Job ID = 16438099 SRX = ERX9193377 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: 00:21:48 78498585 reads; of these: 78498585 (100.00%) were unpaired; of these: 48624433 (61.94%) aligned 0 times 22280299 (28.38%) aligned exactly 1 time 7593853 (9.67%) aligned >1 times 38.06% overall alignment rate Time searching: 00:21:49 Overall time: 00:21:49 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 16 files... [bam_rmdupse_core] 6835842 / 29874152 = 0.2288 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 14:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.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 14:08:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:08:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:08:55: 1000000 INFO @ Tue, 02 Aug 2022 14:09:01: 2000000 INFO @ Tue, 02 Aug 2022 14:09:07: 3000000 INFO @ Tue, 02 Aug 2022 14:09:13: 4000000 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 14:09:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.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 14:09:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:09:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:09:19: 5000000 INFO @ Tue, 02 Aug 2022 14:09:23: 1000000 INFO @ Tue, 02 Aug 2022 14:09:26: 6000000 INFO @ Tue, 02 Aug 2022 14:09:29: 2000000 INFO @ Tue, 02 Aug 2022 14:09:33: 7000000 INFO @ Tue, 02 Aug 2022 14:09:35: 3000000 INFO @ Tue, 02 Aug 2022 14:09:40: 8000000 INFO @ Tue, 02 Aug 2022 14:09:41: 4000000 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 14:09:47: 5000000 INFO @ Tue, 02 Aug 2022 14:09:47: 9000000 INFO @ Tue, 02 Aug 2022 14:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.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 14:09:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:09:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:09:54: 6000000 INFO @ Tue, 02 Aug 2022 14:09:55: 1000000 INFO @ Tue, 02 Aug 2022 14:09:55: 10000000 INFO @ Tue, 02 Aug 2022 14:10:01: 7000000 INFO @ Tue, 02 Aug 2022 14:10:02: 2000000 INFO @ Tue, 02 Aug 2022 14:10:02: 11000000 INFO @ Tue, 02 Aug 2022 14:10:08: 8000000 INFO @ Tue, 02 Aug 2022 14:10:09: 3000000 INFO @ Tue, 02 Aug 2022 14:10:10: 12000000 INFO @ Tue, 02 Aug 2022 14:10:15: 9000000 INFO @ Tue, 02 Aug 2022 14:10:17: 4000000 INFO @ Tue, 02 Aug 2022 14:10:17: 13000000 INFO @ Tue, 02 Aug 2022 14:10:22: 10000000 INFO @ Tue, 02 Aug 2022 14:10:24: 5000000 INFO @ Tue, 02 Aug 2022 14:10:25: 14000000 INFO @ Tue, 02 Aug 2022 14:10:29: 11000000 INFO @ Tue, 02 Aug 2022 14:10:31: 6000000 INFO @ Tue, 02 Aug 2022 14:10:32: 15000000 INFO @ Tue, 02 Aug 2022 14:10:37: 12000000 INFO @ Tue, 02 Aug 2022 14:10:39: 7000000 INFO @ Tue, 02 Aug 2022 14:10:40: 16000000 INFO @ Tue, 02 Aug 2022 14:10:44: 13000000 INFO @ Tue, 02 Aug 2022 14:10:46: 8000000 INFO @ Tue, 02 Aug 2022 14:10:47: 17000000 INFO @ Tue, 02 Aug 2022 14:10:52: 14000000 INFO @ Tue, 02 Aug 2022 14:10:54: 9000000 INFO @ Tue, 02 Aug 2022 14:10:55: 18000000 INFO @ Tue, 02 Aug 2022 14:10:59: 15000000 INFO @ Tue, 02 Aug 2022 14:11:01: 10000000 INFO @ Tue, 02 Aug 2022 14:11:02: 19000000 INFO @ Tue, 02 Aug 2022 14:11:07: 16000000 INFO @ Tue, 02 Aug 2022 14:11:09: 11000000 INFO @ Tue, 02 Aug 2022 14:11:11: 20000000 INFO @ Tue, 02 Aug 2022 14:11:14: 17000000 INFO @ Tue, 02 Aug 2022 14:11:17: 12000000 INFO @ Tue, 02 Aug 2022 14:11:19: 21000000 INFO @ Tue, 02 Aug 2022 14:11:22: 18000000 INFO @ Tue, 02 Aug 2022 14:11:24: 13000000 INFO @ Tue, 02 Aug 2022 14:11:27: 22000000 INFO @ Tue, 02 Aug 2022 14:11:29: 19000000 INFO @ Tue, 02 Aug 2022 14:11:32: 14000000 INFO @ Tue, 02 Aug 2022 14:11:35: 23000000 INFO @ Tue, 02 Aug 2022 14:11:35: #1 tag size is determined as 79 bps INFO @ Tue, 02 Aug 2022 14:11:35: #1 tag size = 79 INFO @ Tue, 02 Aug 2022 14:11:35: #1 total tags in treatment: 23038310 INFO @ Tue, 02 Aug 2022 14:11:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:11:35: #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 14:11:36: #1 tags after filtering in treatment: 23038233 INFO @ Tue, 02 Aug 2022 14:11:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:11:36: #1 finished! INFO @ Tue, 02 Aug 2022 14:11:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:11:38: 20000000 INFO @ Tue, 02 Aug 2022 14:11:38: #2 number of paired peaks: 552 WARNING @ Tue, 02 Aug 2022 14:11:38: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Tue, 02 Aug 2022 14:11:38: start model_add_line... INFO @ Tue, 02 Aug 2022 14:11:38: start X-correlation... INFO @ Tue, 02 Aug 2022 14:11:38: end of X-cor INFO @ Tue, 02 Aug 2022 14:11:38: #2 finished! INFO @ Tue, 02 Aug 2022 14:11:38: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 14:11:38: #2 alternative fragment length(s) may be 2,84,583 bps INFO @ Tue, 02 Aug 2022 14:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.05_model.r WARNING @ Tue, 02 Aug 2022 14:11:38: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:11:38: #2 You may need to consider one of the other alternative