Job ID = 16438974 SRX = SRX10031712 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: 00:38:24 66434450 reads; of these: 66434450 (100.00%) were unpaired; of these: 21390349 (32.20%) aligned 0 times 36601000 (55.09%) aligned exactly 1 time 8443101 (12.71%) aligned >1 times 67.80% overall alignment rate Time searching: 00:38:24 Overall time: 00:38:24 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 20 files... [bam_rmdupse_core] 18108649 / 45044101 = 0.4020 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 15:14:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.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 15:14:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:14:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:14:40: 1000000 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 15:14:53: 2000000 INFO @ Tue, 02 Aug 2022 15:14:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.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 15:14:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:14:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:15:09: 3000000 INFO @ Tue, 02 Aug 2022 15:15:10: 1000000 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 15:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.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 15:15:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:15:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:15:25: 4000000 INFO @ Tue, 02 Aug 2022 15:15:25: 2000000 INFO @ Tue, 02 Aug 2022 15:15:41: 5000000 INFO @ Tue, 02 Aug 2022 15:15:42: 3000000 INFO @ Tue, 02 Aug 2022 15:15:42: 1000000 INFO @ Tue, 02 Aug 2022 15:15:56: 6000000 INFO @ Tue, 02 Aug 2022 15:15:58: 4000000 INFO @ Tue, 02 Aug 2022 15:15:58: 2000000 INFO @ Tue, 02 Aug 2022 15:16:12: 7000000 INFO @ Tue, 02 Aug 2022 15:16:13: 3000000 INFO @ Tue, 02 Aug 2022 15:16:14: 5000000 INFO @ Tue, 02 Aug 2022 15:16:27: 8000000 INFO @ Tue, 02 Aug 2022 15:16:27: 4000000 INFO @ Tue, 02 Aug 2022 15:16:29: 6000000 INFO @ Tue, 02 Aug 2022 15:16:41: 5000000 INFO @ Tue, 02 Aug 2022 15:16:42: 9000000 INFO @ Tue, 02 Aug 2022 15:16:44: 7000000 INFO @ Tue, 02 Aug 2022 15:16:55: 6000000 INFO @ Tue, 02 Aug 2022 15:16:57: 10000000 INFO @ Tue, 02 Aug 2022 15:16:57: 8000000 INFO @ Tue, 02 Aug 2022 15:17:09: 7000000 INFO @ Tue, 02 Aug 2022 15:17:12: 9000000 INFO @ Tue, 02 Aug 2022 15:17:12: 11000000 INFO @ Tue, 02 Aug 2022 15:17:23: 8000000 INFO @ Tue, 02 Aug 2022 15:17:27: 10000000 INFO @ Tue, 02 Aug 2022 15:17:28: 12000000 INFO @ Tue, 02 Aug 2022 15:17:39: 9000000 INFO @ Tue, 02 Aug 2022 15:17:43: 11000000 INFO @ Tue, 02 Aug 2022 15:17:44: 13000000 INFO @ Tue, 02 Aug 2022 15:17:54: 10000000 INFO @ Tue, 02 Aug 2022 15:17:58: 12000000 INFO @ Tue, 02 Aug 2022 15:18:00: 14000000 INFO @ Tue, 02 Aug 2022 15:18:10: 11000000 INFO @ Tue, 02 Aug 2022 15:18:14: 13000000 INFO @ Tue, 02 Aug 2022 15:18:17: 15000000 INFO @ Tue, 02 Aug 2022 15:18:26: 12000000 INFO @ Tue, 02 Aug 2022 15:18:30: 14000000 INFO @ Tue, 02 Aug 2022 15:18:33: 16000000 INFO @ Tue, 02 Aug 2022 15:18:41: 13000000 INFO @ Tue, 02 Aug 2022 15:18:46: 15000000 INFO @ Tue, 02 Aug 2022 15:18:49: 17000000 INFO @ Tue, 02 Aug 2022 15:18:56: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:19:01: 16000000 INFO @ Tue, 02 Aug 2022 15:19:06: 18000000 INFO @ Tue, 02 Aug 2022 15:19:12: 15000000 INFO @ Tue, 02 Aug 2022 15:19:17: 17000000 INFO @ Tue, 02 Aug 2022 15:19:23: 19000000 INFO @ Tue, 02 Aug 2022 15:19:28: 16000000 INFO @ Tue, 02 Aug 2022 15:19:34: 18000000 INFO @ Tue, 02 Aug 2022 15:19:39: 20000000 INFO @ Tue, 02 Aug 2022 15:19:44: 17000000 INFO @ Tue, 02 Aug 2022 15:19:50: 19000000 INFO @ Tue, 02 Aug 2022 15:19:56: 21000000 INFO @ Tue, 02 Aug 2022 15:19:59: 18000000 INFO @ Tue, 02 Aug 2022 15:20:06: 20000000 INFO @ Tue, 02 Aug 2022 15:20:13: 22000000 INFO @ Tue, 02 Aug 2022 15:20:16: 19000000 INFO @ Tue, 02 Aug 2022 15:20:21: 21000000 INFO @ Tue, 02 Aug 2022 15:20:29: 23000000 INFO @ Tue, 02 Aug 2022 15:20:32: 20000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:20:38: 22000000 INFO @ Tue, 02 Aug 2022 15:20:46: 24000000 INFO @ Tue, 02 Aug 2022 15:20:48: 21000000 INFO @ Tue, 02 Aug 2022 15:20:54: 23000000 INFO @ Tue, 02 Aug 2022 15:21:03: 25000000 INFO @ Tue, 02 Aug 2022 15:21:04: 22000000 INFO @ Tue, 02 Aug 2022 15:21:09: 24000000 INFO @ Tue, 02 Aug 2022 15:21:20: 23000000 INFO @ Tue, 02 Aug 2022 15:21:20: 26000000 INFO @ Tue, 02 Aug 2022 15:21:25: 25000000 INFO @ Tue, 02 Aug 2022 15:21:35: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 15:21:35: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 15:21:35: #1 total tags in treatment: 26935452 INFO @ Tue, 02 Aug 2022 15:21:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:21:35: #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 15:21:36: #1 tags after filtering in treatment: 26935393 INFO @ Tue, 02 Aug 2022 15:21:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:21:36: #1 finished! INFO @ Tue, 02 Aug 2022 15:21:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:21:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:21:37: 24000000 INFO @ Tue, 02 Aug 2022 15:21:39: #2 number of paired peaks: 884 WARNING @ Tue, 02 Aug 2022 