Job ID = 6529726 SRX = SRX450798 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: 00:11:16 27371657 reads; of these: 27371657 (100.00%) were unpaired; of these: 4663845 (17.04%) aligned 0 times 19341634 (70.66%) aligned exactly 1 time 3366178 (12.30%) aligned >1 times 82.96% overall alignment rate Time searching: 00:11:16 Overall time: 00:11:16 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] 6311805 / 22707812 = 0.2780 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 02:55:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.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 02:55:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:55:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:55:51: 1000000 INFO @ Tue, 30 Jun 2020 02:56:00: 2000000 INFO @ Tue, 30 Jun 2020 02:56:08: 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 02:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.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 02:56:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:17: 4000000 INFO @ Tue, 30 Jun 2020 02:56:22: 1000000 INFO @ Tue, 30 Jun 2020 02:56:26: 5000000 INFO @ Tue, 30 Jun 2020 02:56:30: 2000000 INFO @ Tue, 30 Jun 2020 02:56:35: 6000000 INFO @ Tue, 30 Jun 2020 02:56:38: 3000000 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 02:56:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.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 02:56:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:44: 7000000 INFO @ Tue, 30 Jun 2020 02:56:47: 4000000 INFO @ Tue, 30 Jun 2020 02:56:51: 1000000 INFO @ Tue, 30 Jun 2020 02:56:53: 8000000 INFO @ Tue, 30 Jun 2020 02:56:56: 5000000 INFO @ Tue, 30 Jun 2020 02:56:59: 2000000 INFO @ Tue, 30 Jun 2020 02:57:02: 9000000 INFO @ Tue, 30 Jun 2020 02:57:04: 6000000 INFO @ Tue, 30 Jun 2020 02:57:07: 3000000 INFO @ Tue, 30 Jun 2020 02:57:10: 10000000 INFO @ Tue, 30 Jun 2020 02:57:13: 7000000 INFO @ Tue, 30 Jun 2020 02:57:15: 4000000 INFO @ Tue, 30 Jun 2020 02:57:19: 11000000 INFO @ Tue, 30 Jun 2020 02:57:22: 8000000 INFO @ Tue, 30 Jun 2020 02:57:23: 5000000 INFO @ Tue, 30 Jun 2020 02:57:28: 12000000 INFO @ Tue, 30 Jun 2020 02:57:31: 9000000 INFO @ Tue, 30 Jun 2020 02:57:31: 6000000 INFO @ Tue, 30 Jun 2020 02:57:37: 13000000 INFO @ Tue, 30 Jun 2020 02:57:39: 7000000 INFO @ Tue, 30 Jun 2020 02:57:39: 10000000 INFO @ Tue, 30 Jun 2020 02:57:46: 14000000 INFO @ Tue, 30 Jun 2020 02:57:46: 8000000 INFO @ Tue, 30 Jun 2020 02:57:48: 11000000 INFO @ Tue, 30 Jun 2020 02:57:54: 9000000 INFO @ Tue, 30 Jun 2020 02:57:55: 15000000 INFO @ Tue, 30 Jun 2020 02:57:57: 12000000 INFO @ Tue, 30 Jun 2020 02:58:02: 10000000 INFO @ Tue, 30 Jun 2020 02:58:03: 16000000 INFO @ Tue, 30 Jun 2020 02:58:06: 13000000 INFO @ Tue, 30 Jun 2020 02:58:07: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:58:07: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:58:07: #1 total tags in treatment: 16396007 INFO @ Tue, 30 Jun 2020 02:58:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:58:07: #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 02:58:08: #1 tags after filtering in treatment: 16395990 INFO @ Tue, 30 Jun 2020 02:58:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:58:08: #1 finished! INFO @ Tue, 30 Jun 2020 02:58:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:58:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:58:09: #2 number of paired peaks: 183 WARNING @ Tue, 30 Jun 2020 02:58:09: 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 02:58:09: start model_add_line... INFO @ Tue, 30 Jun 2020 02:58:09: start X-correlation... INFO @ Tue, 30 Jun 2020 02:58:09: end of X-cor INFO @ Tue, 30 Jun 2020 02:58:09: #2 finished! INFO @ Tue, 30 Jun 2020 02:58:09: #2 predicted fragment length is 92 bps INFO @ Tue, 30 Jun 2020 02:58:09: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 30 Jun 2020 02:58:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.05_model.r WARNING @ Tue, 30 Jun 2020 02:58:09: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:58:09: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Tue, 30 Jun 2020 02:58:09: #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 02:58:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:58:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:58:10: 11000000 INFO @ Tue, 30 Jun 2020 02:58:15: 14000000 INFO @ Tue, 30 Jun 2020 02:58:18: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:58:24: 15000000 INFO @ Tue, 30 Jun 2020 02:58:26: 13000000 INFO @ Tue, 30 Jun 2020 02:58:32: 16000000 INFO @ Tue, 30 Jun 2020 02:58:34: 14000000 INFO @ Tue, 30 Jun 2020 02:58:36: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:58:36: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:58:36: #1 total tags in treatment: 16396007 INFO @ Tue, 30 Jun 2020 02:58:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:58:36: #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 02:58:36: #1 tags after filtering in treatment: 16395990 INFO @ Tue, 30 Jun 2020 02:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:58:36: #1 finished! INFO @ Tue, 30 Jun 2020 02:58:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:58:37: #2 number of paired peaks: 183 WARNING @ Tue, 30 Jun 2020 02:58:37: 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 02:58:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:58:38: start X-correlation... INFO @ Tue, 30 Jun 2020 02:58:38: end of X-cor INFO @ Tue, 30 Jun 2020 02:58:38: #2 finished! INFO @ Tue, 30 Jun 2020 02:58:38: #2 predicted fragment length is 92 bps INFO @ Tue, 30 Jun 2020 02:58:38: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 30 Jun 2020 02:58:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.10_model.r WARNING @ Tue, 30 Jun 2020 02:58:38: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:58:38: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Tue, 30 Jun 2020 02:58:38: #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 02:58:38: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:58:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:58:42: 15000000 INFO @ Tue, 30 Jun 2020 02:58:48: 16000000 INFO @ Tue, 30 Jun 2020 02:58:51: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:58:51: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:58:51: #1 total tags in treatment: 16396007 INFO @ Tue, 30 Jun 2020 02:58:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:58:51: #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 02:58:52: #1 tags after filtering in treatment: 16395990 INFO @ Tue, 30 Jun 2020 02:58:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:58:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:58:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:58:53: #2 number of paired peaks: 183 WARNING @ Tue, 30 Jun 2020 02:58:53: 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 02:58:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:58:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:58:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:58:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:58:53: #2 predicted fragment length is 92 bps INFO @ Tue, 30 Jun 2020 02:58:53: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 30 Jun 2020 02:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.20_model.r WARNING @ Tue, 30 Jun 2020 02:58:53: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:58:53: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Tue, 30 Jun 2020 02:58:53: #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 02:58:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:58:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.05_summits.bed INFO @ Tue, 30 Jun 2020 02:58:55: Done! pass1 - making usageList (398 chroms): 1 millis pass2 - checking and writing primary data (1154 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:59:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:59:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.10_summits.bed INFO @ Tue, 30 Jun 2020 02:59:25: Done! pass1 - making usageList (332 chroms): 1 millis pass2 - checking and writing primary data (737 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:59:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:59:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:59:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX450798/SRX450798.20_summits.bed INFO @ Tue, 30 Jun 2020 02:59:40: Done! pass1 - making usageList (224 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 7 millis CompletedMACS2peakCalling