Job ID = 14170966 SRX = SRX8689091 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: 00:01:55 6859328 reads; of these: 6859328 (100.00%) were unpaired; of these: 266223 (3.88%) aligned 0 times 4377174 (63.81%) aligned exactly 1 time 2215931 (32.31%) aligned >1 times 96.12% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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_rmdupse_core] 517976 / 6593105 = 0.0786 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 09:10:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.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 09:10:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:10:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:10:18: 1000000 INFO @ Sat, 11 Dec 2021 09:10:24: 2000000 INFO @ Sat, 11 Dec 2021 09:10:29: 3000000 INFO @ Sat, 11 Dec 2021 09:10:35: 4000000 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 09:10:41: 5000000 INFO @ Sat, 11 Dec 2021 09:10:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.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 09:10:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:10:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:10:47: 6000000 INFO @ Sat, 11 Dec 2021 09:10:47: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:10:47: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:10:47: #1 total tags in treatment: 6075129 INFO @ Sat, 11 Dec 2021 09:10:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:10:47: #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 09:10:48: #1 tags after filtering in treatment: 6075123 INFO @ Sat, 11 Dec 2021 09:10:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:10:48: #1 finished! INFO @ Sat, 11 Dec 2021 09:10:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:10:48: #2 number of paired peaks: 883 WARNING @ Sat, 11 Dec 2021 09:10:48: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Sat, 11 Dec 2021 09:10:48: start model_add_line... INFO @ Sat, 11 Dec 2021 09:10:48: start X-correlation... INFO @ Sat, 11 Dec 2021 09:10:48: end of X-cor INFO @ Sat, 11 Dec 2021 09:10:48: #2 finished! INFO @ Sat, 11 Dec 2021 09:10:48: #2 predicted fragment length is 73 bps INFO @ Sat, 11 Dec 2021 09:10:48: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 11 Dec 2021 09:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.05_model.r WARNING @ Sat, 11 Dec 2021 09:10:48: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:10:48: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 11 Dec 2021 09:10:48: #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 09:10:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:10:48: 1000000 INFO @ Sat, 11 Dec 2021 09:10:54: 2000000 INFO @ Sat, 11 Dec 2021 09:11:00: 3000000 INFO @ Sat, 11 Dec 2021 09:11:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:11:05: 4000000 INFO @ Sat, 11 Dec 2021 09:11:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:11:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:11:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.05_summits.bed INFO @ Sat, 11 Dec 2021 09:11:08: Done! pass1 - making usageList (581 chroms): 1 millis pass2 - checking and writing primary data (1823 records, 4 fields): 20 millis CompletedMACS2peakCalling 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 09:11:11: 5000000 INFO @ Sat, 11 Dec 2021 09:11:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.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 09:11:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:11:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:11:17: 6000000 INFO @ Sat, 11 Dec 2021 09:11:18: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:11:18: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:11:18: #1 total tags in treatment: 6075129 INFO @ Sat, 11 Dec 2021 09:11:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:11:18: #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 09:11:18: #1 tags after filtering in treatment: 6075123 INFO @ Sat, 11 Dec 2021 09:11:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:11:18: #1 finished! INFO @ Sat, 11 Dec 2021 09:11:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:11:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:11:19: 1000000 INFO @ Sat, 11 Dec 2021 09:11:19: #2 number of paired peaks: 883 WARNING @ Sat, 11 Dec 2021 09:11:19: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Sat, 11 Dec 2021 09:11:19: start model_add_line... INFO @ Sat, 11 Dec 2021 09:11:19: start X-correlation... INFO @ Sat, 11 Dec 2021 09:11:19: end of X-cor INFO @ Sat, 11 Dec 2021 09:11:19: #2 finished! INFO @ Sat, 11 Dec 2021 09:11:19: #2 predicted fragment length is 73 bps INFO @ Sat, 11 Dec 2021 09:11:19: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 11 Dec 2021 09:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.10_model.r WARNING @ Sat, 11 Dec 2021 09:11:19: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:11:19: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 11 Dec 2021 09:11:19: #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 09:11:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:11:24: 2000000 INFO @ Sat, 11 Dec 2021 09:11:30: 3000000 INFO @ Sat, 11 Dec 2021 09:11:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:11:36: 4000000 INFO @ Sat, 11 Dec 2021 09:11:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:11:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:11:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.10_summits.bed BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:11:39: Done! pass1 - making usageList (369 chroms): 1 millis pass2 - checking and writing primary data (821 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:11:41: 5000000 INFO @ Sat, 11 Dec 2021 09:11:47: 6000000 INFO @ Sat, 11 Dec 2021 09:11:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:11:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:11:48: #1 total tags in treatment: 6075129 INFO @ Sat, 11 Dec 2021 09:11:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:11:48: #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 09:11:48: #1 tags after filtering in treatment: 6075123 INFO @ Sat, 11 Dec 2021 09:11:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:11:48: #1 finished! INFO @ Sat, 11 Dec 2021 09:11:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:11:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:11:49: #2 number of paired peaks: 883 WARNING @ Sat, 11 Dec 2021 09:11:49: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Sat, 11 Dec 2021 09:11:49: start model_add_line... INFO @ Sat, 11 Dec 2021 09:11:49: start X-correlation... INFO @ Sat, 11 Dec 2021 09:11:49: end of X-cor INFO @ Sat, 11 Dec 2021 09:11:49: #2 finished! INFO @ Sat, 11 Dec 2021 09:11:49: #2 predicted fragment length is 73 bps INFO @ Sat, 11 Dec 2021 09:11:49: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 11 Dec 2021 09:11:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.20_model.r WARNING @ Sat, 11 Dec 2021 09:11:49: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:11:49: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 11 Dec 2021 09:11:49: #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 09:11:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:11:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:12:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:12:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:12:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:12:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689091/SRX8689091.20_summits.bed INFO @ Sat, 11 Dec 2021 09:12:08: Done! pass1 - making usageList (164 chroms): 1 millis pass2 - checking and writing primary data (304 records, 4 fields): 23 millis CompletedMACS2peakCalling