Job ID = 6627781 SRX = SRX8521406 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: 00:07:52 50924706 reads; of these: 50924706 (100.00%) were unpaired; of these: 41642228 (81.77%) aligned 0 times 6515220 (12.79%) aligned exactly 1 time 2767258 (5.43%) aligned >1 times 18.23% overall alignment rate Time searching: 00:07:52 Overall time: 00:07:52 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] 1634719 / 9282478 = 0.1761 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 13:25:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.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 13:25:01: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:25:01: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:25:08: 1000000 INFO @ Tue, 14 Jul 2020 13:25:14: 2000000 INFO @ Tue, 14 Jul 2020 13:25:21: 3000000 INFO @ Tue, 14 Jul 2020 13:25:27: 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 13:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.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 13:25:31: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:25:31: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:25:33: 5000000 INFO @ Tue, 14 Jul 2020 13:25:38: 1000000 INFO @ Tue, 14 Jul 2020 13:25:40: 6000000 INFO @ Tue, 14 Jul 2020 13:25:45: 2000000 INFO @ Tue, 14 Jul 2020 13:25:47: 7000000 INFO @ Tue, 14 Jul 2020 13:25:51: #1 tag size is determined as 54 bps INFO @ Tue, 14 Jul 2020 13:25:51: #1 tag size = 54 INFO @ Tue, 14 Jul 2020 13:25:51: #1 total tags in treatment: 7647759 INFO @ Tue, 14 Jul 2020 13:25:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:25:51: #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 13:25:52: #1 tags after filtering in treatment: 7647630 INFO @ Tue, 14 Jul 2020 13:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:25:52: #1 finished! INFO @ Tue, 14 Jul 2020 13:25:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:25:52: 3000000 INFO @ Tue, 14 Jul 2020 13:25:52: #2 number of paired peaks: 421 WARNING @ Tue, 14 Jul 2020 13:25:52: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Tue, 14 Jul 2020 13:25:52: start model_add_line... INFO @ Tue, 14 Jul 2020 13:25:52: start X-correlation... INFO @ Tue, 14 Jul 2020 13:25:52: end of X-cor INFO @ Tue, 14 Jul 2020 13:25:52: #2 finished! INFO @ Tue, 14 Jul 2020 13:25:52: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 13:25:52: #2 alternative fragment length(s) may be 4,11,58,148,466,583 bps INFO @ Tue, 14 Jul 2020 13:25:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.05_model.r WARNING @ Tue, 14 Jul 2020 13:25:52: #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 13:25:52: #2 You may need to consider one of the other alternative d(s): 4,11,58,148,466,583 WARNING @ Tue, 14 Jul 2020 13:25:52: #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 13:25:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:25:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:25:58: 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, 14 Jul 2020 13:26:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.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 13:26:01: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:26:01: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:26:05: 5000000 INFO @ Tue, 14 Jul 2020 13:26:08: 1000000 INFO @ Tue, 14 Jul 2020 13:26:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:26:11: 6000000 INFO @ Tue, 14 Jul 2020 13:26:15: 2000000 INFO @ Tue, 14 Jul 2020 13:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.05_peaks.xls INFO @ Tue, 14 Jul 2020 13:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.05_summits.bed INFO @ Tue, 14 Jul 2020 13:26:16: Done! pass1 - making usageList (364 chroms): 1 millis pass2 - checking and writing primary data (945 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 13:26:18: 7000000 INFO @ Tue, 14 Jul 2020 13:26:21: 3000000 INFO @ Tue, 14 Jul 2020 13:26:22: #1 tag size is determined as 54 bps INFO @ Tue, 14 Jul 2020 13:26:22: #1 tag size = 54 INFO @ Tue, 14 Jul 2020 13:26:22: #1 total tags in treatment: 7647759 INFO @ Tue, 14 Jul 2020 13:26:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:26:22: #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 13:26:23: #1 tags after filtering in treatment: 7647630 INFO @ Tue, 14 Jul 2020 13:26:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:26:23: #1 finished! INFO @ Tue, 14 Jul 2020 13:26:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:26:23: #2 number of paired peaks: 421 WARNING @ Tue, 14 Jul 2020 13:26:23: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Tue, 14 Jul 2020 13:26:23: start model_add_line... INFO @ Tue, 14 Jul 2020 13:26:23: start X-correlation... INFO @ Tue, 14 Jul 2020 13:26:23: end of X-cor INFO @ Tue, 14 Jul 2020 13:26:23: #2 finished! INFO @ Tue, 14 Jul 2020 13:26:23: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 13:26:23: #2 alternative fragment length(s) may be 4,11,58,148,466,583 bps INFO @ Tue, 14 Jul 2020 13:26:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.10_model.r WARNING @ Tue, 14 Jul 2020 13:26:23: #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 13:26:23: #2 You may need to consider one of the other alternative d(s): 4,11,58,148,466,583 WARNING @ Tue, 14 Jul 2020 13:26:23: #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 13:26:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:26:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:26:27: 4000000 INFO @ Tue, 14 Jul 2020 13:26:34: 5000000 INFO @ Tue, 14 Jul 2020 13:26:39: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:26:40: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 13:26:46: 7000000 INFO @ Tue, 14 Jul 2020 13:26:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.10_peaks.xls INFO @ Tue, 14 Jul 2020 13:26:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:26:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.10_summits.bed INFO @ Tue, 14 Jul 2020 13:26:47: Done! pass1 - making usageList (177 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 13:26:51: #1 tag size is determined as 54 bps INFO @ Tue, 14 Jul 2020 13:26:51: #1 tag size = 54 INFO @ Tue, 14 Jul 2020 13:26:51: #1 total tags in treatment: 7647759 INFO @ Tue, 14 Jul 2020 13:26:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:26:51: #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 13:26:51: #1 tags after filtering in treatment: 7647630 INFO @ Tue, 14 Jul 2020 13:26:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:26:51: #1 finished! INFO @ Tue, 14 Jul 2020 13:26:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:26:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:26:52: #2 number of paired peaks: 421 WARNING @ Tue, 14 Jul 2020 13:26:52: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Tue, 14 Jul 2020 13:26:52: start model_add_line... INFO @ Tue, 14 Jul 2020 13:26:52: start X-correlation... INFO @ Tue, 14 Jul 2020 13:26:52: end of X-cor INFO @ Tue, 14 Jul 2020 13:26:52: #2 finished! INFO @ Tue, 14 Jul 2020 13:26:52: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 13:26:52: #2 alternative fragment length(s) may be 4,11,58,148,466,583 bps INFO @ Tue, 14 Jul 2020 13:26:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.20_model.r WARNING @ Tue, 14 Jul 2020 13:26:52: #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 13:26:52: #2 You may need to consider one of the other alternative d(s): 4,11,58,148,466,583 WARNING @ Tue, 14 Jul 2020 13:26:52: #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 13:26:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:26:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 13:27:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.20_peaks.xls INFO @ Tue, 14 Jul 2020 13:27:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:27:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521406/SRX8521406.20_summits.bed INFO @ Tue, 14 Jul 2020 13:27:15: Done! pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 4 millis CompletedMACS2peakCalling