Job ID = 12265064 SRX = SRX3032290 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: 00:04:10 9425766 reads; of these: 9425766 (100.00%) were unpaired; of these: 2162941 (22.95%) aligned 0 times 5906615 (62.66%) aligned exactly 1 time 1356210 (14.39%) aligned >1 times 77.05% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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] 1315354 / 7262825 = 0.1811 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:13:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.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 @ Sat, 03 Apr 2021 06:13:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:13:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:13:45: 1000000 INFO @ Sat, 03 Apr 2021 06:13:53: 2000000 INFO @ Sat, 03 Apr 2021 06:14:01: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:14:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.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 @ Sat, 03 Apr 2021 06:14:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:14:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:14:09: 4000000 INFO @ Sat, 03 Apr 2021 06:14:16: 1000000 INFO @ Sat, 03 Apr 2021 06:14:18: 5000000 INFO @ Sat, 03 Apr 2021 06:14:25: 2000000 INFO @ Sat, 03 Apr 2021 06:14:26: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:14:26: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:14:26: #1 total tags in treatment: 5947471 INFO @ Sat, 03 Apr 2021 06:14:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:14:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:14:26: #1 tags after filtering in treatment: 5947408 INFO @ Sat, 03 Apr 2021 06:14:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:14:26: #1 finished! INFO @ Sat, 03 Apr 2021 06:14:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:14:27: #2 number of paired peaks: 724 WARNING @ Sat, 03 Apr 2021 06:14:27: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Sat, 03 Apr 2021 06:14:27: start model_add_line... INFO @ Sat, 03 Apr 2021 06:14:27: start X-correlation... INFO @ Sat, 03 Apr 2021 06:14:27: end of X-cor INFO @ Sat, 03 Apr 2021 06:14:27: #2 finished! INFO @ Sat, 03 Apr 2021 06:14:27: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 06:14:27: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Apr 2021 06:14:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.05_model.r WARNING @ Sat, 03 Apr 2021 06:14:27: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:14:27: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Apr 2021 06:14:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:14:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:14:34: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:14:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.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 @ Sat, 03 Apr 2021 06:14:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:14:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:14:43: 4000000 INFO @ Sat, 03 Apr 2021 06:14:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:14:46: 1000000 INFO @ Sat, 03 Apr 2021 06:14:53: 5000000 INFO @ Sat, 03 Apr 2021 06:14:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:14:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:14:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.05_summits.bed INFO @ Sat, 03 Apr 2021 06:14:54: Done! pass1 - making usageList (315 chroms): 4 millis pass2 - checking and writing primary data (3079 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:14:55: 2000000 INFO @ Sat, 03 Apr 2021 06:15:02: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:15:02: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:15:02: #1 total tags in treatment: 5947471 INFO @ Sat, 03 Apr 2021 06:15:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:15:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:15:02: #1 tags after filtering in treatment: 5947408 INFO @ Sat, 03 Apr 2021 06:15:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:15:02: #1 finished! INFO @ Sat, 03 Apr 2021 06:15:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:15:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:15:03: #2 number of paired peaks: 724 WARNING @ Sat, 03 Apr 2021 06:15:03: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Sat, 03 Apr 2021 06:15:03: start model_add_line... INFO @ Sat, 03 Apr 2021 06:15:03: start X-correlation... INFO @ Sat, 03 Apr 2021 06:15:03: end of X-cor INFO @ Sat, 03 Apr 2021 06:15:03: #2 finished! INFO @ Sat, 03 Apr 2021 06:15:03: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 06:15:03: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Apr 2021 06:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.10_model.r WARNING @ Sat, 03 Apr 2021 06:15:03: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:15:03: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Apr 2021 06:15:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:15:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:15:04: 3000000 INFO @ Sat, 03 Apr 2021 06:15:13: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:15:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:15:23: 5000000 INFO @ Sat, 03 Apr 2021 06:15:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:15:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:15:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.10_summits.bed INFO @ Sat, 03 Apr 2021 06:15:30: Done! pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (692 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:15:32: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:15:32: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:15:32: #1 total tags in treatment: 5947471 INFO @ Sat, 03 Apr 2021 06:15:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:15:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:15:32: #1 tags after filtering in treatment: 5947408 INFO @ Sat, 03 Apr 2021 06:15:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:15:32: #1 finished! INFO @ Sat, 03 Apr 2021 06:15:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:15:33: #2 number of paired peaks: 724 WARNING @ Sat, 03 Apr 2021 06:15:33: Fewer paired peaks (724) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 724 pairs to build model! INFO @ Sat, 03 Apr 2021 06:15:33: start model_add_line... INFO @ Sat, 03 Apr 2021 06:15:33: start X-correlation... INFO @ Sat, 03 Apr 2021 06:15:33: end of X-cor INFO @ Sat, 03 Apr 2021 06:15:33: #2 finished! INFO @ Sat, 03 Apr 2021 06:15:33: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 06:15:33: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Apr 2021 06:15:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.20_model.r WARNING @ Sat, 03 Apr 2021 06:15:33: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:15:33: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Apr 2021 06:15:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:15:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:15:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:15:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032290/SRX3032290.20_summits.bed INFO @ Sat, 03 Apr 2021 06:16:00: Done! pass1 - making usageList (82 chroms): 2 millis pass2 - checking and writing primary data (161 records, 4 fields): 9 millis CompletedMACS2peakCalling