Job ID = 16440719 SRX = SRX15369006 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:58 17539494 reads; of these: 17539494 (100.00%) were unpaired; of these: 1010677 (5.76%) aligned 0 times 10011019 (57.08%) aligned exactly 1 time 6517798 (37.16%) aligned >1 times 94.24% overall alignment rate Time searching: 00:12:59 Overall time: 00:12:59 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4607999 / 16528817 = 0.2788 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 18:10:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.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 @ Tue, 02 Aug 2022 18:10:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:10:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:10:18: 1000000 INFO @ Tue, 02 Aug 2022 18:10:29: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 18:10:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.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 @ Tue, 02 Aug 2022 18:10:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:10:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:10:40: 3000000 INFO @ Tue, 02 Aug 2022 18:10:49: 1000000 INFO @ Tue, 02 Aug 2022 18:10:52: 4000000 INFO @ Tue, 02 Aug 2022 18:11:02: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 18:11:04: 5000000 INFO @ Tue, 02 Aug 2022 18:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.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 @ Tue, 02 Aug 2022 18:11:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:11:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:11:16: 6000000 INFO @ Tue, 02 Aug 2022 18:11:17: 3000000 INFO @ Tue, 02 Aug 2022 18:11:17: 1000000 INFO @ Tue, 02 Aug 2022 18:11:28: 2000000 INFO @ Tue, 02 Aug 2022 18:11:29: 7000000 INFO @ Tue, 02 Aug 2022 18:11:32: 4000000 INFO @ Tue, 02 Aug 2022 18:11:40: 3000000 INFO @ Tue, 02 Aug 2022 18:11:41: 8000000 INFO @ Tue, 02 Aug 2022 18:11:47: 5000000 INFO @ Tue, 02 Aug 2022 18:11:52: 4000000 INFO @ Tue, 02 Aug 2022 18:11:53: 9000000 INFO @ Tue, 02 Aug 2022 18:12:03: 6000000 INFO @ Tue, 02 Aug 2022 18:12:04: 5000000 INFO @ Tue, 02 Aug 2022 18:12:06: 10000000 INFO @ Tue, 02 Aug 2022 18:12:16: 6000000 INFO @ Tue, 02 Aug 2022 18:12:17: 11000000 INFO @ Tue, 02 Aug 2022 18:12:18: 7000000 INFO @ Tue, 02 Aug 2022 18:12:28: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:12:28: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:12:28: #1 total tags in treatment: 11920818 INFO @ Tue, 02 Aug 2022 18:12:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:12:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:12:28: 7000000 INFO @ Tue, 02 Aug 2022 18:12:29: #1 tags after filtering in treatment: 11920815 INFO @ Tue, 02 Aug 2022 18:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:12:29: #1 finished! INFO @ Tue, 02 Aug 2022 18:12:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:12:30: #2 number of paired peaks: 877 WARNING @ Tue, 02 Aug 2022 18:12:30: Fewer paired peaks (877) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 877 pairs to build model! INFO @ Tue, 02 Aug 2022 18:12:30: start model_add_line... INFO @ Tue, 02 Aug 2022 18:12:31: start X-correlation... INFO @ Tue, 02 Aug 2022 18:12:31: end of X-cor INFO @ Tue, 02 Aug 2022 18:12:31: #2 finished! INFO @ Tue, 02 Aug 2022 18:12:31: #2 predicted fragment length is 67 bps INFO @ Tue, 02 Aug 2022 18:12:31: #2 alternative fragment length(s) may be 4,67 bps INFO @ Tue, 02 Aug 2022 18:12:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.05_model.r WARNING @ Tue, 02 Aug 2022 18:12:31: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:12:31: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Tue, 02 Aug 2022 18:12:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:12:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:12:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:12:33: 8000000 INFO @ Tue, 02 Aug 2022 18:12:40: 8000000 INFO @ Tue, 02 Aug 2022 18:12:48: 9000000 INFO @ Tue, 02 Aug 2022 18:12:52: 9000000 INFO @ Tue, 02 Aug 2022 18:13:02: 10000000 INFO @ Tue, 02 Aug 2022 18:13:04: 10000000 INFO @ Tue, 02 Aug 2022 18:13:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:13:15: 11000000 INFO @ Tue, 02 Aug 2022 18:13:16: 11000000 INFO @ Tue, 02 Aug 2022 18:13:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:13:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:13:26: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:13:26: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:13:26: #1 total tags in treatment: 11920818 INFO @ Tue, 02 Aug 2022 18:13:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:13:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:13:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.05_summits.bed INFO @ Tue, 02 Aug 2022 18:13:27: Done! pass1 - making usageList (731 chroms): 2 millis pass2 - checking and writing primary data (2637 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:13:27: #1 tags after filtering in treatment: 11920815 INFO @ Tue, 02 Aug 2022 18:13:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:13:27: #1 finished! INFO @ Tue, 02 Aug 2022 18:13:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:13:28: #2 number of paired peaks: 877 WARNING @ Tue, 02 Aug 2022 18:13:28: Fewer paired peaks (877) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 877 pairs to build model! INFO @ Tue, 02 Aug 2022 18:13:28: start model_add_line... INFO @ Tue, 02 Aug 2022 18:13:28: start X-correlation... INFO @ Tue, 02 Aug 2022 18:13:28: end of X-cor INFO @ Tue, 02 Aug 2022 18:13:28: #2 finished! INFO @ Tue, 02 Aug 2022 18:13:28: #2 predicted fragment length is 67 bps INFO @ Tue, 02 Aug 2022 18:13:28: #2 alternative fragment length(s) may be 4,67 bps INFO @ Tue, 02 Aug 2022 18:13:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.20_model.r WARNING @ Tue, 02 Aug 2022 18:13:28: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:13:28: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Tue, 02 Aug 2022 18:13:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:13:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:13:30: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:13:30: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:13:30: #1 total tags in treatment: 11920818 INFO @ Tue, 02 Aug 2022 18:13:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:13:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:13:30: #1 tags after filtering in treatment: 11920815 INFO @ Tue, 02 Aug 2022 18:13:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:13:30: #1 finished! INFO @ Tue, 02 Aug 2022 18:13:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:13:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:13:32: #2 number of paired peaks: 877 WARNING @ Tue, 02 Aug 2022 18:13:32: Fewer paired peaks (877) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 877 pairs to build model! INFO @ Tue, 02 Aug 2022 18:13:32: start model_add_line... INFO @ Tue, 02 Aug 2022 18:13:32: start X-correlation... INFO @ Tue, 02 Aug 2022 18:13:32: end of X-cor INFO @ Tue, 02 Aug 2022 18:13:32: #2 finished! INFO @ Tue, 02 Aug 2022 18:13:32: #2 predicted fragment length is 67 bps INFO @ Tue, 02 Aug 2022 18:13:32: #2 alternative fragment length(s) may be 4,67 bps INFO @ Tue, 02 Aug 2022 18:13:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.10_model.r WARNING @ Tue, 02 Aug 2022 18:13:32: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:13:32: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Tue, 02 Aug 2022 18:13:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:13:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:13:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:14:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:14:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:14:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:14:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:14:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.20_summits.bed INFO @ Tue, 02 Aug 2022 18:14:23: Done! pass1 - making usageList (518 chroms): 2 millis pass2 - checking and writing primary data (1396 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:14:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:14:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:14:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15369006/SRX15369006.10_summits.bed INFO @ Tue, 02 Aug 2022 18:14:28: Done! pass1 - making usageList (603 chroms): 3 millis pass2 - checking and writing primary data (1720 records, 4 fields): 48 millis CompletedMACS2peakCalling