 INFO @ Fri, 10 Dec 2021 13:15:10: 17000000 INFO @ Fri, 10 Dec 2021 13:15:11: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:15:16: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:15:16: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:15:16: #1 total tags in treatment: 17689945 INFO @ Fri, 10 Dec 2021 13:15:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:15:16: #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 13:15:17: #1 tags after filtering in treatment: 17689940 INFO @ Fri, 10 Dec 2021 13:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:15:17: #1 finished! INFO @ Fri, 10 Dec 2021 13:15:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:15:18: #2 number of paired peaks: 337 WARNING @ Fri, 10 Dec 2021 13:15:18: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Fri, 10 Dec 2021 13:15:18: start model_add_line... INFO @ Fri, 10 Dec 2021 13:15:18: start X-correlation... INFO @ Fri, 10 Dec 2021 13:15:18: end of X-cor INFO @ Fri, 10 Dec 2021 13:15:18: #2 finished! INFO @ Fri, 10 Dec 2021 13:15:18: #2 predicted fragment length is 56 bps INFO @ Fri, 10 Dec 2021 13:15:18: #2 alternative fragment length(s) may be 4,56 bps INFO @ Fri, 10 Dec 2021 13:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.10_model.r WARNING @ Fri, 10 Dec 2021 13:15:18: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:15:18: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Fri, 10 Dec 2021 13:15:18: #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 13:15:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:15:20: 13000000 INFO @ Fri, 10 Dec 2021 13:15:28: 14000000 INFO @ Fri, 10 Dec 2021 13:15:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:15:37: 15000000 INFO @ Fri, 10 Dec 2021 13:15:46: 16000000 INFO @ Fri, 10 Dec 2021 13:15:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:15:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:15:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.05_summits.bed INFO @ Fri, 10 Dec 2021 13:15:52: Done! pass1 - making usageList (616 chroms): 3 millis pass2 - checking and writing primary data (2626 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:15:54: 17000000 INFO @ Fri, 10 Dec 2021 13:16:00: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:16:00: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:16:00: #1 total tags in treatment: 17689945 INFO @ Fri, 10 Dec 2021 13:16:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:16:00: #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 13:16:01: #1 tags after filtering in treatment: 17689940 INFO @ Fri, 10 Dec 2021 13:16:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:16:01: #1 finished! INFO @ Fri, 10 Dec 2021 13:16:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:16:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:16:03: #2 number of paired peaks: 337 WARNING @ Fri, 10 Dec 2021 13:16:03: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Fri, 10 Dec 2021 13:16:03: start model_add_line... INFO @ Fri, 10 Dec 2021 13:16:03: start X-correlation... INFO @ Fri, 10 Dec 2021 13:16:03: end of X-cor INFO @ Fri, 10 Dec 2021 13:16:03: #2 finished! INFO @ Fri, 10 Dec 2021 13:16:03: #2 predicted fragment length is 56 bps INFO @ Fri, 10 Dec 2021 13:16:03: #2 alternative fragment length(s) may be 4,56 bps INFO @ Fri, 10 Dec 2021 13:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.20_model.r WARNING @ Fri, 10 Dec 2021 13:16:03: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:16:03: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Fri, 10 Dec 2021 13:16:03: #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 13:16:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:16:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:16:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:16:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:16:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:16:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.10_summits.bed INFO @ Fri, 10 Dec 2021 13:16:26: Done! pass1 - making usageList (379 chroms): 2 millis pass2 - checking and writing primary data (1168 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:16:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:17:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:17:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712965/SRX4712965.20_summits.bed INFO @ Fri, 10 Dec 2021 13:17:10: Done! pass1 - making usageList (218 chroms): 1 millis pass2 - checking and writing primary data (512 records, 4 fields): 16 millis CompletedMACS2peakCalling