Job ID = 14170991 SRX = SRX8689093 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: 00:10:25 24997723 reads; of these: 24997723 (100.00%) were unpaired; of these: 1146003 (4.58%) aligned 0 times 16909348 (67.64%) aligned exactly 1 time 6942372 (27.77%) aligned >1 times 95.42% overall alignment rate Time searching: 00:10:25 Overall time: 00:10:25 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 12 files... [bam_rmdupse_core] 3529742 / 23851720 = 0.1480 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 09:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.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 09:27:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:27:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:27:40: 1000000 INFO @ Sat, 11 Dec 2021 09:27:48: 2000000 INFO @ Sat, 11 Dec 2021 09:27:57: 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 09:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.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 09:28:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:28:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:28:05: 4000000 INFO @ Sat, 11 Dec 2021 09:28:11: 1000000 INFO @ Sat, 11 Dec 2021 09:28:15: 5000000 INFO @ Sat, 11 Dec 2021 09:28:20: 2000000 INFO @ Sat, 11 Dec 2021 09:28:25: 6000000 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 09:28:30: 3000000 INFO @ Sat, 11 Dec 2021 09:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.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 09:28:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:28:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:28:35: 7000000 INFO @ Sat, 11 Dec 2021 09:28:40: 4000000 INFO @ Sat, 11 Dec 2021 09:28:41: 1000000 INFO @ Sat, 11 Dec 2021 09:28:45: 8000000 INFO @ Sat, 11 Dec 2021 09:28:51: 5000000 INFO @ Sat, 11 Dec 2021 09:28:52: 2000000 INFO @ Sat, 11 Dec 2021 09:28:56: 9000000 INFO @ Sat, 11 Dec 2021 09:29:01: 6000000 INFO @ Sat, 11 Dec 2021 09:29:02: 3000000 INFO @ Sat, 11 Dec 2021 09:29:06: 10000000 INFO @ Sat, 11 Dec 2021 09:29:11: 4000000 INFO @ Sat, 11 Dec 2021 09:29:11: 7000000 INFO @ Sat, 11 Dec 2021 09:29:16: 11000000 INFO @ Sat, 11 Dec 2021 09:29:21: 5000000 INFO @ Sat, 11 Dec 2021 09:29:22: 8000000 INFO @ Sat, 11 Dec 2021 09:29:26: 12000000 INFO @ Sat, 11 Dec 2021 09:29:31: 6000000 INFO @ Sat, 11 Dec 2021 09:29:32: 9000000 INFO @ Sat, 11 Dec 2021 09:29:35: 13000000 INFO @ Sat, 11 Dec 2021 09:29:41: 7000000 INFO @ Sat, 11 Dec 2021 09:29:42: 10000000 INFO @ Sat, 11 Dec 2021 09:29:45: 14000000 INFO @ Sat, 11 Dec 2021 09:29:51: 8000000 INFO @ Sat, 11 Dec 2021 09:29:52: 11000000 INFO @ Sat, 11 Dec 2021 09:29:54: 15000000 INFO @ Sat, 11 Dec 2021 09:30:01: 9000000 INFO @ Sat, 11 Dec 2021 09:30:02: 12000000 INFO @ Sat, 11 Dec 2021 09:30:04: 16000000 INFO @ Sat, 11 Dec 2021 09:30:11: 10000000 INFO @ Sat, 11 Dec 2021 09:30:13: 13000000 INFO @ Sat, 11 Dec 2021 09:30:14: 17000000 INFO @ Sat, 11 Dec 2021 09:30:22: 11000000 INFO @ Sat, 11 Dec 2021 09:30:23: 14000000 INFO @ Sat, 11 Dec 2021 09:30:24: 18000000 INFO @ Sat, 11 Dec 2021 09:30:32: 12000000 INFO @ Sat, 11 Dec 2021 09:30:33: 15000000 INFO @ Sat, 11 Dec 2021 09:30:34: 19000000 INFO @ Sat, 11 Dec 2021 09:30:42: 13000000 INFO @ Sat, 11 Dec 2021 09:30:43: 20000000 INFO @ Sat, 11 Dec 2021 09:30:44: 16000000 INFO @ Sat, 11 Dec 2021 09:30:47: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:30:47: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:30:47: #1 total tags in treatment: 20321978 INFO @ Sat, 11 Dec 2021 09:30:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:30:47: #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 09:30:48: #1 tags after filtering in treatment: 20321946 INFO @ Sat, 11 Dec 2021 09:30:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:30:48: #1 finished! INFO @ Sat, 11 Dec 2021 09:30:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:30:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:30:49: #2 number of paired peaks: 582 WARNING @ Sat, 11 Dec 2021 09:30:49: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sat, 11 Dec 2021 09:30:49: start model_add_line... INFO @ Sat, 11 Dec 2021 09:30:50: start X-correlation... INFO @ Sat, 11 Dec 2021 09:30:50: end of X-cor INFO @ Sat, 11 Dec 2021 09:30:50: #2 finished! INFO @ Sat, 11 Dec 2021 09:30:50: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 09:30:50: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sat, 11 Dec 2021 09:30:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.05_model.r WARNING @ Sat, 11 Dec 2021 09:30:50: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:30:50: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sat, 11 Dec 2021 09:30:50: #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 09:30:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:30:53: 14000000 INFO @ Sat, 11 Dec 2021 09:30:54: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:31:03: 15000000 INFO @ Sat, 11 Dec 2021 09:31:03: 18000000 INFO @ Sat, 11 Dec 2021 09:31:13: 16000000 INFO @ Sat, 11 Dec 2021 09:31:13: 19000000 INFO @ Sat, 11 Dec 2021 09:31:22: 17000000 INFO @ Sat, 11 Dec 2021 09:31:23: 20000000 INFO @ Sat, 11 Dec 2021 09:31:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:31:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:31:26: #1 total tags in treatment: 20321978 INFO @ Sat, 11 Dec 2021 09:31:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:31:26: #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 09:31:27: #1 tags after filtering in treatment: 20321946 INFO @ Sat, 11 Dec 2021 09:31:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:31:27: #1 finished! INFO @ Sat, 11 Dec 2021 09:31:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:31:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:31:29: #2 number of paired peaks: 582 WARNING @ Sat, 11 Dec 2021 09:31:29: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sat, 11 Dec 2021 09:31:29: start model_add_line... INFO @ Sat, 11 Dec 2021 09:31:29: start X-correlation... INFO @ Sat, 11 Dec 2021 09:31:29: end of X-cor INFO @ Sat, 11 Dec 2021 09:31:29: #2 finished! INFO @ Sat, 11 Dec 2021 09:31:29: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 09:31:29: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sat, 11 Dec 2021 09:31:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.10_model.r WARNING @ Sat, 11 Dec 2021 09:31:29: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:31:29: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sat, 11 Dec 2021 09:31:29: #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 09:31:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:31:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:31:31: 18000000 INFO @ Sat, 11 Dec 2021 09:31:40: 19000000 INFO @ Sat, 11 Dec 2021 09:31:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:31:48: 20000000 INFO @ Sat, 11 Dec 2021 09:31:51: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:31:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:31:51: #1 total tags in treatment: 20321978 INFO @ Sat, 11 Dec 2021 09:31:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:31:51: #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 09:31:52: #1 tags after filtering in treatment: 20321946 INFO @ Sat, 11 Dec 2021 09:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:31:52: #1 finished! INFO @ Sat, 11 Dec 2021 09:31:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:31:54: #2 number of paired peaks: 582 WARNING @ Sat, 11 Dec 2021 09:31:54: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sat, 11 Dec 2021 09:31:54: start model_add_line... INFO @ Sat, 11 Dec 2021 09:31:54: start X-correlation... INFO @ Sat, 11 Dec 2021 09:31:54: end of X-cor INFO @ Sat, 11 Dec 2021 09:31:54: #2 finished! INFO @ Sat, 11 Dec 2021 09:31:54: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 09:31:54: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sat, 11 Dec 2021 09:31:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.20_model.r WARNING @ Sat, 11 Dec 2021 09:31:54: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:31:54: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sat, 11 Dec 2021 09:31:54: #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 09:31:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:31:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:32:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:32:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:32:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.05_summits.bed INFO @ Sat, 11 Dec 2021 09:32:10: Done! pass1 - making usageList (719 chroms): 3 millis pass2 - checking and writing primary data (3525 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:32:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:32:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:32:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:32:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:32:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.10_summits.bed INFO @ Sat, 11 Dec 2021 09:32:49: Done! pass1 - making usageList (625 chroms): 2 millis pass2 - checking and writing primary data (2483 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689093/SRX8689093.20_summits.bed INFO @ Sat, 11 Dec 2021 09:33:13: Done! pass1 - making usageList (369 chroms): 3 millis pass2 - checking and writing primary data (854 records, 4 fields): 25 millis CompletedMACS2peakCalling