Job ID = 6529863 SRX = SRX5343097 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: 00:05:15 17300828 reads; of these: 17300828 (100.00%) were unpaired; of these: 877114 (5.07%) aligned 0 times 13761659 (79.54%) aligned exactly 1 time 2662055 (15.39%) aligned >1 times 94.93% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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] 1537526 / 16423714 = 0.0936 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 03:03:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.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 03:03:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:03:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:03:12: 1000000 INFO @ Tue, 30 Jun 2020 03:03:18: 2000000 INFO @ Tue, 30 Jun 2020 03:03:24: 3000000 INFO @ Tue, 30 Jun 2020 03:03:29: 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 03:03:35: 5000000 INFO @ Tue, 30 Jun 2020 03:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.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 03:03:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:03:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:03:41: 6000000 INFO @ Tue, 30 Jun 2020 03:03:43: 1000000 INFO @ Tue, 30 Jun 2020 03:03:47: 7000000 INFO @ Tue, 30 Jun 2020 03:03:49: 2000000 INFO @ Tue, 30 Jun 2020 03:03:53: 8000000 INFO @ Tue, 30 Jun 2020 03:03:55: 3000000 INFO @ Tue, 30 Jun 2020 03:03:59: 9000000 INFO @ Tue, 30 Jun 2020 03:04:01: 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 03:04:06: 10000000 INFO @ Tue, 30 Jun 2020 03:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.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 03:04:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:04:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:04:08: 5000000 INFO @ Tue, 30 Jun 2020 03:04:12: 11000000 INFO @ Tue, 30 Jun 2020 03:04:12: 1000000 INFO @ Tue, 30 Jun 2020 03:04:15: 6000000 INFO @ Tue, 30 Jun 2020 03:04:18: 2000000 INFO @ Tue, 30 Jun 2020 03:04:19: 12000000 INFO @ Tue, 30 Jun 2020 03:04:22: 7000000 INFO @ Tue, 30 Jun 2020 03:04:25: 3000000 INFO @ Tue, 30 Jun 2020 03:04:26: 13000000 INFO @ Tue, 30 Jun 2020 03:04:29: 8000000 INFO @ Tue, 30 Jun 2020 03:04:31: 4000000 INFO @ Tue, 30 Jun 2020 03:04:33: 14000000 INFO @ Tue, 30 Jun 2020 03:04:36: 9000000 INFO @ Tue, 30 Jun 2020 03:04:38: 5000000 INFO @ Tue, 30 Jun 2020 03:04:40: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:04:40: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:04:40: #1 total tags in treatment: 14886188 INFO @ Tue, 30 Jun 2020 03:04:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:04:40: #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 03:04:40: #1 tags after filtering in treatment: 14886186 INFO @ Tue, 30 Jun 2020 03:04:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:04:40: #1 finished! INFO @ Tue, 30 Jun 2020 03:04:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:04:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:04:41: #2 number of paired peaks: 149 WARNING @ Tue, 30 Jun 2020 03:04:41: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 30 Jun 2020 03:04:41: start model_add_line... INFO @ Tue, 30 Jun 2020 03:04:41: start X-correlation... INFO @ Tue, 30 Jun 2020 03:04:42: end of X-cor INFO @ Tue, 30 Jun 2020 03:04:42: #2 finished! INFO @ Tue, 30 Jun 2020 03:04:42: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 03:04:42: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 30 Jun 2020 03:04:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.05_model.r WARNING @ Tue, 30 Jun 2020 03:04:42: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:04:42: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 30 Jun 2020 03:04:42: #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 03:04:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:04:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:04:42: 10000000 INFO @ Tue, 30 Jun 2020 03:04:45: 6000000 INFO @ Tue, 30 Jun 2020 03:04:49: 11000000 INFO @ Tue, 30 Jun 2020 03:04:52: 7000000 INFO @ Tue, 30 Jun 2020 03:04:56: 12000000 INFO @ Tue, 30 Jun 2020 03:04:59: 8000000 INFO @ Tue, 30 Jun 2020 03:05:03: 13000000 INFO @ Tue, 30 Jun 2020 03:05:06: 9000000 INFO @ Tue, 30 Jun 2020 03:05:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:10: 14000000 INFO @ Tue, 30 Jun 2020 03:05:13: 10000000 INFO @ Tue, 30 Jun 2020 03:05:16: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:05:16: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:05:16: #1 total tags in treatment: 14886188 INFO @ Tue, 30 Jun 2020 03:05:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:05:16: #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 03:05:17: #1 tags after filtering in treatment: 14886186 INFO @ Tue, 30 Jun 2020 03:05:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:05:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:05:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:05:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:05:18: #2 number of paired peaks: 149 WARNING @ Tue, 30 Jun 2020 03:05:18: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 30 Jun 2020 03:05:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:05:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:05:18: end of X-cor INFO @ Tue, 30 Jun 2020 03:05:18: #2 finished! INFO @ Tue, 30 Jun 2020 03:05:18: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 03:05:18: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 30 Jun 2020 03:05:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.10_model.r WARNING @ Tue, 30 Jun 2020 03:05:18: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:05:18: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 30 Jun 2020 03:05:18: #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 03:05:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:05:20: 11000000 INFO @ Tue, 30 Jun 2020 03:05:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.05_summits.bed INFO @ Tue, 30 Jun 2020 03:05:24: Done! pass1 - making usageList (346 chroms): 2 millis pass2 - checking and writing primary data (901 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:05:27: 12000000 INFO @ Tue, 30 Jun 2020 03:05:35: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:05:42: 14000000 INFO @ Tue, 30 Jun 2020 03:05:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:49: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:05:49: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:05:49: #1 total tags in treatment: 14886188 INFO @ Tue, 30 Jun 2020 03:05:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:05:49: #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 03:05:50: #1 tags after filtering in treatment: 14886186 INFO @ Tue, 30 Jun 2020 03:05:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:05:50: #1 finished! INFO @ Tue, 30 Jun 2020 03:05:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:05:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:05:51: #2 number of paired peaks: 149 WARNING @ Tue, 30 Jun 2020 03:05:51: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 30 Jun 2020 03:05:51: start model_add_line... INFO @ Tue, 30 Jun 2020 03:05:51: start X-correlation... INFO @ Tue, 30 Jun 2020 03:05:51: end of X-cor INFO @ Tue, 30 Jun 2020 03:05:51: #2 finished! INFO @ Tue, 30 Jun 2020 03:05:51: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 03:05:51: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 30 Jun 2020 03:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.20_model.r WARNING @ Tue, 30 Jun 2020 03:05:51: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:05:51: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 30 Jun 2020 03:05:51: #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 03:05:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:05:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:06:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:06:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:06:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.10_summits.bed INFO @ Tue, 30 Jun 2020 03:06:00: Done! pass1 - making usageList (198 chroms): 1 millis pass2 - checking and writing primary data (407 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:06:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:06:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:06:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:06:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343097/SRX5343097.20_summits.bed INFO @ Tue, 30 Jun 2020 03:06:33: Done! pass1 - making usageList (106 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 8 millis CompletedMACS2peakCalling