Job ID = 6530011 SRX = SRX6386765 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: 00:02:41 9943816 reads; of these: 9943816 (100.00%) were unpaired; of these: 475043 (4.78%) aligned 0 times 6690827 (67.29%) aligned exactly 1 time 2777946 (27.94%) aligned >1 times 95.22% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 1278578 / 9468773 = 0.1350 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 03:10:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.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 03:10:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:21: 1000000 INFO @ Tue, 30 Jun 2020 03:10:27: 2000000 INFO @ Tue, 30 Jun 2020 03:10:33: 3000000 INFO @ Tue, 30 Jun 2020 03:10:39: 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 03:10:45: 5000000 INFO @ Tue, 30 Jun 2020 03:10:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.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 03:10:45: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:45: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:51: 6000000 INFO @ Tue, 30 Jun 2020 03:10:52: 1000000 INFO @ Tue, 30 Jun 2020 03:10:58: 7000000 INFO @ Tue, 30 Jun 2020 03:10:58: 2000000 INFO @ Tue, 30 Jun 2020 03:11:05: 8000000 INFO @ Tue, 30 Jun 2020 03:11:05: 3000000 INFO @ Tue, 30 Jun 2020 03:11:06: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:11:06: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:11:06: #1 total tags in treatment: 8190195 INFO @ Tue, 30 Jun 2020 03:11:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:06: #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 03:11:06: #1 tags after filtering in treatment: 8190173 INFO @ Tue, 30 Jun 2020 03:11:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:06: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:07: #2 number of paired peaks: 911 WARNING @ Tue, 30 Jun 2020 03:11:07: Fewer paired peaks (911) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 911 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:07: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:07: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:07: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:07: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:07: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 03:11:07: #2 alternative fragment length(s) may be 3,41 bps INFO @ Tue, 30 Jun 2020 03:11:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.05_model.r WARNING @ Tue, 30 Jun 2020 03:11:07: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:07: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Tue, 30 Jun 2020 03:11:07: #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 03:11:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:11: 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 03:11:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.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 03:11:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:17: 5000000 INFO @ Tue, 30 Jun 2020 03:11:22: 1000000 INFO @ Tue, 30 Jun 2020 03:11:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:11:23: 6000000 INFO @ Tue, 30 Jun 2020 03:11:29: 2000000 INFO @ Tue, 30 Jun 2020 03:11:30: 7000000 INFO @ Tue, 30 Jun 2020 03:11:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:11:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:11:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.05_summits.bed INFO @ Tue, 30 Jun 2020 03:11:32: Done! pass1 - making usageList (601 chroms): 1 millis pass2 - checking and writing primary data (2312 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:11:35: 3000000 INFO @ Tue, 30 Jun 2020 03:11:37: 8000000 INFO @ Tue, 30 Jun 2020 03:11:38: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:11:38: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:11:38: #1 total tags in treatment: 8190195 INFO @ Tue, 30 Jun 2020 03:11:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:38: #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 03:11:39: #1 tags after filtering in treatment: 8190173 INFO @ Tue, 30 Jun 2020 03:11:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:39: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:39: #2 number of paired peaks: 911 WARNING @ Tue, 30 Jun 2020 03:11:39: Fewer paired peaks (911) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 911 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:39: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:39: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:39: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:39: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:39: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 03:11:39: #2 alternative fragment length(s) may be 3,41 bps INFO @ Tue, 30 Jun 2020 03:11:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.10_model.r WARNING @ Tue, 30 Jun 2020 03:11:39: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:39: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Tue, 30 Jun 2020 03:11:39: #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 03:11:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:41: 4000000 INFO @ Tue, 30 Jun 2020 03:11:47: 5000000 INFO @ Tue, 30 Jun 2020 03:11:53: 6000000 INFO @ Tue, 30 Jun 2020 03:11:56: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:11:59: 7000000 INFO @ Tue, 30 Jun 2020 03:12:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.10_summits.bed INFO @ Tue, 30 Jun 2020 03:12:05: Done! pass1 - making usageList (497 chroms): 1 millis pass2 - checking and writing primary data (1809 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:12:05: 8000000 INFO @ Tue, 30 Jun 2020 03:12:07: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:12:07: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:12:07: #1 total tags in treatment: 8190195 INFO @ Tue, 30 Jun 2020 03:12:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:07: #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 03:12:07: #1 tags after filtering in treatment: 8190173 INFO @ Tue, 30 Jun 2020 03:12:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:07: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:08: #2 number of paired peaks: 911 WARNING @ Tue, 30 Jun 2020 03:12:08: Fewer paired peaks (911) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 911 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:08: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:08: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:08: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:08: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:08: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 03:12:08: #2 alternative fragment length(s) may be 3,41 bps INFO @ Tue, 30 Jun 2020 03:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.20_model.r WARNING @ Tue, 30 Jun 2020 03:12:08: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:08: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Tue, 30 Jun 2020 03:12:08: #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 03:12:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:12:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386765/SRX6386765.20_summits.bed INFO @ Tue, 30 Jun 2020 03:12:33: Done! pass1 - making usageList (352 chroms): 0 millis pass2 - checking and writing primary data (902 records, 4 fields): 12 millis CompletedMACS2peakCalling