Job ID = 16438092 SRX = SRX12261337 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: 00:10:24 20513815 reads; of these: 20513815 (100.00%) were unpaired; of these: 987363 (4.81%) aligned 0 times 12594999 (61.40%) aligned exactly 1 time 6931453 (33.79%) aligned >1 times 95.19% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 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] 4864756 / 19526452 = 0.2491 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.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, 02 Aug 2022 13:51:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:51:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:51:44: 1000000 INFO @ Tue, 02 Aug 2022 13:51:51: 2000000 INFO @ Tue, 02 Aug 2022 13:51:58: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:52:06: 4000000 INFO @ Tue, 02 Aug 2022 13:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.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, 02 Aug 2022 13:52:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:52:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:52:13: 5000000 INFO @ Tue, 02 Aug 2022 13:52:13: 1000000 INFO @ Tue, 02 Aug 2022 13:52:20: 2000000 INFO @ Tue, 02 Aug 2022 13:52:21: 6000000 INFO @ Tue, 02 Aug 2022 13:52:28: 3000000 INFO @ Tue, 02 Aug 2022 13:52:31: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:52:35: 4000000 INFO @ Tue, 02 Aug 2022 13:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.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, 02 Aug 2022 13:52:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:52:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:52:39: 8000000 INFO @ Tue, 02 Aug 2022 13:52:43: 5000000 INFO @ Tue, 02 Aug 2022 13:52:46: 1000000 INFO @ Tue, 02 Aug 2022 13:52:48: 9000000 INFO @ Tue, 02 Aug 2022 13:52:51: 6000000 INFO @ Tue, 02 Aug 2022 13:52:55: 2000000 INFO @ Tue, 02 Aug 2022 13:52:57: 10000000 INFO @ Tue, 02 Aug 2022 13:52:58: 7000000 INFO @ Tue, 02 Aug 2022 13:53:05: 3000000 INFO @ Tue, 02 Aug 2022 13:53:06: 8000000 INFO @ Tue, 02 Aug 2022 13:53:07: 11000000 INFO @ Tue, 02 Aug 2022 13:53:14: 9000000 INFO @ Tue, 02 Aug 2022 13:53:15: 4000000 INFO @ Tue, 02 Aug 2022 13:53:17: 12000000 INFO @ Tue, 02 Aug 2022 13:53:22: 10000000 INFO @ Tue, 02 Aug 2022 13:53:24: 5000000 INFO @ Tue, 02 Aug 2022 13:53:27: 13000000 INFO @ Tue, 02 Aug 2022 13:53:30: 11000000 INFO @ Tue, 02 Aug 2022 13:53:33: 6000000 INFO @ Tue, 02 Aug 2022 13:53:37: 14000000 INFO @ Tue, 02 Aug 2022 13:53:39: 12000000 INFO @ Tue, 02 Aug 2022 13:53:43: 7000000 INFO @ Tue, 02 Aug 2022 13:53:43: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 13:53:43: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 13:53:43: #1 total tags in treatment: 14661696 INFO @ Tue, 02 Aug 2022 13:53:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:53:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:53:45: #1 tags after filtering in treatment: 14661696 INFO @ Tue, 02 Aug 2022 13:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:53:45: #1 finished! INFO @ Tue, 02 Aug 2022 13:53:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:53:46: #2 number of paired peaks: 800 WARNING @ Tue, 02 Aug 2022 13:53:46: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Tue, 02 Aug 2022 13:53:46: start model_add_line... INFO @ Tue, 02 Aug 2022 13:53:46: start X-correlation... INFO @ Tue, 02 Aug 2022 13:53:46: end of X-cor INFO @ Tue, 02 Aug 2022 13:53:46: #2 finished! INFO @ Tue, 02 Aug 2022 13:53:46: #2 predicted fragment length is 58 bps INFO @ Tue, 02 Aug 2022 13:53:46: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 02 Aug 2022 13:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.05_model.r WARNING @ Tue, 02 Aug 2022 13:53:46: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:53:46: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 02 Aug 2022 13:53:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:53:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:53:47: 13000000 INFO @ Tue, 02 Aug 2022 13:53:52: 8000000 INFO @ Tue, 02 Aug 2022 13:53:54: 14000000 INFO @ Tue, 02 Aug 2022 13:54:00: 9000000 INFO @ Tue, 02 Aug 2022 13:54:00: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 13:54:00: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 