Job ID = 6627449 SRX = SRX8521315 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: 00:06:20 42795210 reads; of these: 42795210 (100.00%) were unpaired; of these: 37744396 (88.20%) aligned 0 times 3772744 (8.82%) aligned exactly 1 time 1278070 (2.99%) aligned >1 times 11.80% overall alignment rate Time searching: 00:06:20 Overall time: 00:06:20 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] 846982 / 5050814 = 0.1677 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 11:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.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 11:40:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:40:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:40:48: 1000000 INFO @ Tue, 14 Jul 2020 11:40:54: 2000000 INFO @ Tue, 14 Jul 2020 11:41:01: 3000000 INFO @ Tue, 14 Jul 2020 11:41:07: 4000000 INFO @ Tue, 14 Jul 2020 11:41:08: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:41:08: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:41:08: #1 total tags in treatment: 4203832 INFO @ Tue, 14 Jul 2020 11:41:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:41:08: #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 11:41:09: #1 tags after filtering in treatment: 4203618 INFO @ Tue, 14 Jul 2020 11:41:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:41:09: #1 finished! INFO @ Tue, 14 Jul 2020 11:41:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:41:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:41:09: #2 number of paired peaks: 751 WARNING @ Tue, 14 Jul 2020 11:41:09: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Tue, 14 Jul 2020 11:41:09: start model_add_line... INFO @ Tue, 14 Jul 2020 11:41:09: start X-correlation... INFO @ Tue, 14 Jul 2020 11:41:09: end of X-cor INFO @ Tue, 14 Jul 2020 11:41:09: #2 finished! INFO @ Tue, 14 Jul 2020 11:41:09: #2 predicted fragment length is 67 bps INFO @ Tue, 14 Jul 2020 11:41:09: #2 alternative fragment length(s) may be 67,528 bps INFO @ Tue, 14 Jul 2020 11:41:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.05_model.r WARNING @ Tue, 14 Jul 2020 11:41:09: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:41:09: #2 You may need to consider one of the other alternative d(s): 67,528 WARNING @ Tue, 14 Jul 2020 11:41:09: #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 11:41:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:41:09: #3 Pre-compute pvalue-qvalue table... 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 11:41:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.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 11:41:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:41:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:41:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:41:18: 1000000 INFO @ Tue, 14 Jul 2020 11:41:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:41:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.05_summits.bed INFO @ Tue, 14 Jul 2020 11:41:23: Done! pass1 - making usageList (240 chroms): 0 millis pass2 - checking and writing primary data (766 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:41:25: 2000000 INFO @ Tue, 14 Jul 2020 11:41:31: 3000000 INFO @ Tue, 14 Jul 2020 11:41:37: 4000000 INFO @ Tue, 14 Jul 2020 11:41:39: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:41:39: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:41:39: #1 total tags in treatment: 4203832 INFO @ Tue, 14 Jul 2020 11:41:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:41:39: #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 11:41:39: #1 tags after filtering in treatment: 4203618 INFO @ Tue, 14 Jul 2020 11:41:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:41:39: #1 finished! INFO @ Tue, 14 Jul 2020 11:41:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:41:39: #2 number of paired peaks: 751 WARNING @ Tue, 14 Jul 2020 11:41:39: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Tue, 14 Jul 2020 11:41:39: start model_add_line... INFO @ Tue, 14 Jul 2020 11:41:39: start X-correlation... INFO @ Tue, 14 Jul 2020 11:41:39: end of X-cor INFO @ Tue, 14 Jul 2020 11:41:39: #2 finished! INFO @ Tue, 14 Jul 2020 11:41:39: #2 predicted fragment length is 67 bps INFO @ Tue, 14 Jul 2020 11:41:39: #2 alternative fragment length(s) may be 67,528 bps INFO @ Tue, 14 Jul 2020 11:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.10_model.r WARNING @ Tue, 14 Jul 2020 11:41:39: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:41:39: #2 You may need to consider one of the other alternative d(s): 67,528 WARNING @ Tue, 14 Jul 2020 11:41:39: #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 11:41:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:41:39: #3 Pre-compute pvalue-qvalue table... 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 11:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.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 11:41:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:41:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:41:48: 1000000 INFO @ Tue, 14 Jul 2020 11:41:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:41:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:41:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:41:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.10_summits.bed INFO @ Tue, 14 Jul 2020 11:41:53: Done! pass1 - making usageList (136 chroms): 0 millis pass2 - checking and writing primary data (338 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:41:54: 2000000 INFO @ Tue, 14 Jul 2020 11:42:00: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:42:07: 4000000 INFO @ Tue, 14 Jul 2020 11:42:09: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:42:09: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:42:09: #1 total tags in treatment: 4203832 INFO @ Tue, 14 Jul 2020 11:42:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:42:09: #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 11:42:09: #1 tags after filtering in treatment: 4203618 INFO @ Tue, 14 Jul 2020 11:42:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:42:09: #1 finished! INFO @ Tue, 14 Jul 2020 11:42:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:42:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:42:09: #2 number of paired peaks: 751 WARNING @ Tue, 14 Jul 2020 11:42:09: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Tue, 14 Jul 2020 11:42:09: start model_add_line... INFO @ Tue, 14 Jul 2020 11:42:09: start X-correlation... INFO @ Tue, 14 Jul 2020 11:42:09: end of X-cor INFO @ Tue, 14 Jul 2020 11:42:09: #2 finished! INFO @ Tue, 14 Jul 2020 11:42:09: #2 predicted fragment length is 67 bps INFO @ Tue, 14 Jul 2020 11:42:09: #2 alternative fragment length(s) may be 67,528 bps INFO @ Tue, 14 Jul 2020 11:42:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.20_model.r WARNING @ Tue, 14 Jul 2020 11:42:09: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:42:09: #2 You may need to consider one of the other alternative d(s): 67,528 WARNING @ Tue, 14 Jul 2020 11:42:09: #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 11:42:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:42:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:42:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:42:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:42:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521315/SRX8521315.20_summits.bed INFO @ Tue, 14 Jul 2020 11:42:23: Done! pass1 - making usageList (78 chroms): 0 millis pass2 - checking and writing primary data (137 records, 4 fields): 6 millis CompletedMACS2peakCalling