Job ID = 14168837 SRX = SRX8688975 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:17 17109445 reads; of these: 17109445 (100.00%) were unpaired; of these: 460990 (2.69%) aligned 0 times 11796534 (68.95%) aligned exactly 1 time 4851921 (28.36%) aligned >1 times 97.31% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 2184627 / 16648455 = 0.1312 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 21:06:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.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 @ Fri, 10 Dec 2021 21:06:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:06:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:06:41: 1000000 INFO @ Fri, 10 Dec 2021 21:06:48: 2000000 INFO @ Fri, 10 Dec 2021 21:06:55: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 21:07:03: 4000000 INFO @ Fri, 10 Dec 2021 21:07:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.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 @ Fri, 10 Dec 2021 21:07:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:07:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:07:10: 5000000 INFO @ Fri, 10 Dec 2021 21:07:12: 1000000 INFO @ Fri, 10 Dec 2021 21:07:18: 6000000 INFO @ Fri, 10 Dec 2021 21:07:20: 2000000 INFO @ Fri, 10 Dec 2021 21:07:25: 7000000 INFO @ Fri, 10 Dec 2021 21:07:28: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 21:07:32: 8000000 INFO @ Fri, 10 Dec 2021 21:07:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.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 @ Fri, 10 Dec 2021 21:07:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:07:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:07:37: 4000000 INFO @ Fri, 10 Dec 2021 21:07:40: 9000000 INFO @ Fri, 10 Dec 2021 21:07:40: 1000000 INFO @ Fri, 10 Dec 2021 21:07:46: 5000000 INFO @ Fri, 10 Dec 2021 21:07:47: 2000000 INFO @ Fri, 10 Dec 2021 21:07:47: 10000000 INFO @ Fri, 10 Dec 2021 21:07:54: 3000000 INFO @ Fri, 10 Dec 2021 21:07:54: 6000000 INFO @ Fri, 10 Dec 2021 21:07:55: 11000000 INFO @ Fri, 10 Dec 2021 21:08:01: 4000000 INFO @ Fri, 10 Dec 2021 21:08:03: 7000000 INFO @ Fri, 10 Dec 2021 21:08:03: 12000000 INFO @ Fri, 10 Dec 2021 21:08:08: 5000000 INFO @ Fri, 10 Dec 2021 21:08:11: 13000000 INFO @ Fri, 10 Dec 2021 21:08:12: 8000000 INFO @ Fri, 10 Dec 2021 21:08:15: 6000000 INFO @ Fri, 10 Dec 2021 21:08:18: 14000000 INFO @ Fri, 10 Dec 2021 21:08:20: 9000000 INFO @ Fri, 10 Dec 2021 21:08:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 21:08:22: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 21:08:22: #1 total tags in treatment: 14463828 INFO @ Fri, 10 Dec 2021 21:08:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:08:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:08:22: 7000000 INFO @ Fri, 10 Dec 2021 21:08:23: #1 tags after filtering in treatment: 14463718 INFO @ Fri, 10 Dec 2021 21:08:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 21:08:23: #1 finished! INFO @ Fri, 10 Dec 2021 21:08:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:08:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:08:24: #2 number of paired peaks: 810 WARNING @ Fri, 10 Dec 2021 21:08:24: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Fri, 10 Dec 2021 21:08:24: start model_add_line... INFO @ Fri, 10 Dec 2021 21:08:24: start X-correlation... INFO @ Fri, 10 Dec 2021 21:08:24: end of X-cor INFO @ Fri, 10 Dec 2021 21:08:24: #2 finished! INFO @ Fri, 10 Dec 2021 21:08:24: #2 predicted fragment length is 64 bps INFO @ Fri, 10 Dec 2021 21:08:24: #2 alternative fragment length(s) may be 4,64 bps INFO @ Fri, 10 Dec 2021 21:08:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.05_model.r WARNING @ Fri, 10 Dec 2021 21:08:24: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:08:24: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Fri, 10 Dec 2021 21:08:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:08:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:08:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:08:29: 10000000 INFO @ Fri, 10 Dec 2021 21:08:29: 8000000 INFO @ Fri, 10 Dec 2021 21:08:36: 9000000 INFO @ Fri, 10 Dec 2021 21:08:37: 11000000 INFO @ Fri, 10 Dec 2021 21:08:43: 10000000 INFO @ Fri, 10 Dec 