13:54:00: #1 total tags in treatment: 14661696 INFO @ Tue, 02 Aug 2022 13:54:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:54:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:54:01: #1 tags after filtering in treatment: 14661696 INFO @ Tue, 02 Aug 2022 13:54:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:54:01: #1 finished! INFO @ Tue, 02 Aug 2022 13:54:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:54:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:54:02: #2 number of paired peaks: 800 WARNING @ Tue, 02 Aug 2022 13:54:02: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Tue, 02 Aug 2022 13:54:02: start model_add_line... INFO @ Tue, 02 Aug 2022 13:54:02: start X-correlation... INFO @ Tue, 02 Aug 2022 13:54:02: end of X-cor INFO @ Tue, 02 Aug 2022 13:54:02: #2 finished! INFO @ Tue, 02 Aug 2022 13:54:02: #2 predicted fragment length is 58 bps INFO @ Tue, 02 Aug 2022 13:54:02: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 02 Aug 2022 13:54:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.10_model.r WARNING @ Tue, 02 Aug 2022 13:54:02: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:54:02: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 02 Aug 2022 13:54:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:54:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:54:07: 10000000 INFO @ Tue, 02 Aug 2022 13:54:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:54:15: 11000000 INFO @ Tue, 02 Aug 2022 13:54:24: 12000000 INFO @ Tue, 02 Aug 2022 13:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.05_summits.bed INFO @ Tue, 02 Aug 2022 13:54:27: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (688 chroms): 2 millis pass2 - checking and writing primary data (2240 records, 4 fields): 157 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:54:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:54:32: 13000000 INFO @ Tue, 02 Aug 2022 13:54:39: 14000000 INFO @ Tue, 02 Aug 2022 13:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.10_summits.bed INFO @ Tue, 02 Aug 2022 13:54:41: Done! pass1 - making usageList (578 chroms): 2 millis pass2 - checking and writing primary data (1687 records, 4 fields): 53 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:54:45: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 13:54:45: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 13:54:45: #1 total tags in treatment: 14661696 INFO @ Tue, 02 Aug 2022 13:54:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:54:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:54:46: #1 tags after filtering in treatment: 14661696 INFO @ Tue, 02 Aug 2022 13:54:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:54:46: #1 finished! INFO @ Tue, 02 Aug 2022 13:54:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:54:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:54:47: #2 number of paired peaks: 800 WARNING @ Tue, 02 Aug 2022 13:54:47: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Tue, 02 Aug 2022 13:54:47: start model_add_line... INFO @ Tue, 02 Aug 2022 13:54:47: start X-correlation... INFO @ Tue, 02 Aug 2022 13:54:47: end of X-cor INFO @ Tue, 02 Aug 2022 13:54:47: #2 finished! INFO @ Tue, 02 Aug 2022 13:54:47: #2 predicted fragment length is 58 bps INFO @ Tue, 02 Aug 2022 13:54:47: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 02 Aug 2022 13:54:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.20_model.r WARNING @ Tue, 02 Aug 2022 13:54:47: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:54:47: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 02 Aug 2022 13:54:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:54:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:54:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:55:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:55:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:55:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:55:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261337/SRX12261337.20_summits.bed INFO @ Tue, 02 Aug 2022 13:55:26: Done! pass1 - making usageList (487 chroms): 1 millis pass2 - checking and writing primary data (1385 records, 4 fields): 62 millis CompletedMACS2peakCalling