15:21:39: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Tue, 02 Aug 2022 15:21:39: start model_add_line... INFO @ Tue, 02 Aug 2022 15:21:39: start X-correlation... INFO @ Tue, 02 Aug 2022 15:21:39: end of X-cor INFO @ Tue, 02 Aug 2022 15:21:39: #2 finished! INFO @ Tue, 02 Aug 2022 15:21:39: #2 predicted fragment length is 38 bps INFO @ Tue, 02 Aug 2022 15:21:39: #2 alternative fragment length(s) may be 4,38 bps INFO @ Tue, 02 Aug 2022 15:21:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.05_model.r WARNING @ Tue, 02 Aug 2022 15:21:39: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:21:39: #2 You may need to consider one of the other alternative d(s): 4,38 WARNING @ Tue, 02 Aug 2022 15:21:39: #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 15:21:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:21:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:21:41: 26000000 INFO @ Tue, 02 Aug 2022 15:21:53: 25000000 INFO @ Tue, 02 Aug 2022 15:21:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 15:21:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 15:21:55: #1 total tags in treatment: 26935452 INFO @ Tue, 02 Aug 2022 15:21:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:21:55: #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 15:21:56: #1 tags after filtering in treatment: 26935393 INFO @ Tue, 02 Aug 2022 15:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:21:56: #1 finished! INFO @ Tue, 02 Aug 2022 15:21:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:21:59: #2 number of paired peaks: 884 WARNING @ Tue, 02 Aug 2022 15:21:59: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Tue, 02 Aug 2022 15:21:59: start model_add_line... INFO @ Tue, 02 Aug 2022 15:21:59: start X-correlation... INFO @ Tue, 02 Aug 2022 15:21:59: end of X-cor INFO @ Tue, 02 Aug 2022 15:21:59: #2 finished! INFO @ Tue, 02 Aug 2022 15:21:59: #2 predicted fragment length is 38 bps INFO @ Tue, 02 Aug 2022 15:21:59: #2 alternative fragment length(s) may be 4,38 bps INFO @ Tue, 02 Aug 2022 15:21:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.10_model.r WARNING @ Tue, 02 Aug 2022 15:21:59: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:21:59: #2 You may need to consider one of the other alternative d(s): 4,38 WARNING @ Tue, 02 Aug 2022 15:21:59: #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 15:21:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:21:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:22:09: 26000000 INFO @ Tue, 02 Aug 2022 15:22:24: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 15:22:24: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 15:22:24: #1 total tags in treatment: 26935452 INFO @ Tue, 02 Aug 2022 15:22:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:22:24: #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 15:22:25: #1 tags after filtering in treatment: 26935393 INFO @ Tue, 02 Aug 2022 15:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:22:25: #1 finished! INFO @ Tue, 02 Aug 2022 15:22:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:22:28: #2 number of paired peaks: 884 WARNING @ Tue, 02 Aug 2022 15:22:28: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Tue, 02 Aug 2022 15:22:28: start model_add_line... INFO @ Tue, 02 Aug 2022 15:22:28: start X-correlation... INFO @ Tue, 02 Aug 2022 15:22:28: end of X-cor INFO @ Tue, 02 Aug 2022 15:22:28: #2 finished! INFO @ Tue, 02 Aug 2022 15:22:28: #2 predicted fragment length is 38 bps INFO @ Tue, 02 Aug 2022 15:22:28: #2 alternative fragment length(s) may be 4,38 bps INFO @ Tue, 02 Aug 2022 15:22:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.20_model.r WARNING @ Tue, 02 Aug 2022 15:22:28: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:22:28: #2 You may need to consider one of the other alternative d(s): 4,38 WARNING @ Tue, 02 Aug 2022 15:22:28: #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 15:22:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:22:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:22:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:23:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.05_summits.bed INFO @ Tue, 02 Aug 2022 15:23:36: Done! pass1 - making usageList (617 chroms): 6 millis pass2 - checking and writing primary data (20360 records, 4 fields): 95 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:23:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:23:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:23:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:23:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.10_summits.bed INFO @ Tue, 02 Aug 2022 15:23:52: Done! pass1 - making usageList (396 chroms): 8 millis pass2 - checking and writing primary data (12619 records, 4 fields): 125 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:24:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:24:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:24:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031712/SRX10031712.20_summits.bed INFO @ Tue, 02 Aug 2022 15:24:19: Done! pass1 - making usageList (179 chroms): 4 millis pass2 - checking and writing primary data (4438 records, 4 fields): 26 millis CompletedMACS2peakCalling