Job ID = 16438068 SRX = SRX12261329 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: 00:09:21 21432070 reads; of these: 21432070 (100.00%) were unpaired; of these: 976257 (4.56%) aligned 0 times 13270180 (61.92%) aligned exactly 1 time 7185633 (33.53%) aligned >1 times 95.44% overall alignment rate Time searching: 00:09:21 Overall time: 00:09:21 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 12 files... [bam_rmdupse_core] 7535067 / 20455813 = 0.3684 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 13:42:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.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 13:42:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:42:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:42:47: 1000000 INFO @ Tue, 02 Aug 2022 13:42:53: 2000000 INFO @ Tue, 02 Aug 2022 13:42:59: 3000000 INFO @ Tue, 02 Aug 2022 13:43:05: 4000000 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 13:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.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 13:43:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:43:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:43:11: 5000000 INFO @ Tue, 02 Aug 2022 13:43:16: 1000000 INFO @ Tue, 02 Aug 2022 13:43:17: 6000000 INFO @ Tue, 02 Aug 2022 13:43:23: 2000000 INFO @ Tue, 02 Aug 2022 13:43:23: 7000000 INFO @ Tue, 02 Aug 2022 13:43:29: 3000000 INFO @ Tue, 02 Aug 2022 13:43:30: 8000000 INFO @ Tue, 02 Aug 2022 13:43:35: 4000000 INFO @ Tue, 02 Aug 2022 13:43:36: 9000000 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 13:43:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.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 13:43:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:43:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:43:41: 5000000 INFO @ Tue, 02 Aug 2022 13:43:42: 10000000 INFO @ Tue, 02 Aug 2022 13:43:47: 1000000 INFO @ Tue, 02 Aug 2022 13:43:48: 6000000 INFO @ Tue, 02 Aug 2022 13:43:49: 11000000 INFO @ Tue, 02 Aug 2022 13:43:54: 2000000 INFO @ Tue, 02 Aug 2022 13:43:54: 7000000 INFO @ Tue, 02 Aug 2022 13:43:56: 12000000 INFO @ Tue, 02 Aug 2022 13:44:00: 8000000 INFO @ Tue, 02 Aug 2022 13:44:01: 3000000 INFO @ Tue, 02 Aug 2022 13:44:03: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:44:03: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:44:03: #1 total tags in treatment: 12920746 INFO @ Tue, 02 Aug 2022 13:44:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:44:03: #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 13:44:03: #1 tags after filtering in treatment: 12920745 INFO @ Tue, 02 Aug 2022 13:44:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:44:03: #1 finished! INFO @ Tue, 02 Aug 2022 13:44:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:44:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:44:04: #2 number of paired peaks: 865 WARNING @ Tue, 02 Aug 2022 13:44:04: Fewer paired peaks (865) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 865 pairs to build model! INFO @ Tue, 02 Aug 2022 13:44:04: start model_add_line... INFO @ Tue, 02 Aug 2022 13:44:04: start X-correlation... INFO @ Tue, 02 Aug 2022 13:44:04: end of X-cor INFO @ Tue, 02 Aug 2022 13:44:04: #2 finished! INFO @ Tue, 02 Aug 2022 13:44:04: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 13:44:04: #2 alternative fragment length(s) may be 4,68 bps INFO @ Tue, 02 Aug 2022 13:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.05_model.r WARNING @ Tue, 02 Aug 2022 13:44:04: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:44:04: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Tue, 02 Aug 2022 13:44:04: #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 13:44:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:44:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:44:07: 9000000 INFO @ Tue, 02 Aug 2022 13:44:07: 4000000 INFO @ Tue, 02 Aug 2022 13:44:13: 10000000 INFO @ Tue, 02 Aug 2022 13:44:14: 5000000 INFO @ Tue, 02 Aug 2022 13:44:20: 11000000 INFO @ Tue, 02 Aug 2022 13:44:21: 6000000 INFO @ Tue, 02 Aug 2022 13:44:27: 12000000 INFO @ Tue, 02 Aug 2022 13:44:28: 7000000 INFO @ Tue, 02 Aug 2022 13:44:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:44:33: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:44:33: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:44:33: #1 total tags in treatment: 12920746 INFO @ Tue, 02 Aug 2022 13:44:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:44:33: #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 13:44:34: #1 tags after filtering in treatment: 12920745 INFO @ Tue, 02 Aug 2022 13:44:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:44:34: #1 finished! INFO @ Tue, 02 Aug 2022 13:44:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:44:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:44:34: 8000000 INFO @ Tue, 02 Aug 2022 13:44:35: #2 number of paired peaks: 865 WARNING @ Tue, 02 Aug 2022 13:44:35: Fewer paired peaks (865) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 865 pairs to build model! INFO @ Tue, 02 Aug 2022 13:44:35: start model_add_line... INFO @ Tue, 02 Aug 2022 13:44:35: start X-correlation... INFO @ Tue, 02 Aug 2022 13:44:35: end of X-cor INFO @ Tue, 02 Aug 2022 13:44:35: #2 finished! INFO @ Tue, 02 Aug 2022 13:44:35: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 13:44:35: #2 alternative fragment length(s) may be 4,68 bps INFO @ Tue, 02 Aug 2022 13:44:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.10_model.r WARNING @ Tue, 02 Aug 2022 13:44:35: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:44:35: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Tue, 02 Aug 2022 13:44:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:44:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:44:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:44:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:44:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:44:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.05_summits.bed INFO @ Tue, 02 Aug 2022 13:44:40: Done! pass1 - making usageList (703 chroms): 1 millis pass2 - checking and writing primary data (2559 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:44:41: 9000000 INFO @ Tue, 02 Aug 2022 13:44:47: 10000000 INFO @ Tue, 02 Aug 2022 13:44:53: 11000000 INFO @ Tue, 02 Aug 2022 13:44:59: 12000000 INFO @ Tue, 02 Aug 2022 13:44:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:45:04: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:45:04: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:45:04: #1 total tags in treatment: 12920746 INFO @ Tue, 02 Aug 2022 13:45:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:45:04: #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 13:45:04: #1 tags after filtering in treatment: 12920745 INFO @ Tue, 02 Aug 2022 13:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:45:04: #1 finished! INFO @ Tue, 02 Aug 2022 13:45:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:45:05: #2 number of paired peaks: 865 WARNING @ Tue, 02 Aug 2022 13:45:05: Fewer paired peaks (865) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 865 pairs to build model! INFO @ Tue, 02 Aug 2022 13:45:05: start model_add_line... INFO @ Tue, 02 Aug 2022 13:45:05: start X-correlation... INFO @ Tue, 02 Aug 2022 13:45:05: end of X-cor INFO @ Tue, 02 Aug 2022 13:45:05: #2 finished! INFO @ Tue, 02 Aug 2022 13:45:05: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 13:45:05: #2 alternative fragment length(s) may be 4,68 bps INFO @ Tue, 02 Aug 2022 13:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.20_model.r WARNING @ Tue, 02 Aug 2022 13:45:05: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:45:05: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Tue, 02 Aug 2022 13:45:05: #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 13:45:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:45:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:45:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:45:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:45:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.10_summits.bed INFO @ Tue, 02 Aug 2022 13:45:11: Done! pass1 - making usageList (589 chroms): 2 millis pass2 - checking and writing primary data (1736 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:45:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:45:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:45:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:45:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261329/SRX12261329.20_summits.bed INFO @ Tue, 02 Aug 2022 13:45:42: Done! pass1 - making usageList (502 chroms): 1 millis pass2 - checking and writing primary data (1373 records, 4 fields): 30 millis CompletedMACS2peakCalling