Job ID = 14171957 SRX = SRX9137153 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: 00:04:42 5557043 reads; of these: 5557043 (100.00%) were unpaired; of these: 1031161 (18.56%) aligned 0 times 3238473 (58.28%) aligned exactly 1 time 1287409 (23.17%) aligned >1 times 81.44% overall alignment rate Time searching: 00:04:42 Overall time: 00:04:42 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] 323361 / 4525882 = 0.0714 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 13:40:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.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 13:40:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:40:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:40:56: 1000000 INFO @ Sat, 11 Dec 2021 13:41:03: 2000000 INFO @ Sat, 11 Dec 2021 13:41:11: 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 13:41:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.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 13:41:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:41:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:41:19: 4000000 INFO @ Sat, 11 Dec 2021 13:41:21: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 13:41:21: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 13:41:21: #1 total tags in treatment: 4202521 INFO @ Sat, 11 Dec 2021 13:41:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:41:21: #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 13:41:21: #1 tags after filtering in treatment: 4202293 INFO @ Sat, 11 Dec 2021 13:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:41:21: #1 finished! INFO @ Sat, 11 Dec 2021 13:41:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:41:21: #2 number of paired peaks: 970 WARNING @ Sat, 11 Dec 2021 13:41:21: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sat, 11 Dec 2021 13:41:21: start model_add_line... INFO @ Sat, 11 Dec 2021 13:41:21: start X-correlation... INFO @ Sat, 11 Dec 2021 13:41:21: end of X-cor INFO @ Sat, 11 Dec 2021 13:41:21: #2 finished! INFO @ Sat, 11 Dec 2021 13:41:21: #2 predicted fragment length is 144 bps INFO @ Sat, 11 Dec 2021 13:41:21: #2 alternative fragment length(s) may be 144 bps INFO @ Sat, 11 Dec 2021 13:41:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.05_model.r WARNING @ Sat, 11 Dec 2021 13:41:22: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:41:22: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Sat, 11 Dec 2021 13:41:22: #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 13:41:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:41:26: 1000000 INFO @ Sat, 11 Dec 2021 13:41:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:41:34: 2000000 INFO @ Sat, 11 Dec 2021 13:41:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:41:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:41:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.05_summits.bed INFO @ Sat, 11 Dec 2021 13:41:36: Done! pass1 - making usageList (563 chroms): 1 millis pass2 - checking and writing primary data (1270 records, 4 fields): 404 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:41:42: 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 13:41:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.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 13:41:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:41:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:41:50: 4000000 INFO @ Sat, 11 Dec 2021 13:41:52: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 13:41:52: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 13:41:52: #1 total tags in treatment: 4202521 INFO @ Sat, 11 Dec 2021 13:41:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:41:52: #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 13:41:52: #1 tags after filtering in treatment: 4202293 INFO @ Sat, 11 Dec 2021 13:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:41:52: #1 finished! INFO @ Sat, 11 Dec 2021 13:41:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:41:52: #2 number of paired peaks: 970 WARNING @ Sat, 11 Dec 2021 13:41:52: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sat, 11 Dec 2021 13:41:52: start model_add_line... INFO @ Sat, 11 Dec 2021 13:41:52: start X-correlation... INFO @ Sat, 11 Dec 2021 13:41:52: end of X-cor INFO @ Sat, 11 Dec 2021 13:41:52: #2 finished! INFO @ Sat, 11 Dec 2021 13:41:52: #2 predicted fragment length is 144 bps INFO @ Sat, 11 Dec 2021 13:41:52: #2 alternative fragment length(s) may be 144 bps INFO @ Sat, 11 Dec 2021 13:41:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.10_model.r WARNING @ Sat, 11 Dec 2021 13:41:53: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:41:53: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Sat, 11 Dec 2021 13:41:53: #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 13:41:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:41:57: 1000000 INFO @ Sat, 11 Dec 2021 13:42:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:42:05: 2000000 INFO @ Sat, 11 Dec 2021 13:42:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:42:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:42:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.10_summits.bed INFO @ Sat, 11 Dec 2021 13:42:07: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (974 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:42:12: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:42:20: 4000000 INFO @ Sat, 11 Dec 2021 13:42:22: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 13:42:22: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 13:42:22: #1 total tags in treatment: 4202521 INFO @ Sat, 11 Dec 2021 13:42:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:42:22: #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 13:42:22: #1 tags after filtering in treatment: 4202293 INFO @ Sat, 11 Dec 2021 13:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:42:22: #1 finished! INFO @ Sat, 11 Dec 2021 13:42:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:42:23: #2 number of paired peaks: 970 WARNING @ Sat, 11 Dec 2021 13:42:23: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sat, 11 Dec 2021 13:42:23: start model_add_line... INFO @ Sat, 11 Dec 2021 13:42:23: start X-correlation... INFO @ Sat, 11 Dec 2021 13:42:23: end of X-cor INFO @ Sat, 11 Dec 2021 13:42:23: #2 finished! INFO @ Sat, 11 Dec 2021 13:42:23: #2 predicted fragment length is 144 bps INFO @ Sat, 11 Dec 2021 13:42:23: #2 alternative fragment length(s) may be 144 bps INFO @ Sat, 11 Dec 2021 13:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.20_model.r WARNING @ Sat, 11 Dec 2021 13:42:23: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:42:23: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Sat, 11 Dec 2021 13:42:23: #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 13:42:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:42:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:42:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:42:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:42:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:42:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9137153/SRX9137153.20_summits.bed INFO @ Sat, 11 Dec 2021 13:42:37: Done! pass1 - making usageList (381 chroms): 1 millis pass2 - checking and writing primary data (631 records, 4 fields): 13 millis CompletedMACS2peakCalling