Job ID = 14171817 SRX = SRX9986159 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: 00:04:03 17245690 reads; of these: 17245690 (100.00%) were unpaired; of these: 2389768 (13.86%) aligned 0 times 10968718 (63.60%) aligned exactly 1 time 3887204 (22.54%) aligned >1 times 86.14% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 2804839 / 14855922 = 0.1888 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 13:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.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 13:08:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:08:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:08:14: 1000000 INFO @ Sat, 11 Dec 2021 13:08:19: 2000000 INFO @ Sat, 11 Dec 2021 13:08:25: 3000000 INFO @ Sat, 11 Dec 2021 13:08:30: 4000000 INFO @ Sat, 11 Dec 2021 13:08:35: 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 @ Sat, 11 Dec 2021 13:08:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.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 13:08:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:08:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:08:42: 6000000 INFO @ Sat, 11 Dec 2021 13:08:46: 1000000 INFO @ Sat, 11 Dec 2021 13:08:49: 7000000 INFO @ Sat, 11 Dec 2021 13:08:54: 2000000 INFO @ Sat, 11 Dec 2021 13:08:56: 8000000 INFO @ Sat, 11 Dec 2021 13:09:01: 3000000 INFO @ Sat, 11 Dec 2021 13:09:02: 9000000 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 13:09:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.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 13:09:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:09:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:09:09: 4000000 INFO @ Sat, 11 Dec 2021 13:09:10: 10000000 INFO @ Sat, 11 Dec 2021 13:09:16: 1000000 INFO @ Sat, 11 Dec 2021 13:09:17: 5000000 INFO @ Sat, 11 Dec 2021 13:09:17: 11000000 INFO @ Sat, 11 Dec 2021 13:09:23: 2000000 INFO @ Sat, 11 Dec 2021 13:09:24: 12000000 INFO @ Sat, 11 Dec 2021 13:09:24: 6000000 INFO @ Sat, 11 Dec 2021 13:09:25: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:09:25: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:09:25: #1 total tags in treatment: 12051083 INFO @ Sat, 11 Dec 2021 13:09:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:09:25: #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 13:09:25: #1 tags after filtering in treatment: 12050991 INFO @ Sat, 11 Dec 2021 13:09:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:09:25: #1 finished! INFO @ Sat, 11 Dec 2021 13:09:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:09:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:09:26: #2 number of paired peaks: 206 WARNING @ Sat, 11 Dec 2021 13:09:26: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 11 Dec 2021 13:09:26: start model_add_line... INFO @ Sat, 11 Dec 2021 13:09:26: start X-correlation... INFO @ Sat, 11 Dec 2021 13:09:26: end of X-cor INFO @ Sat, 11 Dec 2021 13:09:26: #2 finished! INFO @ Sat, 11 Dec 2021 13:09:26: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 13:09:26: #2 alternative fragment length(s) may be 19,48,82,110,134,480,515,567,589 bps INFO @ Sat, 11 Dec 2021 13:09:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.05_model.r WARNING @ Sat, 11 Dec 2021 13:09:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:09:26: #2 You may need to consider one of the other alternative d(s): 19,48,82,110,134,480,515,567,589 WARNING @ Sat, 11 Dec 2021 13:09:26: #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 13:09:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:09:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:09:31: 3000000 INFO @ Sat, 11 Dec 2021 13:09:32: 7000000 INFO @ Sat, 11 Dec 2021 13:09:38: 4000000 INFO @ Sat, 11 Dec 2021 13:09:40: 8000000 INFO @ Sat, 11 Dec 2021 13:09:46: 5000000 INFO @ Sat, 11 Dec 2021 13:09:47: 9000000 INFO @ Sat, 11 Dec 2021 13:09:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:09:53: 6000000 INFO @ Sat, 11 Dec 2021 13:09:55: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:10:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:10:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:10:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.05_summits.bed INFO @ Sat, 11 Dec 2021 13:10:00: Done! pass1 - making usageList (415 chroms): 1 millis pass2 - checking and writing primary data (1244 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:10:01: 7000000 INFO @ Sat, 11 Dec 2021 13:10:03: 11000000 INFO @ Sat, 11 Dec 2021 13:10:08: 8000000 INFO @ Sat, 11 Dec 2021 13:10:10: 12000000 INFO @ Sat, 11 Dec 2021 13:10:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:10:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:10:11: #1 total tags in treatment: 12051083 INFO @ Sat, 11 Dec 2021 13:10:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:10:11: #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 13:10:11: #1 tags after filtering in treatment: 12050991 INFO @ Sat, 11 Dec 2021 13:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:10:11: #1 finished! INFO @ Sat, 11 Dec 2021 13:10:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:10:12: #2 number of paired peaks: 206 WARNING @ Sat, 11 Dec 2021 13:10:12: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 11 Dec 2021 13:10:12: start model_add_line... INFO @ Sat, 11 Dec 2021 13:10:12: start X-correlation... INFO @ Sat, 11 Dec 2021 13:10:12: end of X-cor INFO @ Sat, 11 Dec 2021 13:10:12: #2 finished! INFO @ Sat, 11 Dec 2021 13:10:12: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 13:10:12: #2 alternative fragment length(s) may be 19,48,82,110,134,480,515,567,589 bps INFO @ Sat, 11 Dec 2021 13:10:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.10_model.r WARNING @ Sat, 11 Dec 2021 13:10:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:10:12: #2 You may need to consider one of the other alternative d(s): 19,48,82,110,134,480,515,567,589 WARNING @ Sat, 11 Dec 2021 13:10:12: #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 13:10:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:10:15: 9000000 INFO @ Sat, 11 Dec 2021 13:10:22: 10000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:10:29: 11000000 INFO @ Sat, 11 Dec 2021 13:10:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:10:36: 12000000 INFO @ Sat, 11 Dec 2021 13:10:36: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:10:36: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:10:36: #1 total tags in treatment: 12051083 INFO @ Sat, 11 Dec 2021 13:10:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:10:36: #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 13:10:36: #1 tags after filtering in treatment: 12050991 INFO @ Sat, 11 Dec 2021 13:10:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:10:36: #1 finished! INFO @ Sat, 11 Dec 2021 13:10:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:10:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:10:37: #2 number of paired peaks: 206 WARNING @ Sat, 11 Dec 2021 13:10:37: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 11 Dec 2021 13:10:37: start model_add_line... INFO @ Sat, 11 Dec 2021 13:10:37: start X-correlation... INFO @ Sat, 11 Dec 2021 13:10:37: end of X-cor INFO @ Sat, 11 Dec 2021 13:10:37: #2 finished! INFO @ Sat, 11 Dec 2021 13:10:37: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 13:10:37: #2 alternative fragment length(s) may be 19,48,82,110,134,480,515,567,589 bps INFO @ Sat, 11 Dec 2021 13:10:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.20_model.r WARNING @ Sat, 11 Dec 2021 13:10:37: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:10:37: #2 You may need to consider one of the other alternative d(s): 19,48,82,110,134,480,515,567,589 WARNING @ Sat, 11 Dec 2021 13:10:37: #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 13:10:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:10:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:10:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:10:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:10:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.10_summits.bed INFO @ Sat, 11 Dec 2021 13:10:46: Done! pass1 - making usageList (150 chroms): 2 millis pass2 - checking and writing primary data (324 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:11:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:11:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:11:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:11:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986159/SRX9986159.20_summits.bed INFO @ Sat, 11 Dec 2021 13:11:12: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 3 millis CompletedMACS2peakCalling