Job ID = 14167821 SRX = SRX8688914 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:09 5979372 reads; of these: 5979372 (100.00%) were unpaired; of these: 223126 (3.73%) aligned 0 times 4402569 (73.63%) aligned exactly 1 time 1353677 (22.64%) aligned >1 times 96.27% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 334653 / 5756246 = 0.0581 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 13:36:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.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 13:36:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:36:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:36:07: 1000000 INFO @ Fri, 10 Dec 2021 13:36:13: 2000000 INFO @ Fri, 10 Dec 2021 13:36:19: 3000000 INFO @ Fri, 10 Dec 2021 13:36:24: 4000000 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 13:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.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 13:36:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:36:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:36:31: 5000000 INFO @ Fri, 10 Dec 2021 13:36:36: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:36:36: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:36:36: #1 total tags in treatment: 5421593 INFO @ Fri, 10 Dec 2021 13:36:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:36:36: #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 13:36:37: #1 tags after filtering in treatment: 5421385 INFO @ Fri, 10 Dec 2021 13:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:36:37: #1 finished! INFO @ Fri, 10 Dec 2021 13:36:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:36:38: #2 number of paired peaks: 754 WARNING @ Fri, 10 Dec 2021 13:36:38: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Fri, 10 Dec 2021 13:36:38: start model_add_line... INFO @ Fri, 10 Dec 2021 13:36:38: start X-correlation... INFO @ Fri, 10 Dec 2021 13:36:38: 1000000 INFO @ Fri, 10 Dec 2021 13:36:38: end of X-cor INFO @ Fri, 10 Dec 2021 13:36:38: #2 finished! INFO @ Fri, 10 Dec 2021 13:36:38: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 13:36:38: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 13:36:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.05_model.r WARNING @ Fri, 10 Dec 2021 13:36:38: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:36:38: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 13:36:38: #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 13:36:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:36:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:36:44: 2000000 INFO @ Fri, 10 Dec 2021 13:36:50: 3000000 INFO @ Fri, 10 Dec 2021 13:36:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:36:55: 4000000 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 13:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:37:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.05_summits.bed INFO @ Fri, 10 Dec 2021 13:37:01: Done! INFO @ Fri, 10 Dec 2021 13:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.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 13:37:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:37:01: #1 read treatment tags... pass1 - making usageList (519 chroms): 1 millis pass2 - checking and writing primary data (1817 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:37:02: 5000000 INFO @ Fri, 10 Dec 2021 13:37:06: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:37:06: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:37:06: #1 total tags in treatment: 5421593 INFO @ Fri, 10 Dec 2021 13:37:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:37:06: #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 13:37:06: #1 tags after filtering in treatment: 5421385 INFO @ Fri, 10 Dec 2021 13:37:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:37:06: #1 finished! INFO @ Fri, 10 Dec 2021 13:37:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:37:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:37:07: #2 number of paired peaks: 754 WARNING @ Fri, 10 Dec 2021 13:37:07: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Fri, 10 Dec 2021 13:37:07: start model_add_line... INFO @ Fri, 10 Dec 2021 13:37:07: start X-correlation... INFO @ Fri, 10 Dec 2021 13:37:07: 1000000 INFO @ Fri, 10 Dec 2021 13:37:08: end of X-cor INFO @ Fri, 10 Dec 2021 13:37:08: #2 finished! INFO @ Fri, 10 Dec 2021 13:37:08: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 13:37:08: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 13:37:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.10_model.r WARNING @ Fri, 10 Dec 2021 13:37:08: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:37:08: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 13:37:08: #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 13:37:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:37:13: 2000000 INFO @ Fri, 10 Dec 2021 13:37:19: 3000000 INFO @ Fri, 10 Dec 2021 13:37:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:37:25: 4000000 INFO @ Fri, 10 Dec 2021 13:37:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:37:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:37:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.10_summits.bed INFO @ Fri, 10 Dec 2021 13:37:32: Done! pass1 - making usageList (325 chroms): 1 millis pass2 - checking and writing primary data (644 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:37:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:37:37: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:37:37: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:37:37: #1 total tags in treatment: 5421593 INFO @ Fri, 10 Dec 2021 13:37:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:37:37: #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 13:37:38: #1 tags after filtering in treatment: 5421385 INFO @ Fri, 10 Dec 2021 13:37:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:37:38: #1 finished! INFO @ Fri, 10 Dec 2021 13:37:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:37:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:37:38: #2 number of paired peaks: 754 WARNING @ Fri, 10 Dec 2021 13:37:38: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Fri, 10 Dec 2021 13:37:38: start model_add_line... INFO @ Fri, 10 Dec 2021 13:37:38: start X-correlation... INFO @ Fri, 10 Dec 2021 13:37:39: end of X-cor INFO @ Fri, 10 Dec 2021 13:37:39: #2 finished! INFO @ Fri, 10 Dec 2021 13:37:39: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 13:37:39: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 13:37:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.20_model.r WARNING @ Fri, 10 Dec 2021 13:37:39: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:37:39: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 13:37:39: #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 13:37:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:37:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:37:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:38:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:38:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:38:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688914/SRX8688914.20_summits.bed INFO @ Fri, 10 Dec 2021 13:38:03: Done! pass1 - making usageList (107 chroms): 3 millis pass2 - checking and writing primary data (175 records, 4 fields): 10 millis CompletedMACS2peakCalling