Job ID = 6529592 SRX = SRX331397 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: 00:04:52 17761171 reads; of these: 17761171 (100.00%) were unpaired; of these: 1061787 (5.98%) aligned 0 times 12962668 (72.98%) aligned exactly 1 time 3736716 (21.04%) aligned >1 times 94.02% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 1639693 / 16699384 = 0.0982 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 02:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.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 02:24:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:25:01: 1000000 INFO @ Tue, 30 Jun 2020 02:25:06: 2000000 INFO @ Tue, 30 Jun 2020 02:25:12: 3000000 INFO @ Tue, 30 Jun 2020 02:25:17: 4000000 INFO @ Tue, 30 Jun 2020 02:25:22: 5000000 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 02:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.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 02:25:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:25:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:25:28: 6000000 INFO @ Tue, 30 Jun 2020 02:25:32: 1000000 INFO @ Tue, 30 Jun 2020 02:25:34: 7000000 INFO @ Tue, 30 Jun 2020 02:25:38: 2000000 INFO @ Tue, 30 Jun 2020 02:25:40: 8000000 INFO @ Tue, 30 Jun 2020 02:25:44: 3000000 INFO @ Tue, 30 Jun 2020 02:25:46: 9000000 INFO @ Tue, 30 Jun 2020 02:25:50: 4000000 INFO @ Tue, 30 Jun 2020 02:25:52: 10000000 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 02:25:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.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 02:25:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:25:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:25:56: 5000000 INFO @ Tue, 30 Jun 2020 02:25:59: 11000000 INFO @ Tue, 30 Jun 2020 02:26:01: 1000000 INFO @ Tue, 30 Jun 2020 02:26:02: 6000000 INFO @ Tue, 30 Jun 2020 02:26:05: 12000000 INFO @ Tue, 30 Jun 2020 02:26:06: 2000000 INFO @ Tue, 30 Jun 2020 02:26:08: 7000000 INFO @ Tue, 30 Jun 2020 02:26:11: 3000000 INFO @ Tue, 30 Jun 2020 02:26:12: 13000000 INFO @ Tue, 30 Jun 2020 02:26:15: 8000000 INFO @ Tue, 30 Jun 2020 02:26:17: 4000000 INFO @ Tue, 30 Jun 2020 02:26:18: 14000000 INFO @ Tue, 30 Jun 2020 02:26:21: 9000000 INFO @ Tue, 30 Jun 2020 02:26:22: 5000000 INFO @ Tue, 30 Jun 2020 02:26:24: 15000000 INFO @ Tue, 30 Jun 2020 02:26:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:26:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:26:25: #1 total tags in treatment: 15059691 INFO @ Tue, 30 Jun 2020 02:26:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:26:25: #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 02:26:25: #1 tags after filtering in treatment: 15059690 INFO @ Tue, 30 Jun 2020 02:26:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:26:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:26:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:26:26: #2 number of paired peaks: 317 WARNING @ Tue, 30 Jun 2020 02:26:26: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 30 Jun 2020 02:26:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:26:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:26:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:26:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:26:26: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:26:26: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 30 Jun 2020 02:26:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.05_model.r WARNING @ Tue, 30 Jun 2020 02:26:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:26:26: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 30 Jun 2020 02:26:26: #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 02:26:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:26:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:26:27: 10000000 INFO @ Tue, 30 Jun 2020 02:26:27: 6000000 INFO @ Tue, 30 Jun 2020 02:26:33: 7000000 INFO @ Tue, 30 Jun 2020 02:26:33: 11000000 INFO @ Tue, 30 Jun 2020 02:26:38: 8000000 INFO @ Tue, 30 Jun 2020 02:26:39: 12000000 INFO @ Tue, 30 Jun 2020 02:26:44: 9000000 INFO @ Tue, 30 Jun 2020 02:26:46: 13000000 INFO @ Tue, 30 Jun 2020 02:26:49: 10000000 INFO @ Tue, 30 Jun 2020 02:26:52: 14000000 INFO @ Tue, 30 Jun 2020 02:26:55: 11000000 INFO @ Tue, 30 Jun 2020 02:26:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:26:58: 15000000 INFO @ Tue, 30 Jun 2020 02:26:59: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:26:59: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:26:59: #1 total tags in treatment: 15059691 INFO @ Tue, 30 Jun 2020 02:26:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:26:59: #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 02:26:59: #1 tags after filtering in treatment: 15059690 INFO @ Tue, 30 Jun 2020 02:26:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:26:59: #1 finished! INFO @ Tue, 30 Jun 2020 02:26:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:26:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:27:00: 12000000 INFO @ Tue, 30 Jun 2020 02:27:00: #2 number of paired peaks: 317 WARNING @ Tue, 30 Jun 2020 02:27:00: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 30 Jun 2020 02:27:00: start model_add_line... INFO @ Tue, 30 Jun 2020 02:27:01: start X-correlation... INFO @ Tue, 30 Jun 2020 02:27:01: end of X-cor INFO @ Tue, 30 Jun 2020 02:27:01: #2 finished! INFO @ Tue, 30 Jun 2020 02:27:01: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:27:01: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 30 Jun 2020 02:27:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.10_model.r WARNING @ Tue, 30 Jun 2020 02:27:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:27:01: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 30 Jun 2020 02:27:01: #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 02:27:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:27:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:27:11: 14000000 INFO @ Tue, 30 Jun 2020 02:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.05_summits.bed INFO @ Tue, 30 Jun 2020 02:27:12: Done! pass1 - making usageList (524 chroms): 1 millis pass2 - checking and writing primary data (2006 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:27:16: 15000000 INFO @ Tue, 30 Jun 2020 02:27:17: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:27:17: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:27:17: #1 total tags in treatment: 15059691 INFO @ Tue, 30 Jun 2020 02:27:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:27:17: #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 02:27:17: #1 tags after filtering in treatment: 15059690 INFO @ Tue, 30 Jun 2020 02:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:27:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:27:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:27:18: #2 number of paired peaks: 317 WARNING @ Tue, 30 Jun 2020 02:27:18: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 30 Jun 2020 02:27:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:27:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:27:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:27:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:27:18: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:27:18: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 30 Jun 2020 02:27:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.20_model.r WARNING @ Tue, 30 Jun 2020 02:27:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:27:18: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 30 Jun 2020 02:27:18: #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 02:27:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:27:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:27:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:27:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:27:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.10_summits.bed INFO @ Tue, 30 Jun 2020 02:27:47: Done! pass1 - making usageList (443 chroms): 2 millis pass2 - checking and writing primary data (1625 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331397/SRX331397.20_summits.bed INFO @ Tue, 30 Jun 2020 02:28:02: Done! pass1 - making usageList (296 chroms): 1 millis pass2 - checking and writing primary data (599 records, 4 fields): 11 millis CompletedMACS2peakCalling