d(s): 2,84,583 WARNING @ Tue, 02 Aug 2022 14:11:38: #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 14:11:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:11:39: 15000000 INFO @ Tue, 02 Aug 2022 14:11:45: 21000000 INFO @ Tue, 02 Aug 2022 14:11:47: 16000000 INFO @ Tue, 02 Aug 2022 14:11:53: 22000000 INFO @ Tue, 02 Aug 2022 14:11:54: 17000000 INFO @ Tue, 02 Aug 2022 14:12:00: 23000000 INFO @ Tue, 02 Aug 2022 14:12:01: #1 tag size is determined as 79 bps INFO @ Tue, 02 Aug 2022 14:12:01: #1 tag size = 79 INFO @ Tue, 02 Aug 2022 14:12:01: #1 total tags in treatment: 23038310 INFO @ Tue, 02 Aug 2022 14:12:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:12:01: #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 14:12:02: #1 tags after filtering in treatment: 23038233 INFO @ Tue, 02 Aug 2022 14:12:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:12:02: #1 finished! INFO @ Tue, 02 Aug 2022 14:12:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:12:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:12:02: 18000000 INFO @ Tue, 02 Aug 2022 14:12:03: #2 number of paired peaks: 552 WARNING @ Tue, 02 Aug 2022 14:12:03: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Tue, 02 Aug 2022 14:12:03: start model_add_line... INFO @ Tue, 02 Aug 2022 14:12:04: start X-correlation... INFO @ Tue, 02 Aug 2022 14:12:04: end of X-cor INFO @ Tue, 02 Aug 2022 14:12:04: #2 finished! INFO @ Tue, 02 Aug 2022 14:12:04: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 14:12:04: #2 alternative fragment length(s) may be 2,84,583 bps INFO @ Tue, 02 Aug 2022 14:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.10_model.r WARNING @ Tue, 02 Aug 2022 14:12:04: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:12:04: #2 You may need to consider one of the other alternative d(s): 2,84,583 WARNING @ Tue, 02 Aug 2022 14:12:04: #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 14:12:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:12:09: 19000000 INFO @ Tue, 02 Aug 2022 14:12:17: 20000000 INFO @ Tue, 02 Aug 2022 14:12:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:12:25: 21000000 INFO @ Tue, 02 Aug 2022 14:12:33: 22000000 INFO @ Tue, 02 Aug 2022 14:12:40: 23000000 INFO @ Tue, 02 Aug 2022 14:12:41: #1 tag size is determined as 79 bps INFO @ Tue, 02 Aug 2022 14:12:41: #1 tag size = 79 INFO @ Tue, 02 Aug 2022 14:12:41: #1 total tags in treatment: 23038310 INFO @ Tue, 02 Aug 2022 14:12:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:12:41: #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 14:12:42: #1 tags after filtering in treatment: 23038233 INFO @ Tue, 02 Aug 2022 14:12:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:12:42: #1 finished! INFO @ Tue, 02 Aug 2022 14:12:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:12:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:12:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:12:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:12:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.05_summits.bed INFO @ Tue, 02 Aug 2022 14:12:44: Done! INFO @ Tue, 02 Aug 2022 14:12:44: #2 number of paired peaks: 552 WARNING @ Tue, 02 Aug 2022 14:12:44: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Tue, 02 Aug 2022 14:12:44: start model_add_line... INFO @ Tue, 02 Aug 2022 14:12:44: start X-correlation... INFO @ Tue, 02 Aug 2022 14:12:44: end of X-cor INFO @ Tue, 02 Aug 2022 14:12:44: #2 finished! INFO @ Tue, 02 Aug 2022 14:12:44: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 14:12:44: #2 alternative fragment length(s) may be 2,84,583 bps INFO @ Tue, 02 Aug 2022 14:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.20_model.r WARNING @ Tue, 02 Aug 2022 14:12:44: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:12:44: #2 You may need to consider one of the other alternative d(s): 2,84,583 WARNING @ Tue, 02 Aug 2022 14:12:44: #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 14:12:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:12:44: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (668 chroms): 2 millis pass2 - checking and writing primary data (3402 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:12:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:13:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:13:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:13:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.10_summits.bed INFO @ Tue, 02 Aug 2022 14:13:11: Done! pass1 - making usageList (542 chroms): 2 millis pass2 - checking and writing primary data (1775 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:13:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:13:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX9193377/ERX9193377.20_summits.bed INFO @ Tue, 02 Aug 2022 14:13:51: Done! pass1 - making usageList (352 chroms): 2 millis pass2 - checking and writing primary data (751 records, 4 fields): 63 millis CompletedMACS2peakCalling