Job ID = 6529618 SRX = SRX3511951 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: 00:00:01 Multiseed full-index search: 00:04:27 9924189 reads; of these: 9924189 (100.00%) were unpaired; of these: 1633207 (16.46%) aligned 0 times 6556162 (66.06%) aligned exactly 1 time 1734820 (17.48%) aligned >1 times 83.54% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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] 474344 / 8290982 = 0.0572 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 02:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.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 02:28:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:28:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:28:09: 1000000 INFO @ Tue, 30 Jun 2020 02:28:15: 2000000 INFO @ Tue, 30 Jun 2020 02:28:22: 3000000 INFO @ Tue, 30 Jun 2020 02:28:28: 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 02:28:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.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 02:28:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:28:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:28:34: 5000000 INFO @ Tue, 30 Jun 2020 02:28:39: 1000000 INFO @ Tue, 30 Jun 2020 02:28:40: 6000000 INFO @ Tue, 30 Jun 2020 02:28:46: 2000000 INFO @ Tue, 30 Jun 2020 02:28:47: 7000000 INFO @ Tue, 30 Jun 2020 02:28:52: 3000000 INFO @ Tue, 30 Jun 2020 02:28:54: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:28:54: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:28:54: #1 total tags in treatment: 7816638 INFO @ Tue, 30 Jun 2020 02:28:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:28:54: #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 02:28:54: #1 tags after filtering in treatment: 7816611 INFO @ Tue, 30 Jun 2020 02:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:28:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:28:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:28:55: #2 number of paired peaks: 345 WARNING @ Tue, 30 Jun 2020 02:28:55: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Tue, 30 Jun 2020 02:28:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:28:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:28:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:28:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:28:55: #2 predicted fragment length is 106 bps INFO @ Tue, 30 Jun 2020 02:28:55: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 30 Jun 2020 02:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.05_model.r WARNING @ Tue, 30 Jun 2020 02:28:55: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:28:55: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Tue, 30 Jun 2020 02:28:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:28:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:28:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:28:59: 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 02:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.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 02:29:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:29:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:29:05: 5000000 INFO @ Tue, 30 Jun 2020 02:29:10: 1000000 INFO @ Tue, 30 Jun 2020 02:29:11: 6000000 INFO @ Tue, 30 Jun 2020 02:29:13: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:29:18: 2000000 INFO @ Tue, 30 Jun 2020 02:29:19: 7000000 INFO @ Tue, 30 Jun 2020 02:29:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:29:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:29:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.05_summits.bed INFO @ Tue, 30 Jun 2020 02:29:21: Done! pass1 - making usageList (525 chroms): 1 millis pass2 - checking and writing primary data (1254 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:29:24: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:29:24: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:29:24: #1 total tags in treatment: 7816638 INFO @ Tue, 30 Jun 2020 02:29:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:29:24: #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 02:29:25: #1 tags after filtering in treatment: 7816611 INFO @ Tue, 30 Jun 2020 02:29:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:29:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:29:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:29:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:29:25: #2 number of paired peaks: 345 WARNING @ Tue, 30 Jun 2020 02:29:25: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Tue, 30 Jun 2020 02:29:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:29:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:29:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:29:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:29:25: #2 predicted fragment length is 106 bps INFO @ Tue, 30 Jun 2020 02:29:25: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 30 Jun 2020 02:29:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.10_model.r WARNING @ Tue, 30 Jun 2020 02:29:25: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:29:25: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Tue, 30 Jun 2020 02:29:25: #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 02:29:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:29:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:29:26: 3000000 INFO @ Tue, 30 Jun 2020 02:29:34: 4000000 INFO @ Tue, 30 Jun 2020 02:29:42: 5000000 INFO @ Tue, 30 Jun 2020 02:29:43: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:29:49: 6000000 INFO @ Tue, 30 Jun 2020 02:29:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:29:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:29:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.10_summits.bed INFO @ Tue, 30 Jun 2020 02:29:51: Done! pass1 - making usageList (350 chroms): 1 millis pass2 - checking and writing primary data (668 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:29:57: 7000000 INFO @ Tue, 30 Jun 2020 02:30:03: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:30:03: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:30:03: #1 total tags in treatment: 7816638 INFO @ Tue, 30 Jun 2020 02:30:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:30:03: #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 02:30:03: #1 tags after filtering in treatment: 7816611 INFO @ Tue, 30 Jun 2020 02:30:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:30:03: #1 finished! INFO @ Tue, 30 Jun 2020 02:30:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:30:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:30:04: #2 number of paired peaks: 345 WARNING @ Tue, 30 Jun 2020 02:30:04: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Tue, 30 Jun 2020 02:30:04: start model_add_line... INFO @ Tue, 30 Jun 2020 02:30:04: start X-correlation... INFO @ Tue, 30 Jun 2020 02:30:04: end of X-cor INFO @ Tue, 30 Jun 2020 02:30:04: #2 finished! INFO @ Tue, 30 Jun 2020 02:30:04: #2 predicted fragment length is 106 bps INFO @ Tue, 30 Jun 2020 02:30:04: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 30 Jun 2020 02:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.20_model.r WARNING @ Tue, 30 Jun 2020 02:30:04: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:30:04: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Tue, 30 Jun 2020 02:30:04: #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 02:30:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:30:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:30:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:30:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:30:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:30:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511951/SRX3511951.20_summits.bed INFO @ Tue, 30 Jun 2020 02:30:31: Done! pass1 - making usageList (166 chroms): 1 millis pass2 - checking and writing primary data (266 records, 4 fields): 7 millis CompletedMACS2peakCalling