Job ID = 6529612 SRX = SRX348464 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: 00:09:34 41812299 reads; of these: 41812299 (100.00%) were unpaired; of these: 29795679 (71.26%) aligned 0 times 8738982 (20.90%) aligned exactly 1 time 3277638 (7.84%) aligned >1 times 28.74% overall alignment rate Time searching: 00:09:34 Overall time: 00:09:34 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] 2581502 / 12016620 = 0.2148 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 02:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.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 02:50:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:50:17: 1000000 INFO @ Tue, 30 Jun 2020 02:50:22: 2000000 INFO @ Tue, 30 Jun 2020 02:50:28: 3000000 INFO @ Tue, 30 Jun 2020 02:50:33: 4000000 INFO @ Tue, 30 Jun 2020 02:50:39: 5000000 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 02:50:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.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 02:50:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:50:44: 6000000 INFO @ Tue, 30 Jun 2020 02:50:48: 1000000 INFO @ Tue, 30 Jun 2020 02:50:50: 7000000 INFO @ Tue, 30 Jun 2020 02:50:55: 2000000 INFO @ Tue, 30 Jun 2020 02:50:56: 8000000 INFO @ Tue, 30 Jun 2020 02:51:01: 9000000 INFO @ Tue, 30 Jun 2020 02:51:02: 3000000 INFO @ Tue, 30 Jun 2020 02:51:04: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:51:04: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:51:04: #1 total tags in treatment: 9435118 INFO @ Tue, 30 Jun 2020 02:51:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:04: #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 02:51:04: #1 tags after filtering in treatment: 9435113 INFO @ Tue, 30 Jun 2020 02:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:04: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:05: #2 number of paired peaks: 694 WARNING @ Tue, 30 Jun 2020 02:51:05: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:05: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:05: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 02:51:05: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 30 Jun 2020 02:51:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.05_model.r WARNING @ Tue, 30 Jun 2020 02:51:05: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:51:05: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 30 Jun 2020 02:51:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:51:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:08: 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 02:51:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.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 02:51:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:14: 5000000 INFO @ Tue, 30 Jun 2020 02:51:18: 1000000 INFO @ Tue, 30 Jun 2020 02:51:20: 6000000 INFO @ Tue, 30 Jun 2020 02:51:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:25: 2000000 INFO @ Tue, 30 Jun 2020 02:51:26: 7000000 INFO @ Tue, 30 Jun 2020 02:51:32: 3000000 INFO @ Tue, 30 Jun 2020 02:51:32: 8000000 INFO @ Tue, 30 Jun 2020 02:51:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.05_summits.bed INFO @ Tue, 30 Jun 2020 02:51:33: Done! pass1 - making usageList (679 chroms): 1 millis pass2 - checking and writing primary data (3115 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:51:38: 9000000 INFO @ Tue, 30 Jun 2020 02:51:39: 4000000 INFO @ Tue, 30 Jun 2020 02:51:41: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:51:41: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:51:41: #1 total tags in treatment: 9435118 INFO @ Tue, 30 Jun 2020 02:51:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:41: #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 02:51:41: #1 tags after filtering in treatment: 9435113 INFO @ Tue, 30 Jun 2020 02:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:41: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:42: #2 number of paired peaks: 694 WARNING @ Tue, 30 Jun 2020 02:51:42: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:42: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:42: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:42: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:42: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:42: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 02:51:42: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 30 Jun 2020 02:51:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.10_model.r WARNING @ Tue, 30 Jun 2020 02:51:42: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:51:42: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 30 Jun 2020 02:51:42: #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 02:51:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:45: 5000000 INFO @ Tue, 30 Jun 2020 02:51:52: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:51:58: 7000000 INFO @ Tue, 30 Jun 2020 02:52:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:05: 8000000 INFO @ Tue, 30 Jun 2020 02:52:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.10_summits.bed INFO @ Tue, 30 Jun 2020 02:52:11: Done! pass1 - making usageList (557 chroms): 1 millis pass2 - checking and writing primary data (2031 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:52:12: 9000000 INFO @ Tue, 30 Jun 2020 02:52:15: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:52:15: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:52:15: #1 total tags in treatment: 9435118 INFO @ Tue, 30 Jun 2020 02:52:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:15: #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 02:52:15: #1 tags after filtering in treatment: 9435113 INFO @ Tue, 30 Jun 2020 02:52:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:15: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:16: #2 number of paired peaks: 694 WARNING @ Tue, 30 Jun 2020 02:52:16: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:16: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:16: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:16: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 02:52:16: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 30 Jun 2020 02:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.20_model.r WARNING @ Tue, 30 Jun 2020 02:52:16: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:16: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 30 Jun 2020 02:52:16: #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 02:52:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:52:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348464/SRX348464.20_summits.bed INFO @ Tue, 30 Jun 2020 02:52:45: Done! pass1 - making usageList (396 chroms): 1 millis pass2 - checking and writing primary data (939 records, 4 fields): 11 millis CompletedMACS2peakCalling