Job ID = 14167395 SRX = SRX8574266 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: 00:00:04 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:42 27653315 reads; of these: 27653315 (100.00%) were unpaired; of these: 1254928 (4.54%) aligned 0 times 19526510 (70.61%) aligned exactly 1 time 6871877 (24.85%) aligned >1 times 95.46% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:47 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] 4237215 / 26398387 = 0.1605 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 12:19:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.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 12:19:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:19:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:19:10: 1000000 INFO @ Fri, 10 Dec 2021 12:19:15: 2000000 INFO @ Fri, 10 Dec 2021 12:19:20: 3000000 INFO @ Fri, 10 Dec 2021 12:19:25: 4000000 INFO @ Fri, 10 Dec 2021 12:19:30: 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 @ Fri, 10 Dec 2021 12:19:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.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 12:19:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:19:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:19:35: 6000000 INFO @ Fri, 10 Dec 2021 12:19:41: 7000000 INFO @ Fri, 10 Dec 2021 12:19:42: 1000000 INFO @ Fri, 10 Dec 2021 12:19:47: 8000000 INFO @ Fri, 10 Dec 2021 12:19:48: 2000000 INFO @ Fri, 10 Dec 2021 12:19:53: 9000000 INFO @ Fri, 10 Dec 2021 12:19:54: 3000000 INFO @ Fri, 10 Dec 2021 12:19:58: 10000000 INFO @ Fri, 10 Dec 2021 12:20:00: 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 12:20:04: 11000000 INFO @ Fri, 10 Dec 2021 12:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.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 12:20:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:20:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:20:06: 5000000 INFO @ Fri, 10 Dec 2021 12:20:10: 12000000 INFO @ Fri, 10 Dec 2021 12:20:11: 1000000 INFO @ Fri, 10 Dec 2021 12:20:12: 6000000 INFO @ Fri, 10 Dec 2021 12:20:16: 13000000 INFO @ Fri, 10 Dec 2021 12:20:17: 2000000 INFO @ Fri, 10 Dec 2021 12:20:19: 7000000 INFO @ Fri, 10 Dec 2021 12:20:22: 14000000 INFO @ Fri, 10 Dec 2021 12:20:23: 3000000 INFO @ Fri, 10 Dec 2021 12:20:25: 8000000 INFO @ Fri, 10 Dec 2021 12:20:27: 15000000 INFO @ Fri, 10 Dec 2021 12:20:28: 4000000 INFO @ Fri, 10 Dec 2021 12:20:31: 9000000 INFO @ Fri, 10 Dec 2021 12:20:33: 16000000 INFO @ Fri, 10 Dec 2021 12:20:34: 5000000 INFO @ Fri, 10 Dec 2021 12:20:37: 10000000 INFO @ Fri, 10 Dec 2021 12:20:39: 17000000 INFO @ Fri, 10 Dec 2021 12:20:40: 6000000 INFO @ Fri, 10 Dec 2021 12:20:43: 11000000 INFO @ Fri, 10 Dec 2021 12:20:45: 18000000 INFO @ Fri, 10 Dec 2021 12:20:46: 7000000 INFO @ Fri, 10 Dec 2021 12:20:49: 12000000 INFO @ Fri, 10 Dec 2021 12:20:51: 19000000 INFO @ Fri, 10 Dec 2021 12:20:51: 8000000 INFO @ Fri, 10 Dec 2021 12:20:55: 13000000 INFO @ Fri, 10 Dec 2021 12:20:56: 20000000 INFO @ Fri, 10 Dec 2021 12:20:57: 9000000 INFO @ Fri, 10 Dec 2021 12:21:01: 14000000 INFO @ Fri, 10 Dec 2021 12:21:02: 21000000 INFO @ Fri, 10 Dec 2021 12:21:03: 10000000 INFO @ Fri, 10 Dec 2021 12:21:07: 15000000 INFO @ Fri, 10 Dec 2021 12:21:08: 22000000 INFO @ Fri, 10 Dec 2021 12:21:08: 11000000 INFO @ Fri, 10 Dec 2021 12:21:09: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:21:09: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:21:09: #1 total tags in treatment: 22161172 INFO @ Fri, 10 Dec 2021 12:21:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:21:09: #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 12:21:09: #1 tags after filtering in treatment: 22161172 INFO @ Fri, 10 Dec 2021 12:21:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:21:09: #1 finished! INFO @ Fri, 10 Dec 2021 12:21:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:21:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:21:11: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 12:21:11: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 12:21:11: start model_add_line... INFO @ Fri, 10 Dec 2021 12:21:11: start X-correlation... INFO @ Fri, 10 Dec 2021 12:21:11: end of X-cor INFO @ Fri, 10 Dec 2021 12:21:11: #2 finished! INFO @ Fri, 10 Dec 2021 12:21:11: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:21:11: #2 alternative fragment length(s) may be 2,45,598 bps INFO @ Fri, 10 Dec 2021 12:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.05_model.r WARNING @ Fri, 10 Dec 2021 12:21:11: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:21:11: #2 You may need to consider one of the other alternative d(s): 2,45,598 WARNING @ Fri, 10 Dec 2021 12:21:11: #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 12:21:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:21:13: 16000000 INFO @ Fri, 