Job ID = 14170889 SRX = SRX8689051 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: 00:01:27 5680752 reads; of these: 5680752 (100.00%) were unpaired; of these: 704997 (12.41%) aligned 0 times 3974946 (69.97%) aligned exactly 1 time 1000809 (17.62%) aligned >1 times 87.59% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 312566 / 4975755 = 0.0628 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 08:59:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.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 08:59:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:59:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:59:47: 1000000 INFO @ Sat, 11 Dec 2021 08:59:53: 2000000 INFO @ Sat, 11 Dec 2021 08:59:58: 3000000 INFO @ Sat, 11 Dec 2021 09:00:04: 4000000 INFO @ Sat, 11 Dec 2021 09:00:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:00:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:00:08: #1 total tags in treatment: 4663189 INFO @ Sat, 11 Dec 2021 09:00:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:00:08: #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 09:00:08: #1 tags after filtering in treatment: 4663165 INFO @ Sat, 11 Dec 2021 09:00:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:00:08: #1 finished! INFO @ Sat, 11 Dec 2021 09:00:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:00:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:00:08: #2 number of paired peaks: 141 WARNING @ Sat, 11 Dec 2021 09:00:08: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Sat, 11 Dec 2021 09:00:08: start model_add_line... INFO @ Sat, 11 Dec 2021 09:00:08: start X-correlation... INFO @ Sat, 11 Dec 2021 09:00:08: end of X-cor INFO @ Sat, 11 Dec 2021 09:00:08: #2 finished! INFO @ Sat, 11 Dec 2021 09:00:08: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:00:08: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Dec 2021 09:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.05_model.r WARNING @ Sat, 11 Dec 2021 09:00:08: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:00:08: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Dec 2021 09:00:08: #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 09:00:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:00:08: #3 Pre-compute pvalue-qvalue table... 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 09:00:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.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 09:00:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:00:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:00:17: 1000000 INFO @ Sat, 11 Dec 2021 09:00:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:00:23: 2000000 INFO @ Sat, 11 Dec 2021 09:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.05_summits.bed INFO @ Sat, 11 Dec 2021 09:00:25: Done! pass1 - making usageList (130 chroms): 1 millis pass2 - checking and writing primary data (357 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:00:28: 3000000 INFO @ Sat, 11 Dec 2021 09:00:34: 4000000 INFO @ Sat, 11 Dec 2021 09:00:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:00:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:00:38: #1 total tags in treatment: 4663189 INFO @ Sat, 11 Dec 2021 09:00:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:00:38: #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 09:00:38: #1 tags after filtering in treatment: 4663165 INFO @ Sat, 11 Dec 2021 09:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:00:38: #1 finished! INFO @ Sat, 11 Dec 2021 09:00:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:00:39: #2 number of paired peaks: 141 WARNING @ Sat, 11 Dec 2021 09:00:39: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Sat, 11 Dec 2021 09:00:39: start model_add_line... INFO @ Sat, 11 Dec 2021 09:00:39: start X-correlation... INFO @ Sat, 11 Dec 2021 09:00:39: end of X-cor INFO @ Sat, 11 Dec 2021 09:00:39: #2 finished! INFO @ Sat, 11 Dec 2021 09:00:39: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:00:39: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Dec 2021 09:00:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.10_model.r WARNING @ Sat, 11 Dec 2021 09:00:39: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:00:39: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Dec 2021 09:00:39: #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 09:00:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:00:39: #3 Pre-compute pvalue-qvalue table... 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 09:00:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.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 09:00:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:00:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:00:47: 1000000 INFO @ Sat, 11 Dec 2021 09:00:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:00:53: 2000000 INFO @ Sat, 11 Dec 2021 09:00:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:00:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:00:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.10_summits.bed INFO @ Sat, 11 Dec 2021 09:00:55: Done! pass1 - making usageList (94 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:00:58: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:01:04: 4000000 INFO @ Sat, 11 Dec 2021 09:01:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:01:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:01:08: #1 total tags in treatment: 4663189 INFO @ Sat, 11 Dec 2021 09:01:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:01:08: #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 09:01:08: #1 tags after filtering in treatment: 4663165 INFO @ Sat, 11 Dec 2021 09:01:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:01:08: #1 finished! INFO @ Sat, 11 Dec 2021 09:01:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:01:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:01:09: #2 number of paired peaks: 141 WARNING @ Sat, 11 Dec 2021 09:01:09: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Sat, 11 Dec 2021 09:01:09: start model_add_line... INFO @ Sat, 11 Dec 2021 09:01:09: start X-correlation... INFO @ Sat, 11 Dec 2021 09:01:09: end of X-cor INFO @ Sat, 11 Dec 2021 09:01:09: #2 finished! INFO @ Sat, 11 Dec 2021 09:01:09: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:01:09: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Dec 2021 09:01:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.20_model.r WARNING @ Sat, 11 Dec 2021 09:01:09: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:01:09: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Dec 2021 09:01:09: #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 09:01:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:01:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:01:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:01:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:01:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:01:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689051/SRX8689051.20_summits.bed INFO @ Sat, 11 Dec 2021 09:01:25: Done! pass1 - making usageList (59 chroms): 1 millis pass2 - checking and writing primary data (99 records, 4 fields): 48 millis CompletedMACS2peakCalling