Job ID = 14167751 SRX = SRX6407574 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: 00:03:31 7742110 reads; of these: 7742110 (100.00%) were unpaired; of these: 402976 (5.20%) aligned 0 times 6536924 (84.43%) aligned exactly 1 time 802210 (10.36%) aligned >1 times 94.80% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 399054 / 7339134 = 0.0544 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 13:25:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.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 13:25:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:25:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:25:40: 1000000 INFO @ Fri, 10 Dec 2021 13:25:51: 2000000 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 13:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.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 13:26:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:26:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:26:01: 3000000 INFO @ Fri, 10 Dec 2021 13:26:11: 4000000 INFO @ Fri, 10 Dec 2021 13:26:14: 1000000 INFO @ Fri, 10 Dec 2021 13:26:22: 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 13:26:28: 2000000 INFO @ Fri, 10 Dec 2021 13:26:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.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 13:26:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:26:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:26:33: 6000000 INFO @ Fri, 10 Dec 2021 13:26:41: 1000000 INFO @ Fri, 10 Dec 2021 13:26:42: 3000000 INFO @ Fri, 10 Dec 2021 13:26:43: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 13:26:43: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 13:26:43: #1 total tags in treatment: 6940080 INFO @ Fri, 10 Dec 2021 13:26:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:26:43: #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 13:26:44: #1 tags after filtering in treatment: 6939806 INFO @ Fri, 10 Dec 2021 13:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:26:44: #1 finished! INFO @ Fri, 10 Dec 2021 13:26:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:26:44: #2 number of paired peaks: 399 WARNING @ Fri, 10 Dec 2021 13:26:44: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Fri, 10 Dec 2021 13:26:44: start model_add_line... INFO @ Fri, 10 Dec 2021 13:26:45: start X-correlation... INFO @ Fri, 10 Dec 2021 13:26:45: end of X-cor INFO @ Fri, 10 Dec 2021 13:26:45: #2 finished! INFO @ Fri, 10 Dec 2021 13:26:45: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Dec 2021 13:26:45: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Dec 2021 13:26:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.05_model.r WARNING @ Fri, 10 Dec 2021 13:26:45: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:26:45: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 10 Dec 2021 13:26:45: #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 13:26:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:26:53: 2000000 INFO @ Fri, 10 Dec 2021 13:26:56: 4000000 INFO @ Fri, 10 Dec 2021 13:27:04: 3000000 INFO @ Fri, 10 Dec 2021 13:27:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:27:10: 5000000 INFO @ Fri, 10 Dec 2021 13:27:16: 4000000 INFO @ Fri, 10 Dec 2021 13:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.05_summits.bed INFO @ Fri, 10 Dec 2021 13:27:17: Done! pass1 - making usageList (173 chroms): 2 millis pass2 - checking and writing primary data (979 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:27:24: 6000000 INFO @ Fri, 10 Dec 2021 13:27:27: 5000000 INFO @ Fri, 10 Dec 2021 13:27:37: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 13:27:37: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 13:27:37: #1 total tags in treatment: 6940080 INFO @ Fri, 10 Dec 2021 13:27:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:27:37: #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 13:27:38: #1 tags after filtering in treatment: 6939806 INFO @ Fri, 10 Dec 2021 13:27:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:27:38: #1 finished! INFO @ Fri, 10 Dec 2021 13:27:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:27:38: #2 number of paired peaks: 399 WARNING @ Fri, 10 Dec 2021 13:27:38: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Fri, 10 Dec 2021 13:27:38: start model_add_line... INFO @ Fri, 10 Dec 2021 13:27:39: start X-correlation... INFO @ Fri, 10 Dec 2021 13:27:39: end of X-cor INFO @ Fri, 10 Dec 2021 13:27:39: #2 finished! INFO @ Fri, 10 Dec 2021 13:27:39: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Dec 2021 13:27:39: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Dec 2021 13:27:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.10_model.r WARNING @ Fri, 10 Dec 2021 13:27:39: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:27:39: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 10 Dec 2021 13:27:39: #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 13:27:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:27:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:27:39: 6000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:27:50: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 13:27:50: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 13:27:50: #1 total tags in treatment: 6940080 INFO @ Fri, 10 Dec 2021 13:27:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:27:50: #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 13:27:50: #1 tags after filtering in treatment: 6939806 INFO @ Fri, 10 Dec 2021 13:27:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:27:50: #1 finished! INFO @ Fri, 10 Dec 2021 13:27:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:27:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:27:51: #2 number of paired peaks: 399 WARNING @ Fri, 10 Dec 2021 13:27:51: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Fri, 10 Dec 2021 13:27:51: start model_add_line... INFO @ Fri, 10 Dec 2021 13:27:51: start X-correlation... INFO @ Fri, 10 Dec 2021 13:27:51: end of X-cor INFO @ Fri, 10 Dec 2021 13:27:51: #2 finished! INFO @ Fri, 10 Dec 2021 13:27:51: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Dec 2021 13:27:51: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Dec 2021 13:27:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.20_model.r WARNING @ Fri, 10 Dec 2021 13:27:51: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:27:51: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 10 Dec 2021 13:27:51: #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 13:27:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:27:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:28:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:28:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:28:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:28:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.10_summits.bed INFO @ Fri, 10 Dec 2021 13:28:11: Done! pass1 - making usageList (110 chroms): 1 millis pass2 - checking and writing primary data (291 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:28:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407574/SRX6407574.20_summits.bed INFO @ Fri, 10 Dec 2021 13:28:23: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (131 records, 4 fields): 8 millis CompletedMACS2peakCalling