Job ID = 6529567 SRX = SRX318786 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: 00:05:04 18412477 reads; of these: 18412477 (100.00%) were unpaired; of these: 1075289 (5.84%) aligned 0 times 13617936 (73.96%) aligned exactly 1 time 3719252 (20.20%) aligned >1 times 94.16% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 1588030 / 17337188 = 0.0916 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 02:33:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.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 02:33:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:33:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:31: 1000000 INFO @ Tue, 30 Jun 2020 02:33:38: 2000000 INFO @ Tue, 30 Jun 2020 02:33:45: 3000000 INFO @ Tue, 30 Jun 2020 02:33:52: 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 02:33:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.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 02:33:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:33:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:59: 5000000 INFO @ Tue, 30 Jun 2020 02:34:02: 1000000 INFO @ Tue, 30 Jun 2020 02:34:07: 6000000 INFO @ Tue, 30 Jun 2020 02:34:10: 2000000 INFO @ Tue, 30 Jun 2020 02:34:15: 7000000 INFO @ Tue, 30 Jun 2020 02:34:19: 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 02:34:23: 8000000 INFO @ Tue, 30 Jun 2020 02:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.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 02:34:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:34:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:34:27: 4000000 INFO @ Tue, 30 Jun 2020 02:34:31: 9000000 INFO @ Tue, 30 Jun 2020 02:34:32: 1000000 INFO @ Tue, 30 Jun 2020 02:34:35: 5000000 INFO @ Tue, 30 Jun 2020 02:34:40: 10000000 INFO @ Tue, 30 Jun 2020 02:34:40: 2000000 INFO @ Tue, 30 Jun 2020 02:34:44: 6000000 INFO @ Tue, 30 Jun 2020 02:34:47: 3000000 INFO @ Tue, 30 Jun 2020 02:34:48: 11000000 INFO @ Tue, 30 Jun 2020 02:34:52: 7000000 INFO @ Tue, 30 Jun 2020 02:34:55: 4000000 INFO @ Tue, 30 Jun 2020 02:34:56: 12000000 INFO @ Tue, 30 Jun 2020 02:35:01: 8000000 INFO @ Tue, 30 Jun 2020 02:35:03: 5000000 INFO @ Tue, 30 Jun 2020 02:35:04: 13000000 INFO @ Tue, 30 Jun 2020 02:35:09: 9000000 INFO @ Tue, 30 Jun 2020 02:35:10: 6000000 INFO @ Tue, 30 Jun 2020 02:35:13: 14000000 INFO @ Tue, 30 Jun 2020 02:35:18: 10000000 INFO @ Tue, 30 Jun 2020 02:35:18: 7000000 INFO @ Tue, 30 Jun 2020 02:35:21: 15000000 INFO @ Tue, 30 Jun 2020 02:35:26: 8000000 INFO @ Tue, 30 Jun 2020 02:35:26: 11000000 INFO @ Tue, 30 Jun 2020 02:35:27: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:35:27: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:35:27: #1 total tags in treatment: 15749158 INFO @ Tue, 30 Jun 2020 02:35:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:35:27: #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 02:35:28: #1 tags after filtering in treatment: 15749157 INFO @ Tue, 30 Jun 2020 02:35:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:35:28: #1 finished! INFO @ Tue, 30 Jun 2020 02:35:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:35:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:35:29: #2 number of paired peaks: 248 WARNING @ Tue, 30 Jun 2020 02:35:29: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 30 Jun 2020 02:35:29: start model_add_line... INFO @ Tue, 30 Jun 2020 02:35:29: start X-correlation... INFO @ Tue, 30 Jun 2020 02:35:29: end of X-cor INFO @ Tue, 30 Jun 2020 02:35:29: #2 finished! INFO @ Tue, 30 Jun 2020 02:35:29: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:35:29: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:35:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.05_model.r WARNING @ Tue, 30 Jun 2020 02:35:29: #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 02:35:29: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:35:29: #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 02:35:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:35:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:35:34: 9000000 INFO @ Tue, 30 Jun 2020 02:35:35: 12000000 INFO @ Tue, 30 Jun 2020 02:35:42: 10000000 INFO @ Tue, 30 Jun 2020 02:35:44: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:35:49: 11000000 INFO @ Tue, 30 Jun 2020 02:35:52: 14000000 INFO @ Tue, 30 Jun 2020 02:35:56: 12000000 INFO @ Tue, 30 Jun 2020 02:36:00: 15000000 INFO @ Tue, 30 Jun 2020 02:36:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:36:04: 13000000 INFO @ Tue, 30 Jun 2020 02:36:07: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:36:07: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:36:07: #1 total tags in treatment: 15749158 INFO @ Tue, 30 Jun 2020 02:36:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:36:07: #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 02:36:07: #1 tags after filtering in treatment: 15749157 INFO @ Tue, 30 Jun 2020 02:36:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:36:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:36:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:36:08: #2 number of paired peaks: 248 WARNING @ Tue, 30 Jun 2020 02:36:08: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 30 Jun 2020 02:36:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:36:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:36:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:36:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:36:08: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:36:08: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:36:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.10_model.r WARNING @ Tue, 30 Jun 2020 02:36:08: #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 02:36:08: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:36:08: #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 02:36:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:36:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:36:11: 14000000 INFO @ Tue, 30 Jun 2020 02:36:18: 15000000 INFO @ Tue, 30 Jun 2020 02:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.05_summits.bed INFO @ Tue, 30 Jun 2020 02:36:20: Done! pass1 - making usageList (510 chroms): 1 millis pass2 - checking and writing primary data (2080 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:36:23: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:36:23: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:36:23: #1 total tags in treatment: 15749158 INFO @ Tue, 30 Jun 2020 02:36:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:36:23: #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 02:36:24: #1 tags after filtering in treatment: 15749157 INFO @ Tue, 30 Jun 2020 02:36:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:36:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:36:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:36:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:36:25: #2 number of paired peaks: 248 WARNING @ Tue, 30 Jun 2020 02:36:25: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 30 Jun 2020 02:36:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:36:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:36:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:36:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:36:25: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:36:25: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:36:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.20_model.r WARNING @ Tue, 30 Jun 2020 02:36:25: #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 02:36:25: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:36:25: #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 02:36:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:36:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:36:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:36:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:36:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:36:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.10_summits.bed INFO @ Tue, 30 Jun 2020 02:36:58: Done! pass1 - making usageList (408 chroms): 1 millis pass2 - checking and writing primary data (1322 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:36:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:37:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:37:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:37:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318786/SRX318786.20_summits.bed INFO @ Tue, 30 Jun 2020 02:37:15: Done! pass1 - making usageList (215 chroms): 2 millis pass2 - checking and writing primary data (438 records, 4 fields): 8 millis CompletedMACS2peakCalling