Job ID = 6627762 SRX = SRX8521407 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: 00:06:39 54854040 reads; of these: 54854040 (100.00%) were unpaired; of these: 48763831 (88.90%) aligned 0 times 4650761 (8.48%) aligned exactly 1 time 1439448 (2.62%) aligned >1 times 11.10% overall alignment rate Time searching: 00:06:39 Overall time: 00:06:39 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] 778633 / 6090209 = 0.1278 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 13:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.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 13:14:15: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:14:15: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:14:22: 1000000 INFO @ Tue, 14 Jul 2020 13:14:29: 2000000 INFO @ Tue, 14 Jul 2020 13:14:35: 3000000 INFO @ Tue, 14 Jul 2020 13:14:42: 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 13:14:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.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 13:14:45: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:14:45: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:14:49: 5000000 INFO @ Tue, 14 Jul 2020 13:14:52: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 13:14:52: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 13:14:52: #1 total tags in treatment: 5311576 INFO @ Tue, 14 Jul 2020 13:14:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:14:52: #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 13:14:53: #1 tags after filtering in treatment: 5311379 INFO @ Tue, 14 Jul 2020 13:14:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:14:53: #1 finished! INFO @ Tue, 14 Jul 2020 13:14:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:14:53: #2 number of paired peaks: 658 WARNING @ Tue, 14 Jul 2020 13:14:53: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Tue, 14 Jul 2020 13:14:53: start model_add_line... INFO @ Tue, 14 Jul 2020 13:14:53: start X-correlation... INFO @ Tue, 14 Jul 2020 13:14:53: end of X-cor INFO @ Tue, 14 Jul 2020 13:14:53: #2 finished! INFO @ Tue, 14 Jul 2020 13:14:53: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 13:14:53: #2 alternative fragment length(s) may be 4,53,534 bps INFO @ Tue, 14 Jul 2020 13:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.05_model.r WARNING @ Tue, 14 Jul 2020 13:14:53: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:14:53: #2 You may need to consider one of the other alternative d(s): 4,53,534 WARNING @ Tue, 14 Jul 2020 13:14:53: #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 13:14:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:14:53: 1000000 INFO @ Tue, 14 Jul 2020 13:15:01: 2000000 INFO @ Tue, 14 Jul 2020 13:15:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:15:10: 3000000 INFO @ Tue, 14 Jul 2020 13:15:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.05_peaks.xls INFO @ Tue, 14 Jul 2020 13:15:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:15:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.05_summits.bed INFO @ Tue, 14 Jul 2020 13:15:11: Done! pass1 - making usageList (177 chroms): 0 millis pass2 - checking and writing primary data (816 records, 4 fields): 8 millis CompletedMACS2peakCalling 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 13:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.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 13:15:15: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:15:15: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:15:18: 4000000 INFO @ Tue, 14 Jul 2020 13:15:24: 1000000 INFO @ Tue, 14 Jul 2020 13:15:27: 5000000 INFO @ Tue, 14 Jul 2020 13:15:30: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 13:15:30: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 13:15:30: #1 total tags in treatment: 5311576 INFO @ Tue, 14 Jul 2020 13:15:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:15:30: #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 13:15:30: #1 tags after filtering in treatment: 5311379 INFO @ Tue, 14 Jul 2020 13:15:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:15:30: #1 finished! INFO @ Tue, 14 Jul 2020 13:15:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:15:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:15:31: #2 number of paired peaks: 658 WARNING @ Tue, 14 Jul 2020 13:15:31: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Tue, 14 Jul 2020 13:15:31: start model_add_line... INFO @ Tue, 14 Jul 2020 13:15:31: start X-correlation... INFO @ Tue, 14 Jul 2020 13:15:31: end of X-cor INFO @ Tue, 14 Jul 2020 13:15:31: #2 finished! INFO @ Tue, 14 Jul 2020 13:15:31: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 13:15:31: #2 alternative fragment length(s) may be 4,53,534 bps INFO @ Tue, 14 Jul 2020 13:15:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.10_model.r WARNING @ Tue, 14 Jul 2020 13:15:31: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:15:31: #2 You may need to consider one of the other alternative d(s): 4,53,534 WARNING @ Tue, 14 Jul 2020 13:15:31: #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 13:15:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:15:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:15:31: 2000000 INFO @ Tue, 14 Jul 2020 13:15:38: 3000000 INFO @ Tue, 14 Jul 2020 13:15:42: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 13:15:44: 4000000 INFO @ Tue, 14 Jul 2020 13:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.10_peaks.xls INFO @ Tue, 14 Jul 2020 13:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:15:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.10_summits.bed INFO @ Tue, 14 Jul 2020 13:15:47: Done! pass1 - making usageList (123 chroms): 0 millis pass2 - checking and writing primary data (359 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 13:15:51: 5000000 INFO @ Tue, 14 Jul 2020 13:15:53: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 13:15:53: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 13:15:53: #1 total tags in treatment: 5311576 INFO @ Tue, 14 Jul 2020 13:15:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:15:53: #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 13:15:53: #1 tags after filtering in treatment: 5311379 INFO @ Tue, 14 Jul 2020 13:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:15:53: #1 finished! INFO @ Tue, 14 Jul 2020 13:15:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:15:54: #2 number of paired peaks: 658 WARNING @ Tue, 14 Jul 2020 13:15:54: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Tue, 14 Jul 2020 13:15:54: start model_add_line... INFO @ Tue, 14 Jul 2020 13:15:54: start X-correlation... INFO @ Tue, 14 Jul 2020 13:15:54: end of X-cor INFO @ Tue, 14 Jul 2020 13:15:54: #2 finished! INFO @ Tue, 14 Jul 2020 13:15:54: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 13:15:54: #2 alternative fragment length(s) may be 4,53,534 bps INFO @ Tue, 14 Jul 2020 13:15:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.20_model.r WARNING @ Tue, 14 Jul 2020 13:15:54: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:15:54: #2 You may need to consider one of the other alternative d(s): 4,53,534 WARNING @ Tue, 14 Jul 2020 13:15:54: #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 13:15:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:15:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 13:16:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:16:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.20_peaks.xls INFO @ Tue, 14 Jul 2020 13:16:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:16:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521407/SRX8521407.20_summits.bed INFO @ Tue, 14 Jul 2020 13:16:11: Done! pass1 - making usageList (65 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 3 millis CompletedMACS2peakCalling