Job ID = 14167782 SRX = SRX8688902 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: 00:02:27 8347060 reads; of these: 8347060 (100.00%) were unpaired; of these: 526577 (6.31%) aligned 0 times 5542471 (66.40%) aligned exactly 1 time 2278012 (27.29%) aligned >1 times 93.69% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 662377 / 7820483 = 0.0847 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 13:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.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 13:30:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:30:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:31:03: 1000000 INFO @ Fri, 10 Dec 2021 13:31:09: 2000000 INFO @ Fri, 10 Dec 2021 13:31:15: 3000000 INFO @ Fri, 10 Dec 2021 13:31:21: 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 13:31:26: 5000000 INFO @ Fri, 10 Dec 2021 13:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.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 13:31:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:31:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:31:33: 1000000 INFO @ Fri, 10 Dec 2021 13:31:33: 6000000 INFO @ Fri, 10 Dec 2021 13:31:40: 2000000 INFO @ Fri, 10 Dec 2021 13:31:40: 7000000 INFO @ Fri, 10 Dec 2021 13:31:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:31:42: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:31:42: #1 total tags in treatment: 7158106 INFO @ Fri, 10 Dec 2021 13:31:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:31:42: #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 13:31:42: #1 tags after filtering in treatment: 7157958 INFO @ Fri, 10 Dec 2021 13:31:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:31:42: #1 finished! INFO @ Fri, 10 Dec 2021 13:31:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:31:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:31:42: #2 number of paired peaks: 1105 INFO @ Fri, 10 Dec 2021 13:31:42: start model_add_line... INFO @ Fri, 10 Dec 2021 13:31:43: start X-correlation... INFO @ Fri, 10 Dec 2021 13:31:43: end of X-cor INFO @ Fri, 10 Dec 2021 13:31:43: #2 finished! INFO @ Fri, 10 Dec 2021 13:31:43: #2 predicted fragment length is 57 bps INFO @ Fri, 10 Dec 2021 13:31:43: #2 alternative fragment length(s) may be 4,57,557 bps INFO @ Fri, 10 Dec 2021 13:31:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.05_model.r WARNING @ Fri, 10 Dec 2021 13:31:43: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:31:43: #2 You may need to consider one of the other alternative d(s): 4,57,557 WARNING @ Fri, 10 Dec 2021 13:31:43: #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 13:31:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:31:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:31:46: 3000000 INFO @ Fri, 10 Dec 2021 13:31:52: 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 13:31:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.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 13:31:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:31:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:31:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:31:58: 5000000 INFO @ Fri, 10 Dec 2021 13:32:03: 1000000 INFO @ Fri, 10 Dec 2021 13:32:06: 6000000 INFO @ Fri, 10 Dec 2021 13:32:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:32:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:32:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.05_summits.bed INFO @ Fri, 10 Dec 2021 13:32:06: Done! pass1 - making usageList (619 chroms): 1 millis pass2 - checking and writing primary data (2430 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:32:10: 2000000 INFO @ Fri, 10 Dec 2021 13:32:12: 7000000 INFO @ Fri, 10 Dec 2021 13:32:14: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:32:14: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:32:14: #1 total tags in treatment: 7158106 INFO @ Fri, 10 Dec 2021 13:32:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:32:14: #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 13:32:14: #1 tags after filtering in treatment: 7157958 INFO @ Fri, 10 Dec 2021 13:32:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:32:14: #1 finished! INFO @ Fri, 10 Dec 2021 13:32:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:32:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:32:15: #2 number of paired peaks: 1105 INFO @ Fri, 10 Dec 2021 13:32:15: start model_add_line... INFO @ Fri, 10 Dec 2021 13:32:15: start X-correlation... INFO @ Fri, 10 Dec 2021 13:32:15: end of X-cor INFO @ Fri, 10 Dec 2021 13:32:15: #2 finished! INFO @ Fri, 10 Dec 2021 13:32:15: #2 predicted fragment length is 57 bps INFO @ Fri, 10 Dec 2021 13:32:15: #2 alternative fragment length(s) may be 4,57,557 bps INFO @ Fri, 10 Dec 2021 13:32:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.10_model.r WARNING @ Fri, 10 Dec 2021 13:32:15: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:32:15: #2 You may need to consider one of the other alternative d(s): 4,57,557 WARNING @ Fri, 10 Dec 2021 13:32:15: #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 13:32:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:32:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:32:17: 3000000 INFO @ Fri, 10 Dec 2021 13:32:23: 4000000 INFO @ Fri, 10 Dec 2021 13:32:29: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:32:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:32:35: 6000000 INFO @ Fri, 10 Dec 2021 13:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.10_summits.bed INFO @ Fri, 10 Dec 2021 13:32:37: Done! pass1 - making usageList (521 chroms): 1 millis pass2 - checking and writing primary data (1613 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:32:41: 7000000 INFO @ Fri, 10 Dec 2021 13:32:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:32:42: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:32:42: #1 total tags in treatment: 7158106 INFO @ Fri, 10 Dec 2021 13:32:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:32:42: #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 13:32:43: #1 tags after filtering in treatment: 7157958 INFO @ Fri, 10 Dec 2021 13:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:32:43: #1 finished! INFO @ Fri, 10 Dec 2021 13:32:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:32:43: #2 number of paired peaks: 1105 INFO @ Fri, 10 Dec 2021 13:32:43: start model_add_line... INFO @ Fri, 10 Dec 2021 13:32:43: start X-correlation... INFO @ Fri, 10 Dec 2021 13:32:43: end of X-cor INFO @ Fri, 10 Dec 2021 13:32:43: #2 finished! INFO @ Fri, 10 Dec 2021 13:32:43: #2 predicted fragment length is 57 bps INFO @ Fri, 10 Dec 2021 13:32:43: #2 alternative fragment length(s) may be 4,57,557 bps INFO @ Fri, 10 Dec 2021 13:32:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.20_model.r WARNING @ Fri, 10 Dec 2021 13:32:43: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:32:43: #2 You may need to consider one of the other alternative d(s): 4,57,557 WARNING @ Fri, 10 Dec 2021 13:32:43: #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 13:32:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:32:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:32:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:33:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:33:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:33:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688902/SRX8688902.20_summits.bed INFO @ Fri, 10 Dec 2021 13:33:06: Done! pass1 - making usageList (267 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 10 millis CompletedMACS2peakCalling