Job ID = 6529383 SRX = SRX2325645 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: 00:10:22 36567916 reads; of these: 36567916 (100.00%) were unpaired; of these: 13573424 (37.12%) aligned 0 times 17988482 (49.19%) aligned exactly 1 time 5006010 (13.69%) aligned >1 times 62.88% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 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] 7410294 / 22994492 = 0.3223 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 02:01:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.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 02:01:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:45: 1000000 INFO @ Tue, 30 Jun 2020 02:01:53: 2000000 INFO @ Tue, 30 Jun 2020 02:02:01: 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 02:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.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 02:02:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:02:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:02:09: 4000000 INFO @ Tue, 30 Jun 2020 02:02:15: 1000000 INFO @ Tue, 30 Jun 2020 02:02:17: 5000000 INFO @ Tue, 30 Jun 2020 02:02:23: 2000000 INFO @ Tue, 30 Jun 2020 02:02:25: 6000000 INFO @ Tue, 30 Jun 2020 02:02:30: 3000000 INFO @ Tue, 30 Jun 2020 02:02:33: 7000000 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 02:02:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.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 02:02:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:02:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:02:38: 4000000 INFO @ Tue, 30 Jun 2020 02:02:41: 8000000 INFO @ Tue, 30 Jun 2020 02:02:45: 1000000 INFO @ Tue, 30 Jun 2020 02:02:46: 5000000 INFO @ Tue, 30 Jun 2020 02:02:49: 9000000 INFO @ Tue, 30 Jun 2020 02:02:53: 2000000 INFO @ Tue, 30 Jun 2020 02:02:54: 6000000 INFO @ Tue, 30 Jun 2020 02:02:57: 10000000 INFO @ Tue, 30 Jun 2020 02:03:01: 3000000 INFO @ Tue, 30 Jun 2020 02:03:02: 7000000 INFO @ Tue, 30 Jun 2020 02:03:06: 11000000 INFO @ Tue, 30 Jun 2020 02:03:08: 4000000 INFO @ Tue, 30 Jun 2020 02:03:10: 8000000 INFO @ Tue, 30 Jun 2020 02:03:14: 12000000 INFO @ Tue, 30 Jun 2020 02:03:16: 5000000 INFO @ Tue, 30 Jun 2020 02:03:18: 9000000 INFO @ Tue, 30 Jun 2020 02:03:22: 13000000 INFO @ Tue, 30 Jun 2020 02:03:24: 6000000 INFO @ Tue, 30 Jun 2020 02:03:26: 10000000 INFO @ Tue, 30 Jun 2020 02:03:30: 14000000 INFO @ Tue, 30 Jun 2020 02:03:32: 7000000 INFO @ Tue, 30 Jun 2020 02:03:34: 11000000 INFO @ Tue, 30 Jun 2020 02:03:39: 15000000 INFO @ Tue, 30 Jun 2020 02:03:40: 8000000 INFO @ Tue, 30 Jun 2020 02:03:42: 12000000 INFO @ Tue, 30 Jun 2020 02:03:44: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:03:44: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:03:44: #1 total tags in treatment: 15584198 INFO @ Tue, 30 Jun 2020 02:03:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:44: #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 02:03:44: #1 tags after filtering in treatment: 15584193 INFO @ Tue, 30 Jun 2020 02:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:45: #2 number of paired peaks: 335 WARNING @ Tue, 30 Jun 2020 02:03:45: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:45: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:45: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:45: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:45: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:45: #2 predicted fragment length is 83 bps INFO @ Tue, 30 Jun 2020 02:03:45: #2 alternative fragment length(s) may be 4,83 bps INFO @ Tue, 30 Jun 2020 02:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.05_model.r WARNING @ Tue, 30 Jun 2020 02:03:45: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:03:45: #2 You may need to consider one of the other alternative d(s): 4,83 WARNING @ Tue, 30 Jun 2020 02:03:45: #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 02:03:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:03:47: 9000000 INFO @ Tue, 30 Jun 2020 02:03:50: 13000000 INFO @ Tue, 30 Jun 2020 02:03:55: 10000000 INFO @ Tue, 30 Jun 2020 02:03:58: 14000000 INFO @ Tue, 30 Jun 2020 02:04:02: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:04:05: 15000000 INFO @ Tue, 30 Jun 2020 02:04:09: 12000000 INFO @ Tue, 30 Jun 2020 02:04:10: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:04:10: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:04:10: #1 total tags in treatment: 15584198 INFO @ Tue, 30 Jun 2020 02:04:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:04:10: #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 02:04:10: #1 tags after filtering in treatment: 15584193 INFO @ Tue, 30 Jun 2020 02:04:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:04:10: #1 finished! INFO @ Tue, 30 Jun 2020 02:04:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:04:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:04:11: #2 number of paired peaks: 335 WARNING @ Tue, 30 Jun 2020 02:04:11: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 30 Jun 2020 02:04:11: start model_add_line... INFO @ Tue, 30 Jun 2020 02:04:12: start X-correlation... INFO @ Tue, 30 Jun 2020 02:04:12: end of X-cor INFO @ Tue, 30 Jun 2020 02:04:12: #2 finished! INFO @ Tue, 30 Jun 2020 02:04:12: #2 predicted fragment length is 83 bps INFO @ Tue, 30 Jun 2020 02:04:12: #2 alternative fragment length(s) may be 4,83 bps INFO @ Tue, 30 Jun 2020 02:04:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.10_model.r WARNING @ Tue, 30 Jun 2020 02:04:12: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:04:12: #2 You may need to consider one of the other alternative d(s): 4,83 WARNING @ Tue, 30 Jun 2020 02:04:12: #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 02:04:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:04:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:04:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:04:16: 13000000 INFO @ Tue, 30 Jun 2020 02:04:23: 14000000 INFO @ Tue, 30 Jun 2020 02:04:29: 15000000 INFO @ Tue, 30 Jun 2020 02:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.05_summits.bed INFO @ Tue, 30 Jun 2020 02:04:30: Done! pass1 - making usageList (620 chroms): 1 millis pass2 - checking and writing primary data (2101 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:04:33: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:04:33: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:04:33: #1 total tags in treatment: 15584198 INFO @ Tue, 30 Jun 2020 02:04:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:04:33: #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 02:04:34: #1 tags after filtering in treatment: 15584193 INFO @ Tue, 30 Jun 2020 02:04:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:04:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:04:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:04:35: #2 number of paired peaks: 335 WARNING @ Tue, 30 Jun 2020 02:04:35: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 30 Jun 2020 02:04:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:04:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:04:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:04:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:04:35: #2 predicted fragment length is 83 bps INFO @ Tue, 30 Jun 2020 02:04:35: #2 alternative fragment length(s) may be 4,83 bps INFO @ Tue, 30 Jun 2020 02:04:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.20_model.r WARNING @ Tue, 30 Jun 2020 02:04:35: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:04:35: #2 You may need to consider one of the other alternative d(s): 4,83 WARNING @ Tue, 30 Jun 2020 02:04:35: #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 02:04:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:04:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:04:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.10_summits.bed INFO @ Tue, 30 Jun 2020 02:04:59: Done! pass1 - making usageList (475 chroms): 1 millis pass2 - checking and writing primary data (1260 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:05:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:05:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:05:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:05:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325645/SRX2325645.20_summits.bed INFO @ Tue, 30 Jun 2020 02:05:19: Done! pass1 - making usageList (277 chroms): 1 millis pass2 - checking and writing primary data (532 records, 4 fields): 9 millis CompletedMACS2peakCalling