Job ID = 6529143 SRX = SRX013010 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:38 6668507 reads; of these: 6668507 (100.00%) were unpaired; of these: 1580251 (23.70%) aligned 0 times 3533165 (52.98%) aligned exactly 1 time 1555091 (23.32%) aligned >1 times 76.30% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 929623 / 5088256 = 0.1827 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 01:36:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.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 01:36:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:36:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:20: 1000000 INFO @ Tue, 30 Jun 2020 01:36:27: 2000000 INFO @ Tue, 30 Jun 2020 01:36:33: 3000000 INFO @ Tue, 30 Jun 2020 01:36:40: 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 01:36:41: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:36:41: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:36:41: #1 total tags in treatment: 4158633 INFO @ Tue, 30 Jun 2020 01:36:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:36:41: #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 01:36:42: #1 tags after filtering in treatment: 4158567 INFO @ Tue, 30 Jun 2020 01:36:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:36:42: #1 finished! INFO @ Tue, 30 Jun 2020 01:36:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:36:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:36:42: #2 number of paired peaks: 1525 INFO @ Tue, 30 Jun 2020 01:36:42: start model_add_line... INFO @ Tue, 30 Jun 2020 01:36:42: start X-correlation... INFO @ Tue, 30 Jun 2020 01:36:42: end of X-cor INFO @ Tue, 30 Jun 2020 01:36:42: #2 finished! INFO @ Tue, 30 Jun 2020 01:36:42: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 01:36:42: #2 alternative fragment length(s) may be 3,36,70,75 bps INFO @ Tue, 30 Jun 2020 01:36:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.05_model.r WARNING @ Tue, 30 Jun 2020 01:36:42: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:36:42: #2 You may need to consider one of the other alternative d(s): 3,36,70,75 WARNING @ Tue, 30 Jun 2020 01:36:42: #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 01:36:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:36:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.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 01:36:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:36:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:36:49: 1000000 INFO @ Tue, 30 Jun 2020 01:36:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:36:55: 2000000 INFO @ Tue, 30 Jun 2020 01:36:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:36:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:36:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.05_summits.bed INFO @ Tue, 30 Jun 2020 01:36:55: Done! pass1 - making usageList (566 chroms): 2 millis pass2 - checking and writing primary data (2560 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:37:01: 3000000 INFO @ Tue, 30 Jun 2020 01:37:08: 4000000 INFO @ Tue, 30 Jun 2020 01:37:09: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:37:09: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:37:09: #1 total tags in treatment: 4158633 INFO @ Tue, 30 Jun 2020 01:37:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:37:09: #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 01:37:10: #1 tags after filtering in treatment: 4158567 INFO @ Tue, 30 Jun 2020 01:37:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:37:10: #1 finished! INFO @ Tue, 30 Jun 2020 01:37:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:37:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:37:10: #2 number of paired peaks: 1525 INFO @ Tue, 30 Jun 2020 01:37:10: start model_add_line... INFO @ Tue, 30 Jun 2020 01:37:10: start X-correlation... INFO @ Tue, 30 Jun 2020 01:37:10: end of X-cor INFO @ Tue, 30 Jun 2020 01:37:10: #2 finished! INFO @ Tue, 30 Jun 2020 01:37:10: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 01:37:10: #2 alternative fragment length(s) may be 3,36,70,75 bps INFO @ Tue, 30 Jun 2020 01:37:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.10_model.r WARNING @ Tue, 30 Jun 2020 01:37:10: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:37:10: #2 You may need to consider one of the other alternative d(s): 3,36,70,75 WARNING @ Tue, 30 Jun 2020 01:37:10: #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 01:37:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:37:10: #3 Pre-compute pvalue-qvalue table... 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 01:37:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.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 01:37:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:37:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:37:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:37:20: 1000000 INFO @ Tue, 30 Jun 2020 01:37:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:37:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:37:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.10_summits.bed INFO @ Tue, 30 Jun 2020 01:37:23: Done! pass1 - making usageList (378 chroms): 1 millis pass2 - checking and writing primary data (1019 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:37:27: 2000000 INFO @ Tue, 30 Jun 2020 01:37:33: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:37:40: 4000000 INFO @ Tue, 30 Jun 2020 01:37:41: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:37:41: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:37:41: #1 total tags in treatment: 4158633 INFO @ Tue, 30 Jun 2020 01:37:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:37:41: #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 01:37:42: #1 tags after filtering in treatment: 4158567 INFO @ Tue, 30 Jun 2020 01:37:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:37:42: #1 finished! INFO @ Tue, 30 Jun 2020 01:37:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:37:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:37:42: #2 number of paired peaks: 1525 INFO @ Tue, 30 Jun 2020 01:37:42: start model_add_line... INFO @ Tue, 30 Jun 2020 01:37:42: start X-correlation... INFO @ Tue, 30 Jun 2020 01:37:42: end of X-cor INFO @ Tue, 30 Jun 2020 01:37:42: #2 finished! INFO @ Tue, 30 Jun 2020 01:37:42: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 01:37:42: #2 alternative fragment length(s) may be 3,36,70,75 bps INFO @ Tue, 30 Jun 2020 01:37:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.20_model.r WARNING @ Tue, 30 Jun 2020 01:37:42: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:37:42: #2 You may need to consider one of the other alternative d(s): 3,36,70,75 WARNING @ Tue, 30 Jun 2020 01:37:42: #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 01:37:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:37:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:37:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:37:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:37:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:37:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013010/SRX013010.20_summits.bed INFO @ Tue, 30 Jun 2020 01:37:55: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 7 millis CompletedMACS2peakCalling