Job ID = 6627535 SRX = SRX8521362 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: 00:07:31 45172109 reads; of these: 45172109 (100.00%) were unpaired; of these: 35871658 (79.41%) aligned 0 times 6142764 (13.60%) aligned exactly 1 time 3157687 (6.99%) aligned >1 times 20.59% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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_rmdupse_core] 2148197 / 9300451 = 0.2310 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, 14 Jul 2020 12:04:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.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, 14 Jul 2020 12:04:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:04:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:04:16: 1000000 INFO @ Tue, 14 Jul 2020 12:04:22: 2000000 INFO @ Tue, 14 Jul 2020 12:04:28: 3000000 INFO @ Tue, 14 Jul 2020 12:04:34: 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, 14 Jul 2020 12:04:40: 5000000 INFO @ Tue, 14 Jul 2020 12:04:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.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, 14 Jul 2020 12:04:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:04:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:04:45: 6000000 INFO @ Tue, 14 Jul 2020 12:04:46: 1000000 INFO @ Tue, 14 Jul 2020 12:04:51: 2000000 INFO @ Tue, 14 Jul 2020 12:04:52: 7000000 INFO @ Tue, 14 Jul 2020 12:04:53: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 12:04:53: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 12:04:53: #1 total tags in treatment: 7152254 INFO @ Tue, 14 Jul 2020 12:04:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:04:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:04:53: #1 tags after filtering in treatment: 7152071 INFO @ Tue, 14 Jul 2020 12:04:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:04:53: #1 finished! INFO @ Tue, 14 Jul 2020 12:04:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:04:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:04:54: #2 number of paired peaks: 548 WARNING @ Tue, 14 Jul 2020 12:04:54: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Tue, 14 Jul 2020 12:04:54: start model_add_line... INFO @ Tue, 14 Jul 2020 12:04:54: start X-correlation... INFO @ Tue, 14 Jul 2020 12:04:54: end of X-cor INFO @ Tue, 14 Jul 2020 12:04:54: #2 finished! INFO @ Tue, 14 Jul 2020 12:04:54: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:04:54: #2 alternative fragment length(s) may be 58,526,546 bps INFO @ Tue, 14 Jul 2020 12:04:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.05_model.r WARNING @ Tue, 14 Jul 2020 12:04:54: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:04:54: #2 You may need to consider one of the other alternative d(s): 58,526,546 WARNING @ Tue, 14 Jul 2020 12:04:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:04:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:04:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:04:56: 3000000 INFO @ Tue, 14 Jul 2020 12:05:01: 4000000 INFO @ Tue, 14 Jul 2020 12:05:07: 5000000 INFO @ Tue, 14 Jul 2020 12:05:08: #3 Call peaks for each chromosome... 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, 14 Jul 2020 12:05:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.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, 14 Jul 2020 12:05:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:05:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:05:12: 6000000 INFO @ Tue, 14 Jul 2020 12:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:05:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:05:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.05_summits.bed INFO @ Tue, 14 Jul 2020 12:05:16: Done! pass1 - making usageList (366 chroms): 1 millis pass2 - checking and writing primary data (1208 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:05:17: 1000000 INFO @ Tue, 14 Jul 2020 12:05:18: 7000000 INFO @ Tue, 14 Jul 2020 12:05:18: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 12:05:18: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 12:05:18: #1 total tags in treatment: 7152254 INFO @ Tue, 14 Jul 2020 12:05:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:05:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:05:19: #1 tags after filtering in treatment: 7152071 INFO @ Tue, 14 Jul 2020 12:05:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:05:19: #1 finished! INFO @ Tue, 14 Jul 2020 12:05:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:05:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:05:19: #2 number of paired peaks: 548 WARNING @ Tue, 14 Jul 2020 12:05:19: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Tue, 14 Jul 2020 12:05:19: start model_add_line... INFO @ Tue, 14 Jul 2020 12:05:19: start X-correlation... INFO @ Tue, 14 Jul 2020 12:05:19: end of X-cor INFO @ Tue, 14 Jul 2020 12:05:19: #2 finished! INFO @ Tue, 14 Jul 2020 12:05:19: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:05:19: #2 alternative fragment length(s) may be 58,526,546 bps INFO @ Tue, 14 Jul 2020 12:05:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.10_model.r WARNING @ Tue, 14 Jul 2020 12:05:19: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:05:19: #2 You may need to consider one of the other alternative d(s): 58,526,546 WARNING @ Tue, 14 Jul 2020 12:05:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:05:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:05:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:05:23: 2000000 INFO @ Tue, 14 Jul 2020 12:05:29: 3000000 INFO @ Tue, 14 Jul 2020 12:05:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:05:35: 4000000 INFO @ Tue, 14 Jul 2020 12:05:41: 5000000 INFO @ Tue, 14 Jul 2020 12:05:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.10_summits.bed INFO @ Tue, 14 Jul 2020 12:05:42: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (465 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:05:46: 6000000 INFO @ Tue, 14 Jul 2020 12:05:53: 7000000 INFO @ Tue, 14 Jul 2020 12:05:54: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 12:05:54: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 12:05:54: #1 total tags in treatment: 7152254 INFO @ Tue, 14 Jul 2020 12:05:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:05:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:05:54: #1 tags after filtering in treatment: 7152071 INFO @ Tue, 14 Jul 2020 12:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:05:54: #1 finished! INFO @ Tue, 14 Jul 2020 12:05:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:05:54: #2 number of paired peaks: 548 WARNING @ Tue, 14 Jul 2020 12:05:54: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Tue, 14 Jul 2020 12:05:54: start model_add_line... INFO @ Tue, 14 Jul 2020 12:05:55: start X-correlation... INFO @ Tue, 14 Jul 2020 12:05:55: end of X-cor INFO @ Tue, 14 Jul 2020 12:05:55: #2 finished! INFO @ Tue, 14 Jul 2020 12:05:55: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:05:55: #2 alternative fragment length(s) may be 58,526,546 bps INFO @ Tue, 14 Jul 2020 12:05:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.20_model.r WARNING @ Tue, 14 Jul 2020 12:05:55: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:05:55: #2 You may need to consider one of the other alternative d(s): 58,526,546 WARNING @ Tue, 14 Jul 2020 12:05:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:05:55: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:05:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:06:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:06:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:06:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521362/SRX8521362.20_summits.bed INFO @ Tue, 14 Jul 2020 12:06:17: Done! pass1 - making usageList (104 chroms): 0 millis pass2 - checking and writing primary data (204 records, 4 fields): 4 millis CompletedMACS2peakCalling