Job ID = 6529971 SRX = SRX5661472 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: 00:03:43 11448701 reads; of these: 11448701 (100.00%) were unpaired; of these: 386186 (3.37%) aligned 0 times 7146364 (62.42%) aligned exactly 1 time 3916151 (34.21%) aligned >1 times 96.63% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 1453100 / 11062515 = 0.1314 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 03:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.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 03:10:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:27: 1000000 INFO @ Tue, 30 Jun 2020 03:10:34: 2000000 INFO @ Tue, 30 Jun 2020 03:10:41: 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 03:10:48: 4000000 INFO @ Tue, 30 Jun 2020 03:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.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 03:10:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:56: 5000000 INFO @ Tue, 30 Jun 2020 03:10:58: 1000000 INFO @ Tue, 30 Jun 2020 03:11:04: 6000000 INFO @ Tue, 30 Jun 2020 03:11:06: 2000000 INFO @ Tue, 30 Jun 2020 03:11:12: 7000000 INFO @ Tue, 30 Jun 2020 03:11:14: 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 03:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.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 03:11:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:20: 8000000 INFO @ Tue, 30 Jun 2020 03:11:22: 4000000 INFO @ Tue, 30 Jun 2020 03:11:27: 1000000 INFO @ Tue, 30 Jun 2020 03:11:28: 9000000 INFO @ Tue, 30 Jun 2020 03:11:30: 5000000 INFO @ Tue, 30 Jun 2020 03:11:33: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:33: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:33: #1 total tags in treatment: 9609415 INFO @ Tue, 30 Jun 2020 03:11:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:33: #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 03:11:34: #1 tags after filtering in treatment: 9609413 INFO @ Tue, 30 Jun 2020 03:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:34: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:35: #2 number of paired peaks: 890 WARNING @ Tue, 30 Jun 2020 03:11:35: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:35: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:35: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:35: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:35: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:35: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:11:35: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 30 Jun 2020 03:11:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.05_model.r WARNING @ Tue, 30 Jun 2020 03:11:35: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:35: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 30 Jun 2020 03:11:35: #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 03:11:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:35: 2000000 INFO @ Tue, 30 Jun 2020 03:11:37: 6000000 INFO @ Tue, 30 Jun 2020 03:11:43: 3000000 INFO @ Tue, 30 Jun 2020 03:11:44: 7000000 INFO @ Tue, 30 Jun 2020 03:11:50: 4000000 INFO @ Tue, 30 Jun 2020 03:11:53: 8000000 INFO @ Tue, 30 Jun 2020 03:11:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:11:58: 5000000 INFO @ Tue, 30 Jun 2020 03:12:00: 9000000 INFO @ Tue, 30 Jun 2020 03:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.05_summits.bed INFO @ Tue, 30 Jun 2020 03:12:03: Done! pass1 - making usageList (690 chroms): 2 millis pass2 - checking and writing primary data (2603 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:12:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:12:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:12:05: #1 total tags in treatment: 9609415 INFO @ Tue, 30 Jun 2020 03:12:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:05: #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 03:12:05: #1 tags after filtering in treatment: 9609413 INFO @ Tue, 30 Jun 2020 03:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:05: 6000000 INFO @ Tue, 30 Jun 2020 03:12:06: #2 number of paired peaks: 890 WARNING @ Tue, 30 Jun 2020 03:12:06: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:06: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:06: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:06: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:06: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:06: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:12:06: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 30 Jun 2020 03:12:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.10_model.r WARNING @ Tue, 30 Jun 2020 03:12:06: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:06: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 30 Jun 2020 03:12:06: #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 03:12:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:13: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:12:21: 8000000 INFO @ Tue, 30 Jun 2020 03:12:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:28: 9000000 INFO @ Tue, 30 Jun 2020 03:12:33: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:12:33: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:12:33: #1 total tags in treatment: 9609415 INFO @ Tue, 30 Jun 2020 03:12:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:33: #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 03:12:33: #1 tags after filtering in treatment: 9609413 INFO @ Tue, 30 Jun 2020 03:12:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:33: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.10_summits.bed INFO @ Tue, 30 Jun 2020 03:12:34: Done! INFO @ Tue, 30 Jun 2020 03:12:34: #2 number of paired peaks: 890 WARNING @ Tue, 30 Jun 2020 03:12:34: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:34: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:34: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:34: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:34: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:34: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:12:34: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 30 Jun 2020 03:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.20_model.r WARNING @ Tue, 30 Jun 2020 03:12:34: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:34: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 30 Jun 2020 03:12:34: #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 03:12:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:34: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (588 chroms): 2 millis pass2 - checking and writing primary data (2010 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:12:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661472/SRX5661472.20_summits.bed INFO @ Tue, 30 Jun 2020 03:13:02: Done! pass1 - making usageList (331 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 20 millis CompletedMACS2peakCalling