Job ID = 14170929 SRX = SRX8689076 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: 00:00:01 Multiseed full-index search: 00:02:24 7679244 reads; of these: 7679244 (100.00%) were unpaired; of these: 874133 (11.38%) aligned 0 times 4957107 (64.55%) aligned exactly 1 time 1848004 (24.06%) aligned >1 times 88.62% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 552815 / 6805111 = 0.0812 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 09:05:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.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 09:05:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:05:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:06:02: 1000000 INFO @ Sat, 11 Dec 2021 09:06:10: 2000000 INFO @ Sat, 11 Dec 2021 09:06:19: 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 @ Sat, 11 Dec 2021 09:06:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.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 09:06:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:06:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:06:27: 4000000 INFO @ Sat, 11 Dec 2021 09:06:32: 1000000 INFO @ Sat, 11 Dec 2021 09:06:36: 5000000 INFO @ Sat, 11 Dec 2021 09:06:40: 2000000 INFO @ Sat, 11 Dec 2021 09:06:45: 6000000 INFO @ Sat, 11 Dec 2021 09:06:47: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:06:47: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:06:47: #1 total tags in treatment: 6252296 INFO @ Sat, 11 Dec 2021 09:06:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:06:47: #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 09:06:48: #1 tags after filtering in treatment: 6252148 INFO @ Sat, 11 Dec 2021 09:06:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:06:48: #1 finished! INFO @ Sat, 11 Dec 2021 09:06:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:06:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:06:48: #2 number of paired peaks: 934 WARNING @ Sat, 11 Dec 2021 09:06:48: Fewer paired peaks (934) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 934 pairs to build model! INFO @ Sat, 11 Dec 2021 09:06:48: start model_add_line... INFO @ Sat, 11 Dec 2021 09:06:48: start X-correlation... INFO @ Sat, 11 Dec 2021 09:06:48: end of X-cor INFO @ Sat, 11 Dec 2021 09:06:48: #2 finished! INFO @ Sat, 11 Dec 2021 09:06:48: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 09:06:48: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 11 Dec 2021 09:06:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.05_model.r WARNING @ Sat, 11 Dec 2021 09:06:48: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:06:48: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 11 Dec 2021 09:06:48: #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 09:06:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:06:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:06:49: 3000000 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 09:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.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 09:06:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:06:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:06:57: 4000000 INFO @ Sat, 11 Dec 2021 09:07:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:07:02: 1000000 INFO @ Sat, 11 Dec 2021 09:07:07: 5000000 INFO @ Sat, 11 Dec 2021 09:07:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:07:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:07:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.05_summits.bed INFO @ Sat, 11 Dec 2021 09:07:09: Done! pass1 - making usageList (559 chroms): 2 millis pass2 - checking and writing primary data (2188 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:07:11: 2000000 INFO @ Sat, 11 Dec 2021 09:07:15: 6000000 INFO @ Sat, 11 Dec 2021 09:07:18: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:18: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:18: #1 total tags in treatment: 6252296 INFO @ Sat, 11 Dec 2021 09:07:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:18: #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 09:07:18: #1 tags after filtering in treatment: 6252148 INFO @ Sat, 11 Dec 2021 09:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:18: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:07:19: #2 number of paired peaks: 934 WARNING @ Sat, 11 Dec 2021 09:07:19: Fewer paired peaks (934) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 934 pairs to build model! INFO @ Sat, 11 Dec 2021 09:07:19: start model_add_line... INFO @ Sat, 11 Dec 2021 09:07:19: start X-correlation... INFO @ Sat, 11 Dec 2021 09:07:19: end of X-cor INFO @ Sat, 11 Dec 2021 09:07:19: #2 finished! INFO @ Sat, 11 Dec 2021 09:07:19: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 09:07:19: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 11 Dec 2021 09:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.10_model.r WARNING @ Sat, 11 Dec 2021 09:07:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:07:19: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 11 Dec 2021 09:07:19: #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 09:07:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:07:19: 3000000 INFO @ Sat, 11 Dec 2021 09:07:27: 4000000 INFO @ Sat, 11 Dec 2021 09:07:31: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:07:36: 5000000 INFO @ Sat, 11 Dec 2021 09:07:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:07:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:07:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.10_summits.bed INFO @ Sat, 11 Dec 2021 09:07:39: Done! pass1 - making usageList (405 chroms): 1 millis pass2 - checking and writing primary data (945 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:07:44: 6000000 INFO @ Sat, 11 Dec 2021 09:07:47: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:47: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:47: #1 total tags in treatment: 6252296 INFO @ Sat, 11 Dec 2021 09:07:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:47: #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 09:07:47: #1 tags after filtering in treatment: 6252148 INFO @ Sat, 11 Dec 2021 09:07:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:47: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:07:48: #2 number of paired peaks: 934 WARNING @ Sat, 11 Dec 2021 09:07:48: Fewer paired peaks (934) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 934 pairs to build model! INFO @ Sat, 11 Dec 2021 09:07:48: start model_add_line... INFO @ Sat, 11 Dec 2021 09:07:48: start X-correlation... INFO @ Sat, 11 Dec 2021 09:07:48: end of X-cor INFO @ Sat, 11 Dec 2021 09:07:48: #2 finished! INFO @ Sat, 11 Dec 2021 09:07:48: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 09:07:48: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 11 Dec 2021 09:07:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.20_model.r WARNING @ Sat, 11 Dec 2021 09:07:48: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:07:48: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 11 Dec 2021 09:07:48: #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 09:07:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:07:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:08:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689076/SRX8689076.20_summits.bed INFO @ Sat, 11 Dec 2021 09:08:08: Done! pass1 - making usageList (133 chroms): 2 millis pass2 - checking and writing primary data (225 records, 4 fields): 10 millis CompletedMACS2peakCalling