2021 21:08:46: 12000000 INFO @ Fri, 10 Dec 2021 21:08:50: 11000000 INFO @ Fri, 10 Dec 2021 21:08:55: 13000000 INFO @ Fri, 10 Dec 2021 21:08:58: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:09:03: 14000000 INFO @ Fri, 10 Dec 2021 21:09:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:09:05: 13000000 INFO @ Fri, 10 Dec 2021 21:09:08: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 21:09:08: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 21:09:08: #1 total tags in treatment: 14463828 INFO @ Fri, 10 Dec 2021 21:09:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:09:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:09:08: #1 tags after filtering in treatment: 14463718 INFO @ Fri, 10 Dec 2021 21:09:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 21:09:08: #1 finished! INFO @ Fri, 10 Dec 2021 21:09:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:09:10: #2 number of paired peaks: 810 WARNING @ Fri, 10 Dec 2021 21:09:10: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Fri, 10 Dec 2021 21:09:10: start model_add_line... INFO @ Fri, 10 Dec 2021 21:09:10: start X-correlation... INFO @ Fri, 10 Dec 2021 21:09:10: end of X-cor INFO @ Fri, 10 Dec 2021 21:09:10: #2 finished! INFO @ Fri, 10 Dec 2021 21:09:10: #2 predicted fragment length is 64 bps INFO @ Fri, 10 Dec 2021 21:09:10: #2 alternative fragment length(s) may be 4,64 bps INFO @ Fri, 10 Dec 2021 21:09:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.10_model.r WARNING @ Fri, 10 Dec 2021 21:09:10: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:09:10: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Fri, 10 Dec 2021 21:09:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:09:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:09:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:09:12: 14000000 INFO @ Fri, 10 Dec 2021 21:09:15: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 21:09:15: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 21:09:15: #1 total tags in treatment: 14463828 INFO @ Fri, 10 Dec 2021 21:09:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:09:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:09:16: #1 tags after filtering in treatment: 14463718 INFO @ Fri, 10 Dec 2021 21:09:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 21:09:16: #1 finished! INFO @ Fri, 10 Dec 2021 21:09:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:09:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:09:17: #2 number of paired peaks: 810 WARNING @ Fri, 10 Dec 2021 21:09:17: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Fri, 10 Dec 2021 21:09:17: start model_add_line... INFO @ Fri, 10 Dec 2021 21:09:17: start X-correlation... INFO @ Fri, 10 Dec 2021 21:09:17: end of X-cor INFO @ Fri, 10 Dec 2021 21:09:17: #2 finished! INFO @ Fri, 10 Dec 2021 21:09:17: #2 predicted fragment length is 64 bps INFO @ Fri, 10 Dec 2021 21:09:17: #2 alternative fragment length(s) may be 4,64 bps INFO @ Fri, 10 Dec 2021 21:09:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.20_model.r WARNING @ Fri, 10 Dec 2021 21:09:17: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:09:17: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Fri, 10 Dec 2021 21:09:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:09:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:09:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.05_summits.bed INFO @ Fri, 10 Dec 2021 21:09:24: Done! pass1 - making usageList (705 chroms): 3 millis pass2 - checking and writing primary data (3562 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:09:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:09:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:10:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.10_summits.bed INFO @ Fri, 10 Dec 2021 21:10:09: Done! pass1 - making usageList (581 chroms): 1 millis pass2 - checking and writing primary data (1977 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688975/SRX8688975.20_summits.bed INFO @ Fri, 10 Dec 2021 21:10:16: Done! pass1 - making usageList (330 chroms): 1 millis pass2 - checking and writing primary data (811 records, 4 fields): 23 millis CompletedMACS2peakCalling