Job ID = 6529384 SRX = SRX2325646 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: 00:06:21 32419504 reads; of these: 32419504 (100.00%) were unpaired; of these: 22295060 (68.77%) aligned 0 times 7976119 (24.60%) aligned exactly 1 time 2148325 (6.63%) aligned >1 times 31.23% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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] 3875371 / 10124444 = 0.3828 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.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 @ Tue, 30 Jun 2020 01:57:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:07: 1000000 INFO @ Tue, 30 Jun 2020 01:57:12: 2000000 INFO @ Tue, 30 Jun 2020 01:57:18: 3000000 INFO @ Tue, 30 Jun 2020 01:57:24: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:57:29: 5000000 INFO @ Tue, 30 Jun 2020 01:57:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.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 @ Tue, 30 Jun 2020 01:57:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:36: 6000000 INFO @ Tue, 30 Jun 2020 01:57:37: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 01:57:37: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 01:57:37: #1 total tags in treatment: 6249073 INFO @ Tue, 30 Jun 2020 01:57:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:57:38: 1000000 INFO @ Tue, 30 Jun 2020 01:57:38: #1 tags after filtering in treatment: 6249065 INFO @ Tue, 30 Jun 2020 01:57:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:38: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:39: #2 number of paired peaks: 508 WARNING @ Tue, 30 Jun 2020 01:57:39: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:39: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:39: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:39: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:39: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:39: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 01:57:39: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 30 Jun 2020 01:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.05_model.r WARNING @ Tue, 30 Jun 2020 01:57:39: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:39: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 30 Jun 2020 01:57:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:57:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:43: 2000000 INFO @ Tue, 30 Jun 2020 01:57:48: 3000000 INFO @ Tue, 30 Jun 2020 01:57:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:57:54: 4000000 INFO @ Tue, 30 Jun 2020 01:57:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:57:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:57:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.05_summits.bed INFO @ Tue, 30 Jun 2020 01:57:58: Done! pass1 - making usageList (458 chroms): 2 millis pass2 - checking and writing primary data (1307 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:57:59: 5000000 INFO @ Tue, 30 Jun 2020 01:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.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 @ Tue, 30 Jun 2020 01:58:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:06: 6000000 INFO @ Tue, 30 Jun 2020 01:58:07: 1000000 INFO @ Tue, 30 Jun 2020 01:58:07: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 01:58:07: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 01:58:07: #1 total tags in treatment: 6249073 INFO @ Tue, 30 Jun 2020 01:58:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:58:08: #1 tags after filtering in treatment: 6249065 INFO @ Tue, 30 Jun 2020 01:58:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:08: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:08: #2 number of paired peaks: 508 WARNING @ Tue, 30 Jun 2020 01:58:08: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:08: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:08: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:08: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:08: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:08: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 01:58:08: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 30 Jun 2020 01:58:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.10_model.r WARNING @ Tue, 30 Jun 2020 01:58:08: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:08: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 30 Jun 2020 01:58:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:58:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:13: 2000000 INFO @ Tue, 30 Jun 2020 01:58:18: 3000000 INFO @ Tue, 30 Jun 2020 01:58:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:24: 4000000 INFO @ Tue, 30 Jun 2020 01:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.10_summits.bed INFO @ Tue, 30 Jun 2020 01:58:27: Done! pass1 - making usageList (315 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:58:30: 5000000 INFO @ Tue, 30 Jun 2020 01:58:36: 6000000 INFO @ Tue, 30 Jun 2020 01:58:38: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 01:58:38: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 01:58:38: #1 total tags in treatment: 6249073 INFO @ Tue, 30 Jun 2020 01:58:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:58:39: #1 tags after filtering in treatment: 6249065 INFO @ Tue, 30 Jun 2020 01:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:39: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:39: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:58:39: #2 number of paired peaks: 508 WARNING @ Tue, 30 Jun 2020 01:58:39: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:39: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:39: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:39: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:39: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:39: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 01:58:39: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 30 Jun 2020 01:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.20_model.r WARNING @ Tue, 30 Jun 2020 01:58:39: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:39: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 30 Jun 2020 01:58:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:58:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325646/SRX2325646.20_summits.bed INFO @ Tue, 30 Jun 2020 01:58:58: Done! pass1 - making usageList (139 chroms): 1 millis pass2 - checking and writing primary data (245 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。