Job ID = 6530100 SRX = SRX969908 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: 00:10:38 38792973 reads; of these: 38792973 (100.00%) were unpaired; of these: 4280726 (11.03%) aligned 0 times 28208387 (72.72%) aligned exactly 1 time 6303860 (16.25%) aligned >1 times 88.97% overall alignment rate Time searching: 00:10:38 Overall time: 00:10:38 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] 6165927 / 34512247 = 0.1787 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.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, 30 Jun 2020 03:39:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:39:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:39:54: 1000000 INFO @ Tue, 30 Jun 2020 03:39:59: 2000000 INFO @ Tue, 30 Jun 2020 03:40:05: 3000000 INFO @ Tue, 30 Jun 2020 03:40:10: 4000000 INFO @ Tue, 30 Jun 2020 03:40:15: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:40:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.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, 30 Jun 2020 03:40:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:40:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:40:21: 6000000 INFO @ Tue, 30 Jun 2020 03:40:25: 1000000 INFO @ Tue, 30 Jun 2020 03:40:26: 7000000 INFO @ Tue, 30 Jun 2020 03:40:31: 2000000 INFO @ Tue, 30 Jun 2020 03:40:32: 8000000 INFO @ Tue, 30 Jun 2020 03:40:36: 3000000 INFO @ Tue, 30 Jun 2020 03:40:38: 9000000 INFO @ Tue, 30 Jun 2020 03:40:42: 4000000 INFO @ Tue, 30 Jun 2020 03:40:44: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:40:48: 5000000 INFO @ Tue, 30 Jun 2020 03:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.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, 30 Jun 2020 03:40:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:40:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:40:49: 11000000 INFO @ Tue, 30 Jun 2020 03:40:55: 6000000 INFO @ Tue, 30 Jun 2020 03:40:55: 12000000 INFO @ Tue, 30 Jun 2020 03:40:56: 1000000 INFO @ Tue, 30 Jun 2020 03:41:01: 13000000 INFO @ Tue, 30 Jun 2020 03:41:01: 7000000 INFO @ Tue, 30 Jun 2020 03:41:03: 2000000 INFO @ Tue, 30 Jun 2020 03:41:07: 14000000 INFO @ Tue, 30 Jun 2020 03:41:08: 8000000 INFO @ Tue, 30 Jun 2020 03:41:10: 3000000 INFO @ Tue, 30 Jun 2020 03:41:13: 15000000 INFO @ Tue, 30 Jun 2020 03:41:14: 9000000 INFO @ Tue, 30 Jun 2020 03:41:17: 4000000 INFO @ Tue, 30 Jun 2020 03:41:19: 16000000 INFO @ Tue, 30 Jun 2020 03:41:21: 10000000 INFO @ Tue, 30 Jun 2020 03:41:24: 5000000 INFO @ Tue, 30 Jun 2020 03:41:25: 17000000 INFO @ Tue, 30 Jun 2020 03:41:27: 11000000 INFO @ Tue, 30 Jun 2020 03:41:31: 6000000 INFO @ Tue, 30 Jun 2020 03:41:31: 18000000 INFO @ Tue, 30 Jun 2020 03:41:33: 12000000 INFO @ Tue, 30 Jun 2020 03:41:37: 19000000 INFO @ Tue, 30 Jun 2020 03:41:38: 7000000 INFO @ Tue, 30 Jun 2020 03:41:40: 13000000 INFO @ Tue, 30 Jun 2020 03:41:43: 20000000 INFO @ Tue, 30 Jun 2020 03:41:45: 8000000 INFO @ Tue, 30 Jun 2020 03:41:46: 14000000 INFO @ Tue, 30 Jun 2020 03:41:50: 21000000 INFO @ Tue, 30 Jun 2020 03:41:52: 9000000 INFO @ Tue, 30 Jun 2020 03:41:53: 15000000 INFO @ Tue, 30 Jun 2020 03:41:56: 22000000 INFO @ Tue, 30 Jun 2020 03:41:59: 16000000 INFO @ Tue, 30 Jun 2020 03:41:59: 10000000 INFO @ Tue, 30 Jun 2020 03:42:02: 23000000 INFO @ Tue, 30 Jun 2020 03:42:05: 17000000 INFO @ Tue, 30 Jun 2020 03:42:06: 11000000 INFO @ Tue, 30 Jun 2020 03:42:08: 24000000 INFO @ Tue, 30 Jun 2020 03:42:11: 18000000 INFO @ Tue, 30 Jun 2020 03:42:13: 12000000 INFO @ Tue, 30 Jun 2020 03:42:15: 25000000 INFO @ Tue, 30 Jun 2020 03:42:18: 19000000 INFO @ Tue, 30 Jun 2020 03:42:20: 13000000 INFO @ Tue, 30 Jun 2020 03:42:21: 26000000 INFO @ Tue, 30 Jun 2020 03:42:24: 20000000 INFO @ Tue, 30 Jun 2020 03:42:27: 14000000 INFO @ Tue, 30 Jun 2020 03:42:27: 27000000 INFO @ Tue, 30 Jun 2020 03:42:30: 21000000 INFO @ Tue, 30 Jun 2020 03:42:33: 15000000 INFO @ Tue, 30 Jun 2020 03:42:33: 28000000 INFO @ Tue, 30 Jun 2020 03:42:36: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:42:36: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:42:36: #1 total tags in treatment: 28346320 INFO @ Tue, 30 Jun 2020 03:42:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:42:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:42:36: 22000000 INFO @ Tue, 30 Jun 2020 03:42:37: #1 tags after filtering in treatment: 28346315 INFO @ Tue, 30 Jun 2020 03:42:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:42:37: #1 finished! INFO @ Tue, 30 Jun 2020 03:42:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:42:38: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 03:42:38: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 03:42:38: start model_add_line... INFO @ Tue, 30 Jun 2020 03:42:39: start X-correlation... INFO @ Tue, 30 Jun 2020 03:42:39: end of X-cor INFO @ Tue, 30 Jun 2020 03:42:39: #2 finished! INFO @ Tue, 30 Jun 2020 03:42:39: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 03:42:39: #2 alternative fragment length(s) may be 3,54 bps INFO @ Tue, 30 Jun 2020 03:42:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.05_model.r WARNING @ Tue, 30 Jun 2020 03:42:39: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:42:39: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Tue, 