Job ID = 14170804 SRX = SRX8689019 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: 00:02:43 7629140 reads; of these: 7629140 (100.00%) were unpaired; of these: 408446 (5.35%) aligned 0 times 4620488 (60.56%) aligned exactly 1 time 2600206 (34.08%) aligned >1 times 94.65% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 790424 / 7220694 = 0.1095 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 @ Sat, 11 Dec 2021 08:52:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.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, 11 Dec 2021 08:52:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:52:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:53:07: 1000000 INFO @ Sat, 11 Dec 2021 08:53:16: 2000000 INFO @ Sat, 11 Dec 2021 08:53:25: 3000000 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 @ Sat, 11 Dec 2021 08:53:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.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, 11 Dec 2021 08:53:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:53:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:53:33: 4000000 INFO @ Sat, 11 Dec 2021 08:53:35: 1000000 INFO @ Sat, 11 Dec 2021 08:53:42: 2000000 INFO @ Sat, 11 Dec 2021 08:53:43: 5000000 INFO @ Sat, 11 Dec 2021 08:53:49: 3000000 INFO @ Sat, 11 Dec 2021 08:53:53: 6000000 INFO @ Sat, 11 Dec 2021 08:53:55: 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 @ Sat, 11 Dec 2021 08:53:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:53:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:53:57: #1 total tags in treatment: 6430270 INFO @ Sat, 11 Dec 2021 08:53:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:53:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:53:58: #1 tags after filtering in treatment: 6430268 INFO @ Sat, 11 Dec 2021 08:53:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:53:58: #1 finished! INFO @ Sat, 11 Dec 2021 08:53:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:53:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:53:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.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, 11 Dec 2021 08:53:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:53:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:53:58: #2 number of paired peaks: 711 WARNING @ Sat, 11 Dec 2021 08:53:58: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sat, 11 Dec 2021 08:53:58: start model_add_line... INFO @ Sat, 11 Dec 2021 08:53:58: start X-correlation... INFO @ Sat, 11 Dec 2021 08:53:58: end of X-cor INFO @ Sat, 11 Dec 2021 08:53:58: #2 finished! INFO @ Sat, 11 Dec 2021 08:53:58: #2 predicted fragment length is 62 bps INFO @ Sat, 11 Dec 2021 08:53:58: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 11 Dec 2021 08:53:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.05_model.r WARNING @ Sat, 11 Dec 2021 08:53:58: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:53:58: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 11 Dec 2021 08:53:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:53:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:53:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:54:02: 5000000 INFO @ Sat, 11 Dec 2021 08:54:07: 1000000 INFO @ Sat, 11 Dec 2021 08:54:10: 6000000 INFO @ Sat, 11 Dec 2021 08:54:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:54:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:54:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:54:14: #1 total tags in treatment: 6430270 INFO @ Sat, 11 Dec 2021 08:54:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:54:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:54:15: #1 tags after filtering in treatment: 6430268 INFO @ Sat, 11 Dec 2021 08:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:54:15: #1 finished! INFO @ Sat, 11 Dec 2021 08:54:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:54:15: #2 number of paired peaks: 711 WARNING @ Sat, 11 Dec 2021 08:54:15: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sat, 11 Dec 2021 08:54:15: start model_add_line... INFO @ Sat, 11 Dec 2021 08:54:15: start X-correlation... INFO @ Sat, 11 Dec 2021 08:54:15: end of X-cor INFO @ Sat, 11 Dec 2021 08:54:15: #2 finished! INFO @ Sat, 11 Dec 2021 08:54:15: #2 predicted fragment length is 62 bps INFO @ Sat, 11 Dec 2021 08:54:15: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 11 Dec 2021 08:54:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.10_model.r WARNING @ Sat, 11 Dec 2021 08:54:16: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:54:16: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 11 Dec 2021 08:54:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:54:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:54:16: 2000000 INFO @ Sat, 11 Dec 2021 08:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.05_summits.bed INFO @ Sat, 11 Dec 2021 08:54:20: Done! pass1 - making usageList (764 chroms): 2 millis pass2 - checking and writing primary data (2276 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:54:26: 3000000 INFO @ Sat, 11 Dec 2021 08:54:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:54:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:54:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:54:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.10_summits.bed INFO @ Sat, 11 Dec 2021 08:54:36: Done! INFO @ Sat, 11 Dec 2021 08:54:36: 4000000 pass1 - making usageList (434 chroms): 1 millis pass2 - checking and writing primary data (868 records, 4 fields): 40 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:54:46: 5000000 INFO @ Sat, 11 Dec 2021 08:54:57: 6000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:55:02: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:55:02: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:55:02: #1 total tags in treatment: 6430270 INFO @ Sat, 11 Dec 2021 08:55:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:55:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:55:02: #1 tags after filtering in treatment: 6430268 INFO @ Sat, 11 Dec 2021 08:55:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:55:02: #1 finished! INFO @ Sat, 11 Dec 2021 08:55:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:55:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:55:03: #2 number of paired peaks: 711 WARNING @ Sat, 11 Dec 2021 08:55:03: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sat, 11 Dec 2021 08:55:03: start model_add_line... INFO @ Sat, 11 Dec 2021 08:55:03: start X-correlation... INFO @ Sat, 11 Dec 2021 08:55:03: end of X-cor INFO @ Sat, 11 Dec 2021 08:55:03: #2 finished! INFO @ Sat, 11 Dec 2021 08:55:03: #2 predicted fragment length is 62 bps INFO @ Sat, 11 Dec 2021 08:55:03: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 11 Dec 2021 08:55:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.20_model.r WARNING @ Sat, 11 Dec 2021 08:55:03: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:55:03: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 11 Dec 2021 08:55:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:55:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:55:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:55:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:55:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:55:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689019/SRX8689019.20_summits.bed INFO @ Sat, 11 Dec 2021 08:55:23: Done! pass1 - making usageList (146 chroms): 1 millis pass2 - checking and writing primary data (272 records, 4 fields): 29 millis CompletedMACS2peakCalling