10 Dec 2021 12:21:14: 12000000 INFO @ Fri, 10 Dec 2021 12:21:19: 13000000 INFO @ Fri, 10 Dec 2021 12:21:19: 17000000 INFO @ Fri, 10 Dec 2021 12:21:25: 14000000 INFO @ Fri, 10 Dec 2021 12:21:26: 18000000 INFO @ Fri, 10 Dec 2021 12:21:30: 15000000 INFO @ Fri, 10 Dec 2021 12:21:32: 19000000 INFO @ Fri, 10 Dec 2021 12:21:36: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:21:38: 20000000 INFO @ Fri, 10 Dec 2021 12:21:42: 17000000 INFO @ Fri, 10 Dec 2021 12:21:44: 21000000 INFO @ Fri, 10 Dec 2021 12:21:48: 18000000 INFO @ Fri, 10 Dec 2021 12:21:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:21:50: 22000000 INFO @ Fri, 10 Dec 2021 12:21:51: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:21:51: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:21:51: #1 total tags in treatment: 22161172 INFO @ Fri, 10 Dec 2021 12:21:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:21:51: #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 12:21:52: #1 tags after filtering in treatment: 22161172 INFO @ Fri, 10 Dec 2021 12:21:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:21:52: #1 finished! INFO @ Fri, 10 Dec 2021 12:21:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:21:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:21:53: 19000000 INFO @ Fri, 10 Dec 2021 12:21:53: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 12:21:53: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 12:21:53: start model_add_line... INFO @ Fri, 10 Dec 2021 12:21:53: start X-correlation... INFO @ Fri, 10 Dec 2021 12:21:53: end of X-cor INFO @ Fri, 10 Dec 2021 12:21:53: #2 finished! INFO @ Fri, 10 Dec 2021 12:21:53: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:21:53: #2 alternative fragment length(s) may be 2,45,598 bps INFO @ Fri, 10 Dec 2021 12:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.10_model.r WARNING @ Fri, 10 Dec 2021 12:21:53: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:21:53: #2 You may need to consider one of the other alternative d(s): 2,45,598 WARNING @ Fri, 10 Dec 2021 12:21:53: #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 12:21:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:21:59: 20000000 INFO @ Fri, 10 Dec 2021 12:22:04: 21000000 INFO @ Fri, 10 Dec 2021 12:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.05_summits.bed INFO @ Fri, 10 Dec 2021 12:22:05: Done! pass1 - making usageList (717 chroms): 1 millis pass2 - checking and writing primary data (3136 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:22:09: 22000000 INFO @ Fri, 10 Dec 2021 12:22:10: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:22:10: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:22:10: #1 total tags in treatment: 22161172 INFO @ Fri, 10 Dec 2021 12:22:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:22:10: #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 12:22:11: #1 tags after filtering in treatment: 22161172 INFO @ Fri, 10 Dec 2021 12:22:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:22:11: #1 finished! INFO @ Fri, 10 Dec 2021 12:22:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:22:12: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 12:22:12: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 12:22:12: start model_add_line... INFO @ Fri, 10 Dec 2021 12:22:12: start X-correlation... INFO @ Fri, 10 Dec 2021 12:22:12: end of X-cor INFO @ Fri, 10 Dec 2021 12:22:12: #2 finished! INFO @ Fri, 10 Dec 2021 12:22:12: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:22:12: #2 alternative fragment length(s) may be 2,45,598 bps INFO @ Fri, 10 Dec 2021 12:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.20_model.r WARNING @ Fri, 10 Dec 2021 12:22:12: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:22:12: #2 You may need to consider one of the other alternative d(s): 2,45,598 WARNING @ Fri, 10 Dec 2021 12:22:12: #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 12:22:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:22:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:22:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:22:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:22:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:22:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.10_summits.bed INFO @ Fri, 10 Dec 2021 12:22:49: Done! INFO @ Fri, 10 Dec 2021 12:22:49: #3 Call peaks for each chromosome... pass1 - making usageList (577 chroms): 1 millis pass2 - checking and writing primary data (2085 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:23:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574266/SRX8574266.20_summits.bed INFO @ Fri, 10 Dec 2021 12:23:07: Done! pass1 - making usageList (284 chroms): 1 millis pass2 - checking and writing primary data (524 records, 4 fields): 9 millis CompletedMACS2peakCalling