Job ID = 14170794 SRX = SRX8689105 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: 00:04:59 17564911 reads; of these: 17564911 (100.00%) were unpaired; of these: 475570 (2.71%) aligned 0 times 12455086 (70.91%) aligned exactly 1 time 4634255 (26.38%) aligned >1 times 97.29% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 1895699 / 17089341 = 0.1109 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 08:53:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.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 08:53:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:53:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:53:42: 1000000 INFO @ Sat, 11 Dec 2021 08:53:47: 2000000 INFO @ Sat, 11 Dec 2021 08:53:53: 3000000 INFO @ Sat, 11 Dec 2021 08:53:59: 4000000 INFO @ Sat, 11 Dec 2021 08:54:04: 5000000 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 08:54:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.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 08:54:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:54:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:54:10: 6000000 INFO @ Sat, 11 Dec 2021 08:54:13: 1000000 INFO @ Sat, 11 Dec 2021 08:54:16: 7000000 INFO @ Sat, 11 Dec 2021 08:54:19: 2000000 INFO @ Sat, 11 Dec 2021 08:54:23: 8000000 INFO @ Sat, 11 Dec 2021 08:54:25: 3000000 INFO @ Sat, 11 Dec 2021 08:54:29: 9000000 INFO @ Sat, 11 Dec 2021 08:54:32: 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 08:54:36: 10000000 INFO @ Sat, 11 Dec 2021 08:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.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 08:54:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:54:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:54:38: 5000000 INFO @ Sat, 11 Dec 2021 08:54:42: 11000000 INFO @ Sat, 11 Dec 2021 08:54:43: 1000000 INFO @ Sat, 11 Dec 2021 08:54:45: 6000000 INFO @ Sat, 11 Dec 2021 08:54:49: 12000000 INFO @ Sat, 11 Dec 2021 08:54:49: 2000000 INFO @ Sat, 11 Dec 2021 08:54:51: 7000000 INFO @ Sat, 11 Dec 2021 08:54:55: 13000000 INFO @ Sat, 11 Dec 2021 08:54:56: 3000000 INFO @ Sat, 11 Dec 2021 08:54:58: 8000000 INFO @ Sat, 11 Dec 2021 08:55:01: 14000000 INFO @ Sat, 11 Dec 2021 08:55:03: 4000000 INFO @ Sat, 11 Dec 2021 08:55:04: 9000000 INFO @ Sat, 11 Dec 2021 08:55:08: 15000000 INFO @ Sat, 11 Dec 2021 08:55:09: 5000000 INFO @ Sat, 11 Dec 2021 08:55:09: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:55:09: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:55:09: #1 total tags in treatment: 15193642 INFO @ Sat, 11 Dec 2021 08:55:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:55:09: #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 08:55:10: #1 tags after filtering in treatment: 15193572 INFO @ Sat, 11 Dec 2021 08:55:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:55:10: #1 finished! INFO @ Sat, 11 Dec 2021 08:55:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:55:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:55:11: 10000000 INFO @ Sat, 11 Dec 2021 08:55:11: #2 number of paired peaks: 680 WARNING @ Sat, 11 Dec 2021 08:55:11: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sat, 11 Dec 2021 08:55:11: start model_add_line... INFO @ Sat, 11 Dec 2021 08:55:11: start X-correlation... INFO @ Sat, 11 Dec 2021 08:55:11: end of X-cor INFO @ Sat, 11 Dec 2021 08:55:11: #2 finished! INFO @ Sat, 11 Dec 2021 08:55:11: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 08:55:11: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sat, 11 Dec 2021 08:55:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.05_model.r WARNING @ Sat, 11 Dec 2021 08:55:11: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:55:11: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sat, 11 Dec 2021 08:55:11: #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 08:55:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:55:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:55:15: 6000000 INFO @ Sat, 11 Dec 2021 08:55:17: 11000000 INFO @ Sat, 11 Dec 2021 08:55:22: 7000000 INFO @ Sat, 11 Dec 2021 08:55:24: 12000000 INFO @ Sat, 11 Dec 2021 08:55:28: 8000000 INFO @ Sat, 11 Dec 2021 08:55:30: 13000000 INFO @ Sat, 11 Dec 2021 08:55:35: 9000000 INFO @ Sat, 11 Dec 2021 08:55:36: 14000000 INFO @ Sat, 11 Dec 2021 08:55:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:55:41: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:55:43: 