Job ID = 6530061 SRX = SRX6962951 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: 00:16:33 49107048 reads; of these: 49107048 (100.00%) were unpaired; of these: 4964389 (10.11%) aligned 0 times 34398457 (70.05%) aligned exactly 1 time 9744202 (19.84%) aligned >1 times 89.89% overall alignment rate Time searching: 00:16:33 Overall time: 00:16:33 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] 14486486 / 44142659 = 0.3282 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 03:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.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 03:39:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:39:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:39:53: 1000000 INFO @ Tue, 30 Jun 2020 03:39:59: 2000000 INFO @ Tue, 30 Jun 2020 03:40:06: 3000000 INFO @ Tue, 30 Jun 2020 03:40:13: 4000000 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 03:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.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 03:40:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:40:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:40:20: 5000000 INFO @ Tue, 30 Jun 2020 03:40:24: 1000000 INFO @ Tue, 30 Jun 2020 03:40:27: 6000000 INFO @ Tue, 30 Jun 2020 03:40:31: 2000000 INFO @ Tue, 30 Jun 2020 03:40:35: 7000000 INFO @ Tue, 30 Jun 2020 03:40:39: 3000000 INFO @ Tue, 30 Jun 2020 03:40:43: 8000000 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 03:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.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 03:40:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:40:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:40:47: 4000000 INFO @ Tue, 30 Jun 2020 03:40:50: 9000000 INFO @ Tue, 30 Jun 2020 03:40:54: 1000000 INFO @ Tue, 30 Jun 2020 03:40:55: 5000000 INFO @ Tue, 30 Jun 2020 03:40:58: 10000000 INFO @ Tue, 30 Jun 2020 03:41:02: 2000000 INFO @ Tue, 30 Jun 2020 03:41:02: 6000000 INFO @ Tue, 30 Jun 2020 03:41:06: 11000000 INFO @ Tue, 30 Jun 2020 03:41:09: 3000000 INFO @ Tue, 30 Jun 2020 03:41:10: 7000000 INFO @ Tue, 30 Jun 2020 03:41:13: 12000000 INFO @ Tue, 30 Jun 2020 03:41:17: 4000000 INFO @ Tue, 30 Jun 2020 03:41:18: 8000000 INFO @ Tue, 30 Jun 2020 03:41:21: 13000000 INFO @ Tue, 30 Jun 2020 03:41:24: 5000000 INFO @ Tue, 30 Jun 2020 03:41:26: 9000000 INFO @ Tue, 30 Jun 2020 03:41:29: 14000000 INFO @ Tue, 30 Jun 2020 03:41:32: 6000000 INFO @ Tue, 30 Jun 2020 03:41:33: 10000000 INFO @ Tue, 30 Jun 2020 03:41:36: 15000000 INFO @ Tue, 30 Jun 2020 03:41:39: 7000000 INFO @ Tue, 30 Jun 2020 03:41:41: 11000000 INFO @ Tue, 30 Jun 2020 03:41:44: 16000000 INFO @ Tue, 30 Jun 2020 03:41:47: 8000000 INFO @ Tue, 30 Jun 2020 03:41:48: 12000000 INFO @ Tue, 30 Jun 2020 03:41:52: 17000000 INFO @ Tue, 30 Jun 2020 03:41:54: 9000000 INFO @ Tue, 30 Jun 2020 03:41:56: 13000000 INFO @ Tue, 30 Jun 2020 03:41:59: 18000000 INFO @ Tue, 30 Jun 2020 03:42:02: 10000000 INFO @ Tue, 30 Jun 2020 03:42:04: 14000000 INFO @ Tue, 30 Jun 2020 03:42:07: 19000000 INFO @ Tue, 30 Jun 2020 03:42:09: 11000000 INFO @ Tue, 30 Jun 2020 