Job ID = 6529447 SRX = SRX287567 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: 00:00:01 Multiseed full-index search: 00:07:37 23008083 reads; of these: 23008083 (100.00%) were unpaired; of these: 1567493 (6.81%) aligned 0 times 14607380 (63.49%) aligned exactly 1 time 6833210 (29.70%) aligned >1 times 93.19% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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 12 files... [bam_rmdupse_core] 4169987 / 21440590 = 0.1945 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 02:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.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 02:21:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:21:13: 1000000 INFO @ Tue, 30 Jun 2020 02:21:21: 2000000 INFO @ Tue, 30 Jun 2020 02:21:29: 3000000 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 02:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.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 02:21:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:21:37: 4000000 INFO @ Tue, 30 Jun 2020 02:21:44: 1000000 INFO @ Tue, 30 Jun 2020 02:21:45: 5000000 INFO @ Tue, 30 Jun 2020 02:21:52: 2000000 INFO @ Tue, 30 Jun 2020 02:21:53: 6000000 INFO @ Tue, 30 Jun 2020 02:22:00: 7000000 INFO @ Tue, 30 Jun 2020 02:22:00: 3000000 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 02:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.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 02:22:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:08: 8000000 INFO @ Tue, 30 Jun 2020 02:22:09: 4000000 INFO @ Tue, 30 Jun 2020 02:22:14: 1000000 INFO @ Tue, 30 Jun 2020 02:22:16: 9000000 INFO @ Tue, 30 Jun 2020 02:22:17: 5000000 INFO @ Tue, 30 Jun 2020 02:22:22: 2000000 INFO @ Tue, 30 Jun 2020 02:22:24: 10000000 INFO @ Tue, 30 Jun 2020 02:22:25: 6000000 INFO @ Tue, 30 Jun 2020 02:22:30: 3000000 INFO @ Tue, 30 Jun 2020 02:22:33: 11000000 INFO @ Tue, 30 Jun 2020 02:22:34: 7000000 INFO @ Tue, 30 Jun 2020 02:22:38: 4000000 INFO @ Tue, 30 Jun 2020 02:22:41: 12000000 INFO @ Tue, 30 Jun 2020 02:22:42: 8000000 INFO @ Tue, 30 Jun 2020 02:22:47: 5000000 INFO @ Tue, 30 Jun 2020 02:22:50: 9000000 INFO @ Tue, 30 Jun 2020 02:22:50: 13000000 INFO @ Tue, 30 Jun 2020 02:22:56: 6000000 INFO @ Tue, 30 Jun 2020 02:22:58: 10000000 INFO @ Tue, 30 Jun 2020 02:23:00: 14000000 INFO @ Tue, 30 Jun 2020 02:23:05: 7000000 INFO @ Tue, 30 Jun 2020 02:23:06: 11000000 INFO @ Tue, 30 Jun 2020 02:23:09: 15000000 INFO @ Tue, 30 Jun 2020 02:23:15: 8000000 INFO @ Tue, 30 Jun 2020 02:23:15: 12000000 INFO @ Tue, 30 Jun 2020 02:23:19: 16000000 INFO @ Tue, 30 Jun 2020 02:23:24: 13000000 INFO @ Tue, 30 Jun 2020 02:23:24: 9000000 INFO @ Tue, 30 Jun 2020 02:23:28: 17000000 INFO @ Tue, 30 Jun 2020 02:23:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:23:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:23:31: #1 total tags in treatment: 17270603 INFO @ Tue, 30 Jun 2020 02:23:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:31: #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 02:23:31: #1 tags after filtering in treatment: 17270603 INFO @ Tue, 30 Jun 2020 02:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:31: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:33: #2 number of paired peaks: 669 WARNING @ Tue, 30 Jun 2020 02:23:33: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:33: 10000000 INFO @ Tue, 30 Jun 2020 02:23:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:33: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:23:33: #2 alternative fragment length(s) may be 2,14,19 bps INFO @ Tue, 30 Jun 2020 02:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.05_model.r WARNING @ Tue, 30 Jun 2020 02:23:33: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:23:33: #2 You may need to consider one of the other alternative d(s): 2,14,19 WARNING @ Tue, 30 Jun 2020 02:23:33: #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 02:23:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:23:34: 14000000 INFO @ Tue, 30 Jun 2020 02:23:42: 11000000 INFO @ Tue, 30 Jun 2020 02:23:42: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:23:51: 12000000 INFO @ Tue, 30 Jun 2020 02:23:52: 16000000 INFO @ Tue, 30 Jun 2020 02:24:00: 13000000 INFO @ Tue, 30 Jun 2020 02:24:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:05: 17000000 INFO @ Tue, 30 Jun 2020 02:24:08: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:24:08: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:24:08: #1 total tags in treatment: 17270603 INFO @ Tue, 30 Jun 2020 02:24:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:08: #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 02:24:09: #1 tags after filtering in treatment: 17270603 INFO @ Tue, 30 Jun 2020 02:24:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:09: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:10: #2 number of paired peaks: 669 WARNING @ Tue, 30 Jun 2020 02:24:10: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:10: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:24:10: #2 alternative fragment length(s) may be 2,14,19 bps INFO @ Tue, 30 Jun 2020 02:24:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.10_model.r WARNING @ Tue, 30 Jun 2020 02:24:10: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:10: #2 You may need to consider one of the other alternative d(s): 2,14,19 WARNING @ Tue, 30 Jun 2020 02:24:10: #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 02:24:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:10: 14000000 INFO @ Tue, 30 Jun 2020 02:24:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.05_summits.bed INFO @ Tue, 30 Jun 2020 02:24:16: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:24:20: 15000000 INFO @ Tue, 30 Jun 2020 02:24:29: 16000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:24:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:39: 17000000 INFO @ Tue, 30 Jun 2020 02:24:42: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:24:42: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:24:42: #1 total tags in treatment: 17270603 INFO @ Tue, 30 Jun 2020 02:24:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:42: #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 02:24:42: #1 tags after filtering in treatment: 17270603 INFO @ Tue, 30 Jun 2020 02:24:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:42: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:44: #2 number of paired peaks: 669 WARNING @ Tue, 30 Jun 2020 02:24:44: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:44: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:44: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:44: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:44: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:44: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:24:44: #2 alternative fragment length(s) may be 2,14,19 bps INFO @ Tue, 30 Jun 2020 02:24:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.20_model.r WARNING @ Tue, 30 Jun 2020 02:24:44: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:44: #2 You may need to consider one of the other alternative d(s): 2,14,19 WARNING @ Tue, 30 Jun 2020 02:24:44: #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 02:24:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.10_summits.bed INFO @ Tue, 30 Jun 2020 02:24:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:25:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:25:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287567/SRX287567.20_summits.bed INFO @ Tue, 30 Jun 2020 02:25:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling