Job ID = 14170908 SRX = SRX8689040 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: 00:04:27 16898507 reads; of these: 16898507 (100.00%) were unpaired; of these: 465159 (2.75%) aligned 0 times 12165696 (71.99%) aligned exactly 1 time 4267652 (25.25%) aligned >1 times 97.25% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 1557591 / 16433348 = 0.0948 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 @ Sat, 11 Dec 2021 09:07:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.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 @ Sat, 11 Dec 2021 09:07:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:07:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:07:48: 1000000 INFO @ Sat, 11 Dec 2021 09:07:54: 2000000 INFO @ Sat, 11 Dec 2021 09:07:59: 3000000 INFO @ Sat, 11 Dec 2021 09:08:05: 4000000 INFO @ Sat, 11 Dec 2021 09:08:10: 5000000 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 @ Sat, 11 Dec 2021 09:08:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.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 @ Sat, 11 Dec 2021 09:08:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:08:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:08:16: 6000000 INFO @ Sat, 11 Dec 2021 09:08:19: 1000000 INFO @ Sat, 11 Dec 2021 09:08:23: 7000000 INFO @ Sat, 11 Dec 2021 09:08:25: 2000000 INFO @ Sat, 11 Dec 2021 09:08:29: 8000000 INFO @ Sat, 11 Dec 2021 09:08:32: 3000000 INFO @ Sat, 11 Dec 2021 09:08:35: 9000000 INFO @ Sat, 11 Dec 2021 09:08:38: 4000000 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 @ Sat, 11 Dec 2021 09:08:42: 10000000 INFO @ Sat, 11 Dec 2021 09:08:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.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 @ Sat, 11 Dec 2021 09:08:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:08:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:08:44: 5000000 INFO @ Sat, 11 Dec 2021 09:08:48: 11000000 INFO @ Sat, 11 Dec 2021 09:08:49: 1000000 INFO @ Sat, 11 Dec 2021 09:08:51: 6000000 INFO @ Sat, 11 Dec 2021 09:08:55: 12000000 INFO @ Sat, 11 Dec 2021 09:08:55: 2000000 INFO @ Sat, 11 Dec 2021 09:08:57: 7000000 INFO @ Sat, 11 Dec 2021 09:09:02: 13000000 INFO @ Sat, 11 Dec 2021 09:09:02: 3000000 INFO @ Sat, 11 Dec 2021 09:09:04: 8000000 INFO @ Sat, 11 Dec 2021 09:09:08: 14000000 INFO @ Sat, 11 Dec 2021 09:09:08: 4000000 INFO @ Sat, 11 Dec 2021 09:09:10: 9000000 INFO @ Sat, 11 Dec 2021 09:09:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:09:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:09:14: #1 total tags in treatment: 14875757 INFO @ Sat, 11 Dec 2021 09:09:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:09:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:09:14: #1 tags after filtering in treatment: 14875696 INFO @ Sat, 11 Dec 2021 09:09:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:09:14: #1 finished! INFO @ Sat, 11 Dec 2021 09:09:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:09:14: 5000000 INFO @ Sat, 11 Dec 2021 09:09:15: #2 number of paired peaks: 660 WARNING @ Sat, 11 Dec 2021 09:09:15: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Sat, 11 Dec 2021 09:09:15: start model_add_line... INFO @ Sat, 11 Dec 2021 09:09:15: start X-correlation... INFO @ Sat, 11 Dec 2021 09:09:15: end of X-cor INFO @ Sat, 11 Dec 2021 09:09:15: #2 finished! INFO @ Sat, 11 Dec 2021 09:09:15: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 09:09:15: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 11 Dec 2021 09:09:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.05_model.r WARNING @ Sat, 11 Dec 2021 09:09:15: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:09:15: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 11 Dec 2021 09:09:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:09:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:09:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:09:17: 10000000 INFO @ Sat, 11 Dec 2021 09:09:21: 6000000 INFO @ Sat, 11 Dec 2021 09:09:23: 11000000 INFO @ Sat, 11 Dec 2021 09:09:27: 7000000 INFO @ Sat, 11 Dec 2021 09:09:30: 12000000 INFO @ Sat, 11 Dec 2021 09:09:34: 8000000 INFO @ Sat, 11 Dec 2021 09:09:36: 13000000 INFO @ Sat, 11 Dec 2021 09:09:40: 9000000 INFO @ Sat, 11 Dec 2021 09:09:42: 14000000 INFO @ Sat, 11 Dec 2021 09:09:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:09:46: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:09:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:09:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:09:48: #1 total tags in treatment: 14875757 INFO @ Sat, 11 Dec 2021 09:09:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:09:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:09:49: #1 tags after filtering in treatment: 14875696 INFO @ Sat, 11 Dec 2021 09:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:09:49: #1 finished! INFO @ Sat, 11 Dec 2021 09:09:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:09:50: #2 number of paired peaks: 660 WARNING @ Sat, 11 Dec 2021 09:09:50: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Sat, 11 Dec 2021 09:09:50: start model_add_line... INFO @ Sat, 11 Dec 2021 09:09:50: start X-correlation... INFO @ Sat, 11 Dec 2021 09:09:50: end of X-cor INFO @ Sat, 11 Dec 2021 09:09:50: #2 finished! INFO @ Sat, 11 Dec 2021 09:09:50: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 09:09:50: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 11 Dec 2021 09:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.10_model.r WARNING @ Sat, 11 Dec 2021 09:09:50: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:09:50: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 11 Dec 2021 09:09:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:09:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:09:52: 11000000 INFO @ Sat, 11 Dec 2021 09:09:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:09:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:09:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.05_summits.bed INFO @ Sat, 11 Dec 2021 09:09:57: Done! pass1 - making usageList (691 chroms): 2 millis pass2 - checking and writing primary data (3180 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:09:58: 12000000 INFO @ Sat, 11 Dec 2021 09:10:04: 13000000 INFO @ Sat, 11 Dec 2021 09:10:10: 14000000 INFO @ Sat, 11 Dec 2021 09:10:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:10:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:10:15: #1 total tags in treatment: 14875757 INFO @ Sat, 11 Dec 2021 09:10:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:10:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:10:15: #1 tags after filtering in treatment: 14875696 INFO @ Sat, 11 Dec 2021 09:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:10:15: #1 finished! INFO @ Sat, 11 Dec 2021 09:10:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:10:16: #2 number of paired peaks: 660 WARNING @ Sat, 11 Dec 2021 09:10:16: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Sat, 11 Dec 2021 09:10:16: start model_add_line... INFO @ Sat, 11 Dec 2021 09:10:16: start X-correlation... INFO @ Sat, 11 Dec 2021 09:10:16: end of X-cor INFO @ Sat, 11 Dec 2021 09:10:16: #2 finished! INFO @ Sat, 11 Dec 2021 09:10:16: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 09:10:16: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 11 Dec 2021 09:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.20_model.r WARNING @ Sat, 11 Dec 2021 09:10:16: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:10:16: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 11 Dec 2021 09:10:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:10:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:10:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.10_summits.bed INFO @ Sat, 11 Dec 2021 09:10:30: Done! pass1 - making usageList (581 chroms): 2 millis pass2 - checking and writing primary data (2058 records, 4 fields): 90 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:10:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:10:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:10:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:10:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689040/SRX8689040.20_summits.bed INFO @ Sat, 11 Dec 2021 09:10:58: Done! pass1 - making usageList (345 chroms): 1 millis pass2 - checking and writing primary data (775 records, 4 fields): 67 millis CompletedMACS2peakCalling