30 Jun 2020 03:42:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:42:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:42:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:42:40: 16000000 INFO @ Tue, 30 Jun 2020 03:42:42: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:42:47: 17000000 INFO @ Tue, 30 Jun 2020 03:42:49: 24000000 INFO @ Tue, 30 Jun 2020 03:42:54: 18000000 INFO @ Tue, 30 Jun 2020 03:42:55: 25000000 INFO @ Tue, 30 Jun 2020 03:43:01: 19000000 INFO @ Tue, 30 Jun 2020 03:43:01: 26000000 INFO @ Tue, 30 Jun 2020 03:43:08: 27000000 INFO @ Tue, 30 Jun 2020 03:43:08: 20000000 INFO @ Tue, 30 Jun 2020 03:43:14: 28000000 INFO @ Tue, 30 Jun 2020 03:43:15: 21000000 INFO @ Tue, 30 Jun 2020 03:43:16: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:43:16: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:43:16: #1 total tags in treatment: 28346320 INFO @ Tue, 30 Jun 2020 03:43:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:43:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:43:17: #1 tags after filtering in treatment: 28346315 INFO @ Tue, 30 Jun 2020 03:43:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:43:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:43:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:43:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:43:19: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 03:43:19: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 03:43:19: start model_add_line... INFO @ Tue, 30 Jun 2020 03:43:19: start X-correlation... INFO @ Tue, 30 Jun 2020 03:43:19: end of X-cor INFO @ Tue, 30 Jun 2020 03:43:19: #2 finished! INFO @ Tue, 30 Jun 2020 03:43:19: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 03:43:19: #2 alternative fragment length(s) may be 3,54 bps INFO @ Tue, 30 Jun 2020 03:43:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.10_model.r WARNING @ Tue, 30 Jun 2020 03:43:19: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:43:19: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Tue, 30 Jun 2020 03:43:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:43:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:43:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:43:22: 22000000 INFO @ Tue, 30 Jun 2020 03:43:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:43:29: 23000000 INFO @ Tue, 30 Jun 2020 03:43:36: 24000000 INFO @ Tue, 30 Jun 2020 03:43:43: 25000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:43:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.05_summits.bed INFO @ Tue, 30 Jun 2020 03:43:46: Done! pass1 - making usageList (292 chroms): 2 millis pass2 - checking and writing primary data (5740 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:43:50: 26000000 INFO @ Tue, 30 Jun 2020 03:43:57: 27000000 INFO @ Tue, 30 Jun 2020 03:44:04: 28000000 INFO @ Tue, 30 Jun 2020 03:44:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:44:06: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:44:06: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:44:06: #1 total tags in treatment: 28346320 INFO @ Tue, 30 Jun 2020 03:44:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:44:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:44:07: #1 tags after filtering in treatment: 28346315 INFO @ Tue, 30 Jun 2020 03:44:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:44:07: #1 finished! INFO @ Tue, 30 Jun 2020 03:44:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:44:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:44:09: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 03:44:09: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 03:44:09: start model_add_line... INFO @ Tue, 30 Jun 2020 03:44:09: start X-correlation... INFO @ Tue, 30 Jun 2020 03:44:09: end of X-cor INFO @ Tue, 30 Jun 2020 03:44:09: #2 finished! INFO @ Tue, 30 Jun 2020 03:44:09: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 03:44:09: #2 alternative fragment length(s) may be 3,54 bps INFO @ Tue, 30 Jun 2020 03:44:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.20_model.r WARNING @ Tue, 30 Jun 2020 03:44:09: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:44:09: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Tue, 30 Jun 2020 03:44:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:44:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:44:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:44:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.10_summits.bed INFO @ Tue, 30 Jun 2020 03:44:26: Done! pass1 - making usageList (167 chroms): 1 millis pass2 - checking and writing primary data (2412 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:44:54: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:45:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:45:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:45:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969908/SRX969908.20_summits.bed INFO @ Tue, 30 Jun 2020 03:45:16: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (749 records, 4 fields): 7 millis CompletedMACS2peakCalling