Job ID = 6529566 SRX = SRX318785 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: 00:04:44 18006243 reads; of these: 18006243 (100.00%) were unpaired; of these: 1246403 (6.92%) aligned 0 times 13106968 (72.79%) aligned exactly 1 time 3652872 (20.29%) aligned >1 times 93.08% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 1765134 / 16759840 = 0.1053 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 02:32:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.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 02:32:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:13: 1000000 INFO @ Tue, 30 Jun 2020 02:32:20: 2000000 INFO @ Tue, 30 Jun 2020 02:32:28: 3000000 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 02:32:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.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 02:32:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:36: 4000000 INFO @ Tue, 30 Jun 2020 02:32:42: 1000000 INFO @ Tue, 30 Jun 2020 02:32:43: 5000000 INFO @ Tue, 30 Jun 2020 02:32:49: 2000000 INFO @ Tue, 30 Jun 2020 02:32:51: 6000000 INFO @ Tue, 30 Jun 2020 02:32:56: 3000000 INFO @ Tue, 30 Jun 2020 02:32:59: 7000000 INFO @ Tue, 30 Jun 2020 02:33:02: 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 02:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.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 02:33:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:33:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:06: 8000000 INFO @ Tue, 30 Jun 2020 02:33:09: 5000000 INFO @ Tue, 30 Jun 2020 02:33:12: 1000000 INFO @ Tue, 30 Jun 2020 02:33:14: 9000000 INFO @ Tue, 30 Jun 2020 02:33:16: 6000000 INFO @ Tue, 30 Jun 2020 02:33:20: 2000000 INFO @ Tue, 30 Jun 2020 02:33:22: 10000000 INFO @ Tue, 30 Jun 2020 02:33:23: 7000000 INFO @ Tue, 30 Jun 2020 02:33:27: 3000000 INFO @ Tue, 30 Jun 2020 02:33:29: 11000000 INFO @ Tue, 30 Jun 2020 02:33:30: 8000000 INFO @ Tue, 30 Jun 2020 02:33:34: 4000000 INFO @ Tue, 30 Jun 2020 02:33:37: 12000000 INFO @ Tue, 30 Jun 2020 02:33:37: 9000000 INFO @ Tue, 30 Jun 2020 02:33:41: 5000000 INFO @ Tue, 30 Jun 2020 02:33:44: 10000000 INFO @ Tue, 30 Jun 2020 02:33:45: 13000000 INFO @ Tue, 30 Jun 2020 02:33:48: 6000000 INFO @ Tue, 30 Jun 2020 02:33:52: 11000000 INFO @ Tue, 30 Jun 2020 02:33:53: 14000000 INFO @ Tue, 30 Jun 2020 02:33:56: 7000000 INFO @ Tue, 30 Jun 2020 02:33:59: 12000000 INFO @ Tue, 30 Jun 2020 02:34:01: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:34:01: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:34:01: #1 total tags in treatment: 14994706 INFO @ Tue, 30 Jun 2020 02:34:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:01: #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 02:34:01: #1 tags after filtering in treatment: 14994705 INFO @ Tue, 30 Jun 2020 02:34:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:01: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:02: #2 number of paired peaks: 183 WARNING @ Tue, 30 Jun 2020 02:34:02: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:02: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:02: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:02: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:02: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:02: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:34:02: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:34:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.05_model.r WARNING @ Tue, 30 Jun 2020 02:34:02: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:02: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:34:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:34:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:03: 8000000 INFO @ Tue, 30 Jun 2020 02:34:06: 13000000 INFO @ Tue, 30 Jun 2020 02:34:10: 9000000 INFO @ Tue, 30 Jun 2020 02:34:12: 14000000 INFO @ Tue, 30 Jun 2020 02:34:17: 10000000 INFO @ Tue, 30 Jun 2020 02:34:19: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:34:19: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:34:19: #1 total tags in treatment: 14994706 INFO @ Tue, 30 Jun 2020 02:34:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:19: #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 02:34:20: #1 tags after filtering in treatment: 14994705 INFO @ Tue, 30 Jun 2020 02:34:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:20: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:20: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:34:21: #2 number of paired peaks: 183 WARNING @ Tue, 30 Jun 2020 02:34:21: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:21: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:21: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:21: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:21: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:34:21: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.10_model.r WARNING @ Tue, 30 Jun 2020 02:34:21: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:21: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:34:21: #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 02:34:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:24: 11000000 INFO @ Tue, 30 Jun 2020 02:34:31: 12000000 INFO @ Tue, 30 Jun 2020 02:34:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:34:38: 13000000 INFO @ Tue, 30 Jun 2020 02:34:44: 14000000 INFO @ Tue, 30 Jun 2020 02:34:51: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:34:51: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:34:51: #1 total tags in treatment: 14994706 INFO @ Tue, 30 Jun 2020 02:34:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:51: #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 02:34:52: #1 tags after filtering in treatment: 14994705 INFO @ Tue, 30 Jun 2020 02:34:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:34:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:34:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:34:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.05_summits.bed INFO @ Tue, 30 Jun 2020 02:34:52: Done! INFO @ Tue, 30 Jun 2020 02:34:53: #2 number of paired peaks: 183 WARNING @ Tue, 30 Jun 2020 02:34:53: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:53: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:34:53: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:34:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.20_model.r WARNING @ Tue, 30 Jun 2020 02:34:53: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:53: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:34:53: #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 02:34:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:53: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (547 chroms): 2 millis pass2 - checking and writing primary data (2110 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:35:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.10_summits.bed INFO @ Tue, 30 Jun 2020 02:35:08: Done! pass1 - making usageList (400 chroms): 1 millis pass2 - checking and writing primary data (1185 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:35:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:35:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318785/SRX318785.20_summits.bed INFO @ Tue, 30 Jun 2020 02:35:40: Done! pass1 - making usageList (150 chroms): 1 millis pass2 - checking and writing primary data (287 records, 4 fields): 6 millis CompletedMACS2peakCalling