Job ID = 6529546 SRX = SRX3068983 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: 00:04:38 18188488 reads; of these: 18188488 (100.00%) were unpaired; of these: 1211335 (6.66%) aligned 0 times 13898038 (76.41%) aligned exactly 1 time 3079115 (16.93%) aligned >1 times 93.34% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5173388 / 16977153 = 0.3047 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 02:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.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 02:21:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:21:08: 1000000 INFO @ Tue, 30 Jun 2020 02:21:14: 2000000 INFO @ Tue, 30 Jun 2020 02:21:20: 3000000 INFO @ Tue, 30 Jun 2020 02:21:26: 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 02:21:32: 5000000 INFO @ Tue, 30 Jun 2020 02:21:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.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 02:21:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:21:38: 6000000 INFO @ Tue, 30 Jun 2020 02:21:39: 1000000 INFO @ Tue, 30 Jun 2020 02:21:44: 7000000 INFO @ Tue, 30 Jun 2020 02:21:45: 2000000 INFO @ Tue, 30 Jun 2020 02:21:51: 8000000 INFO @ Tue, 30 Jun 2020 02:21:52: 3000000 INFO @ Tue, 30 Jun 2020 02:21:57: 9000000 INFO @ Tue, 30 Jun 2020 02:21:58: 4000000 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 02:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.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 02:22:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:04: 10000000 INFO @ Tue, 30 Jun 2020 02:22:05: 5000000 INFO @ Tue, 30 Jun 2020 02:22:09: 1000000 INFO @ Tue, 30 Jun 2020 02:22:11: 11000000 INFO @ Tue, 30 Jun 2020 02:22:11: 6000000 INFO @ Tue, 30 Jun 2020 02:22:16: 2000000 INFO @ Tue, 30 Jun 2020 02:22:17: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:22:17: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:22:17: #1 total tags in treatment: 11803765 INFO @ Tue, 30 Jun 2020 02:22:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:22:17: #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 02:22:17: #1 tags after filtering in treatment: 11803759 INFO @ Tue, 30 Jun 2020 02:22:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:22:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:22:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:22:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:22:18: 7000000 INFO @ Tue, 30 Jun 2020 02:22:18: #2 number of paired peaks: 579 WARNING @ Tue, 30 Jun 2020 02:22:18: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Tue, 30 Jun 2020 02:22:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:22:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:22:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:22:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:22:18: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:22:18: #2 alternative fragment length(s) may be 3,49,577 bps INFO @ Tue, 30 Jun 2020 02:22:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.05_model.r WARNING @ Tue, 30 Jun 2020 02:22:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:22:18: #2 You may need to consider one of the other alternative d(s): 3,49,577 WARNING @ Tue, 30 Jun 2020 02:22:18: #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 02:22:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:22:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:22:23: 3000000 INFO @ Tue, 30 Jun 2020 02:22:24: 8000000 INFO @ Tue, 30 Jun 2020 02:22:29: 4000000 INFO @ Tue, 30 Jun 2020 02:22:30: 9000000 INFO @ Tue, 30 Jun 2020 02:22:36: 5000000 INFO @ Tue, 30 Jun 2020 02:22:37: 10000000 INFO @ Tue, 30 Jun 2020 02:22:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:22:42: 6000000 INFO @ Tue, 30 Jun 2020 02:22:43: 11000000 INFO @ Tue, 30 Jun 2020 02:22:48: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:22:48: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:22:48: #1 total tags in treatment: 11803765 INFO @ Tue, 30 Jun 2020 02:22:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:22:48: #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 02:22:49: #1 tags after filtering in treatment: 11803759 INFO @ Tue, 30 Jun 2020 02:22:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:22:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:22:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:22:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:22:49: 7000000 INFO @ Tue, 30 Jun 2020 02:22:50: #2 number of paired peaks: 579 WARNING @ Tue, 30 Jun 2020 02:22:50: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Tue, 30 Jun 2020 02:22:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:22:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:22:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:22:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:22:50: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:22:50: #2 alternative fragment length(s) may be 3,49,577 bps INFO @ Tue, 30 Jun 2020 02:22:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.10_model.r WARNING @ Tue, 30 Jun 2020 02:22:50: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:22:50: #2 You may need to consider one of the other alternative d(s): 3,49,577 WARNING @ Tue, 30 Jun 2020 02:22:50: #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 02:22:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.05_summits.bed INFO @ Tue, 30 Jun 2020 02:22:52: Done! pass1 - making usageList (492 chroms): 2 millis pass2 - checking and writing primary data (1905 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:22:56: 8000000 INFO @ Tue, 30 Jun 2020 02:23:02: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:23:10: 10000000 INFO @ Tue, 30 Jun 2020 02:23:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:23:16: 11000000 INFO @ Tue, 30 Jun 2020 02:23:22: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:23:22: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:23:22: #1 total tags in treatment: 11803765 INFO @ Tue, 30 Jun 2020 02:23:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:22: #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 02:23:23: #1 tags after filtering in treatment: 11803759 INFO @ Tue, 30 Jun 2020 02:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:23:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:23:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.10_summits.bed INFO @ Tue, 30 Jun 2020 02:23:24: #2 number of paired peaks: 579 WARNING @ Tue, 30 Jun 2020 02:23:24: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:24: Done! INFO @ Tue, 30 Jun 2020 02:23:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:24: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:23:24: #2 alternative fragment length(s) may be 3,49,577 bps INFO @ Tue, 30 Jun 2020 02:23:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.20_model.r WARNING @ Tue, 30 Jun 2020 02:23:24: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:23:24: #2 You may need to consider one of the other alternative d(s): 3,49,577 WARNING @ Tue, 30 Jun 2020 02:23:24: #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 02:23:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:24: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (428 chroms): 2 millis pass2 - checking and writing primary data (1516 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:23:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:23:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:23:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:23:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068983/SRX3068983.20_summits.bed INFO @ Tue, 30 Jun 2020 02:23:58: Done! pass1 - making usageList (265 chroms): 2 millis pass2 - checking and writing primary data (485 records, 4 fields): 15 millis CompletedMACS2peakCalling