Job ID = 14167773 SRX = SRX8688901 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: 00:01:26 6014330 reads; of these: 6014330 (100.00%) were unpaired; of these: 400836 (6.66%) aligned 0 times 4855857 (80.74%) aligned exactly 1 time 757637 (12.60%) aligned >1 times 93.34% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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] 242303 / 5613494 = 0.0432 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 13:28:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.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 @ Fri, 10 Dec 2021 13:28:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:28:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:28:27: 1000000 INFO @ Fri, 10 Dec 2021 13:28:33: 2000000 INFO @ Fri, 10 Dec 2021 13:28:38: 3000000 INFO @ Fri, 10 Dec 2021 13:28:44: 4000000 INFO @ Fri, 10 Dec 2021 13:28:50: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 13:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.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 @ Fri, 10 Dec 2021 13:28:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:28:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:28:52: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:28:52: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:28:52: #1 total tags in treatment: 5371191 INFO @ Fri, 10 Dec 2021 13:28:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:28:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:28:52: #1 tags after filtering in treatment: 5370909 INFO @ Fri, 10 Dec 2021 13:28:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:28:52: #1 finished! INFO @ Fri, 10 Dec 2021 13:28:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:28:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:28:52: #2 number of paired peaks: 124 WARNING @ Fri, 10 Dec 2021 13:28:52: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Fri, 10 Dec 2021 13:28:52: start model_add_line... INFO @ Fri, 10 Dec 2021 13:28:53: start X-correlation... INFO @ Fri, 10 Dec 2021 13:28:53: end of X-cor INFO @ Fri, 10 Dec 2021 13:28:53: #2 finished! INFO @ Fri, 10 Dec 2021 13:28:53: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Dec 2021 13:28:53: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 10 Dec 2021 13:28:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.05_model.r WARNING @ Fri, 10 Dec 2021 13:28:53: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:28:53: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 10 Dec 2021 13:28:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:28:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:28:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:28:57: 1000000 INFO @ Fri, 10 Dec 2021 13:29:03: 2000000 INFO @ Fri, 10 Dec 2021 13:29:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:29:08: 3000000 INFO @ Fri, 10 Dec 2021 13:29:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:29:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:29:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.05_summits.bed INFO @ Fri, 10 Dec 2021 13:29:11: Done! pass1 - making usageList (140 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:29:14: 4000000 INFO @ Fri, 10 Dec 2021 13:29:19: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 13:29:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:29:22: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:29:22: #1 total tags in treatment: 5371191 INFO @ Fri, 10 Dec 2021 13:29:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:29:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:29:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.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 @ Fri, 10 Dec 2021 13:29:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:29:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:29:22: #1 tags after filtering in treatment: 5370909 INFO @ Fri, 10 Dec 2021 13:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:29:22: #1 finished! INFO @ Fri, 10 Dec 2021 13:29:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:29:22: #2 number of paired peaks: 124 WARNING @ Fri, 10 Dec 2021 13:29:22: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Fri, 10 Dec 2021 13:29:22: start model_add_line... INFO @ Fri, 10 Dec 2021 13:29:22: start X-correlation... INFO @ Fri, 10 Dec 2021 13:29:22: end of X-cor INFO @ Fri, 10 Dec 2021 13:29:22: #2 finished! INFO @ Fri, 10 Dec 2021 13:29:22: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Dec 2021 13:29:22: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 10 Dec 2021 13:29:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.10_model.r WARNING @ Fri, 10 Dec 2021 13:29:22: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:29:22: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 10 Dec 2021 13:29:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:29:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:29:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:29:27: 1000000 INFO @ Fri, 10 Dec 2021 13:29:33: 2000000 INFO @ Fri, 10 Dec 2021 13:29:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:29:38: 3000000 INFO @ Fri, 10 Dec 2021 13:29:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:29:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:29:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.10_summits.bed INFO @ Fri, 10 Dec 2021 13:29:40: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (138 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:29:44: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:29:49: 5000000 INFO @ Fri, 10 Dec 2021 13:29:51: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:29:51: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:29:51: #1 total tags in treatment: 5371191 INFO @ Fri, 10 Dec 2021 13:29:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:29:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:29:52: #1 tags after filtering in treatment: 5370909 INFO @ Fri, 10 Dec 2021 13:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:29:52: #1 finished! INFO @ Fri, 10 Dec 2021 13:29:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:29:52: #2 number of paired peaks: 124 WARNING @ Fri, 10 Dec 2021 13:29:52: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Fri, 10 Dec 2021 13:29:52: start model_add_line... INFO @ Fri, 10 Dec 2021 13:29:52: start X-correlation... INFO @ Fri, 10 Dec 2021 13:29:52: end of X-cor INFO @ Fri, 10 Dec 2021 13:29:52: #2 finished! INFO @ Fri, 10 Dec 2021 13:29:52: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Dec 2021 13:29:52: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 10 Dec 2021 13:29:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.20_model.r WARNING @ Fri, 10 Dec 2021 13:29:52: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:29:52: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 10 Dec 2021 13:29:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:29:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:29:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:30:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:30:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:30:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:30:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688901/SRX8688901.20_summits.bed INFO @ Fri, 10 Dec 2021 13:30:10: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 2 millis CompletedMACS2peakCalling