Job ID = 6529828 SRX = SRX495218 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: 00:04:21 17232507 reads; of these: 17232507 (100.00%) were unpaired; of these: 337970 (1.96%) aligned 0 times 12617018 (73.22%) aligned exactly 1 time 4277519 (24.82%) aligned >1 times 98.04% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 3804190 / 16894537 = 0.2252 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 03:03:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.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 03:03:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:03:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:03:14: 1000000 INFO @ Tue, 30 Jun 2020 03:03:21: 2000000 INFO @ Tue, 30 Jun 2020 03:03:27: 3000000 INFO @ Tue, 30 Jun 2020 03:03:33: 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 03:03:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.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 03:03:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:03:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:03:40: 5000000 INFO @ Tue, 30 Jun 2020 03:03:45: 1000000 INFO @ Tue, 30 Jun 2020 03:03:46: 6000000 INFO @ Tue, 30 Jun 2020 03:03:52: 2000000 INFO @ Tue, 30 Jun 2020 03:03:53: 7000000 INFO @ Tue, 30 Jun 2020 03:03:59: 3000000 INFO @ Tue, 30 Jun 2020 03:04:00: 8000000 INFO @ Tue, 30 Jun 2020 03:04:06: 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 03:04:07: 9000000 INFO @ Tue, 30 Jun 2020 03:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.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 03:04:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:04:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:04:12: 5000000 INFO @ Tue, 30 Jun 2020 03:04:14: 10000000 INFO @ Tue, 30 Jun 2020 03:04:14: 1000000 INFO @ Tue, 30 Jun 2020 03:04:19: 6000000 INFO @ Tue, 30 Jun 2020 03:04:21: 2000000 INFO @ Tue, 30 Jun 2020 03:04:21: 11000000 INFO @ Tue, 30 Jun 2020 03:04:26: 7000000 INFO @ Tue, 30 Jun 2020 03:04:27: 3000000 INFO @ Tue, 30 Jun 2020 03:04:28: 12000000 INFO @ Tue, 30 Jun 2020 03:04:33: 4000000 INFO @ Tue, 30 Jun 2020 03:04:33: 8000000 INFO @ Tue, 30 Jun 2020 03:04:35: 13000000 INFO @ Tue, 30 Jun 2020 03:04:35: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:04:35: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:04:35: #1 total tags in treatment: 13090347 INFO @ Tue, 30 Jun 2020 03:04:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:04:35: #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 03:04:36: #1 tags after filtering in treatment: 13090346 INFO @ Tue, 30 Jun 2020 03:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:04:36: #1 finished! INFO @ Tue, 30 Jun 2020 03:04:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:04:37: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 03:04:37: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 03:04:37: start model_add_line... INFO @ Tue, 30 Jun 2020 03:04:37: start X-correlation... INFO @ Tue, 30 Jun 2020 03:04:37: end of X-cor INFO @ Tue, 30 Jun 2020 03:04:37: #2 finished! INFO @ Tue, 30 Jun 2020 03:04:37: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:04:37: #2 alternative fragment length(s) may be 3,12,50,107,555 bps INFO @ Tue, 30 Jun 2020 03:04:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.05_model.r WARNING @ Tue, 30 Jun 2020 03:04:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:04:37: #2 You may need to consider one of the other alternative d(s): 3,12,50,107,555 WARNING @ Tue, 30 Jun 2020 03:04:37: #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 03:04:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:04:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:04:39: 5000000 INFO @ Tue, 30 Jun 2020 03:04:40: 9000000 INFO @ Tue, 30 Jun 2020 03:04:46: 6000000 INFO @ Tue, 30 Jun 2020 03:04:47: 10000000 INFO @ Tue, 30 Jun 2020 03:04:52: 7000000 INFO @ Tue, 30 Jun 2020 03:04:55: 11000000 INFO @ Tue, 30 Jun 2020 03:04:58: 8000000 INFO @ Tue, 30 Jun 2020 03:05:01: 12000000 INFO @ Tue, 30 Jun 2020 03:05:04: 9000000 INFO @ Tue, 30 Jun 2020 03:05:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:08: 13000000 INFO @ Tue, 30 Jun 2020 03:05:08: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:05:08: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:05:08: #1 total tags in treatment: 13090347 INFO @ Tue, 30 Jun 2020 03:05:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:05:08: #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 03:05:09: #1 tags after filtering in treatment: 13090346 INFO @ Tue, 30 Jun 2020 03:05:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:05:09: #1 finished! INFO @ Tue, 30 Jun 2020 03:05:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:05:10: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 03:05:10: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 03:05:10: start model_add_line... INFO @ Tue, 30 Jun 2020 03:05:10: start X-correlation... INFO @ Tue, 30 Jun 2020 03:05:10: end of X-cor INFO @ Tue, 30 Jun 2020 03:05:10: #2 finished! INFO @ Tue, 30 Jun 2020 03:05:10: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:05:10: #2 alternative fragment length(s) may be 3,12,50,107,555 bps INFO @ Tue, 30 Jun 2020 03:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.10_model.r WARNING @ Tue, 30 Jun 2020 03:05:10: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:05:10: #2 You may need to consider one of the other alternative d(s): 3,12,50,107,555 WARNING @ Tue, 30 Jun 2020 03:05:10: #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 03:05:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:05:10: 10000000 INFO @ Tue, 30 Jun 2020 03:05:16: 11000000 INFO @ Tue, 30 Jun 2020 03:05:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.05_summits.bed INFO @ Tue, 30 Jun 2020 03:05:18: Done! pass1 - making usageList (242 chroms): 0 millis pass2 - checking and writing primary data (531 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:05:22: 12000000 INFO @ Tue, 30 Jun 2020 03:05:28: 13000000 INFO @ Tue, 30 Jun 2020 03:05:29: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:05:29: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:05:29: #1 total tags in treatment: 13090347 INFO @ Tue, 30 Jun 2020 03:05:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:05:29: #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 03:05:29: #1 tags after filtering in treatment: 13090346 INFO @ Tue, 30 Jun 2020 03:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:05:29: #1 finished! INFO @ Tue, 30 Jun 2020 03:05:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:05:30: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 03:05:30: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 03:05:30: start model_add_line... INFO @ Tue, 30 Jun 2020 03:05:30: start X-correlation... INFO @ Tue, 30 Jun 2020 03:05:30: end of X-cor INFO @ Tue, 30 Jun 2020 03:05:30: #2 finished! INFO @ Tue, 30 Jun 2020 03:05:30: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:05:30: #2 alternative fragment length(s) may be 3,12,50,107,555 bps INFO @ Tue, 30 Jun 2020 03:05:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.20_model.r WARNING @ Tue, 30 Jun 2020 03:05:30: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:05:30: #2 You may need to consider one of the other alternative d(s): 3,12,50,107,555 WARNING @ Tue, 30 Jun 2020 03:05:30: #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 03:05:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:05:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.10_summits.bed INFO @ Tue, 30 Jun 2020 03:05:48: Done! pass1 - making usageList (98 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:05:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:06:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:06:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:06:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495218/SRX495218.20_summits.bed INFO @ Tue, 30 Jun 2020 03:06:08: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (127 records, 4 fields): 3 millis CompletedMACS2peakCalling