15000000 INFO @ Sat, 11 Dec 2021 08:55:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:55:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:55:44: #1 total tags in treatment: 15193642 INFO @ Sat, 11 Dec 2021 08:55:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:55:44: #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 08:55:45: #1 tags after filtering in treatment: 15193572 INFO @ Sat, 11 Dec 2021 08:55:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:55:45: #1 finished! INFO @ Sat, 11 Dec 2021 08:55:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:55:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:55:46: #2 number of paired peaks: 680 WARNING @ Sat, 11 Dec 2021 08:55:46: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sat, 11 Dec 2021 08:55:46: start model_add_line... INFO @ Sat, 11 Dec 2021 08:55:46: start X-correlation... INFO @ Sat, 11 Dec 2021 08:55:46: end of X-cor INFO @ Sat, 11 Dec 2021 08:55:46: #2 finished! INFO @ Sat, 11 Dec 2021 08:55:46: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 08:55:46: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sat, 11 Dec 2021 08:55:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.10_model.r WARNING @ Sat, 11 Dec 2021 08:55:46: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:55:46: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sat, 11 Dec 2021 08:55:46: #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 08:55:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:55:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:55:47: 11000000 INFO @ Sat, 11 Dec 2021 08:55:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:55:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:55:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.05_summits.bed INFO @ Sat, 11 Dec 2021 08:55:52: Done! pass1 - making usageList (678 chroms): 2 millis pass2 - checking and writing primary data (3043 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:55:53: 12000000 INFO @ Sat, 11 Dec 2021 08:55:59: 13000000 INFO @ Sat, 11 Dec 2021 08:56:05: 14000000 INFO @ Sat, 11 Dec 2021 08:56:10: 15000000 INFO @ Sat, 11 Dec 2021 08:56:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:56:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:56:12: #1 total tags in treatment: 15193642 INFO @ Sat, 11 Dec 2021 08:56:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:56:12: #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 08:56:12: #1 tags after filtering in treatment: 15193572 INFO @ Sat, 11 Dec 2021 08:56:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:56:12: #1 finished! INFO @ Sat, 11 Dec 2021 08:56:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:56:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:56:13: #2 number of paired peaks: 680 WARNING @ Sat, 11 Dec 2021 08:56:13: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sat, 11 Dec 2021 08:56:13: start model_add_line... INFO @ Sat, 11 Dec 2021 08:56:13: start X-correlation... INFO @ Sat, 11 Dec 2021 08:56:13: end of X-cor INFO @ Sat, 11 Dec 2021 08:56:13: #2 finished! INFO @ Sat, 11 Dec 2021 08:56:13: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 08:56:13: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sat, 11 Dec 2021 08:56:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.20_model.r WARNING @ Sat, 11 Dec 2021 08:56:13: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:56:13: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sat, 11 Dec 2021 08:56:13: #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 08:56:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:56:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:56:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.10_summits.bed INFO @ Sat, 11 Dec 2021 08:56:28: Done! pass1 - making usageList (580 chroms): 1 millis pass2 - checking and writing primary data (2159 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:56:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:56:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:56:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:56:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689105/SRX8689105.20_summits.bed INFO @ Sat, 11 Dec 2021 08:56:54: Done! pass1 - making usageList (364 chroms): 1 millis pass2 - checking and writing primary data (817 records, 4 fields): 11 millis CompletedMACS2peakCalling