03:42:11: 15000000 INFO @ Tue, 30 Jun 2020 03:42:15: 20000000 INFO @ Tue, 30 Jun 2020 03:42:17: 12000000 INFO @ Tue, 30 Jun 2020 03:42:19: 16000000 INFO @ Tue, 30 Jun 2020 03:42:22: 21000000 INFO @ Tue, 30 Jun 2020 03:42:24: 13000000 INFO @ Tue, 30 Jun 2020 03:42:26: 17000000 INFO @ Tue, 30 Jun 2020 03:42:30: 22000000 INFO @ Tue, 30 Jun 2020 03:42:32: 14000000 INFO @ Tue, 30 Jun 2020 03:42:34: 18000000 INFO @ Tue, 30 Jun 2020 03:42:37: 23000000 INFO @ Tue, 30 Jun 2020 03:42:39: 15000000 INFO @ Tue, 30 Jun 2020 03:42:41: 19000000 INFO @ Tue, 30 Jun 2020 03:42:45: 24000000 INFO @ Tue, 30 Jun 2020 03:42:47: 16000000 INFO @ Tue, 30 Jun 2020 03:42:49: 20000000 INFO @ Tue, 30 Jun 2020 03:42:53: 25000000 INFO @ Tue, 30 Jun 2020 03:42:54: 17000000 INFO @ Tue, 30 Jun 2020 03:42:56: 21000000 INFO @ Tue, 30 Jun 2020 03:43:01: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:43:02: 18000000 INFO @ Tue, 30 Jun 2020 03:43:04: 22000000 INFO @ Tue, 30 Jun 2020 03:43:08: 27000000 INFO @ Tue, 30 Jun 2020 03:43:09: 19000000 INFO @ Tue, 30 Jun 2020 03:43:11: 23000000 INFO @ Tue, 30 Jun 2020 03:43:16: 28000000 INFO @ Tue, 30 Jun 2020 03:43:17: 20000000 INFO @ Tue, 30 Jun 2020 03:43:19: 24000000 INFO @ Tue, 30 Jun 2020 03:43:24: 29000000 INFO @ Tue, 30 Jun 2020 03:43:24: 21000000 INFO @ Tue, 30 Jun 2020 03:43:27: 25000000 INFO @ Tue, 30 Jun 2020 03:43:29: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:43:29: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:43:29: #1 total tags in treatment: 29656173 INFO @ Tue, 30 Jun 2020 03:43:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:43:29: #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 03:43:30: #1 tags after filtering in treatment: 29656169 INFO @ Tue, 30 Jun 2020 03:43:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:43:30: #1 finished! INFO @ Tue, 30 Jun 2020 03:43:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:43:32: #2 number of paired peaks: 173 WARNING @ Tue, 30 Jun 2020 03:43:32: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 30 Jun 2020 03:43:32: start model_add_line... INFO @ Tue, 30 Jun 2020 03:43:32: start X-correlation... INFO @ Tue, 30 Jun 2020 03:43:32: end of X-cor INFO @ Tue, 30 Jun 2020 03:43:32: #2 finished! INFO @ Tue, 30 Jun 2020 03:43:32: #2 predicted fragment length is 78 bps INFO @ Tue, 30 Jun 2020 03:43:32: #2 alternative fragment length(s) may be 3,78,592 bps INFO @ Tue, 30 Jun 2020 03:43:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.05_model.r WARNING @ Tue, 30 Jun 2020 03:43:32: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:43:32: #2 You may need to consider one of the other alternative d(s): 3,78,592 WARNING @ Tue, 30 Jun 2020 03:43:32: #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 03:43:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:43:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:43:32: 22000000 INFO @ Tue, 30 Jun 2020 03:43:35: 26000000 INFO @ Tue, 30 Jun 2020 03:43:39: 23000000 INFO @ Tue, 30 Jun 2020 03:43:42: 27000000 INFO @ Tue, 30 Jun 2020 03:43:47: 24000000 INFO @ Tue, 30 Jun 2020 03:43:50: 28000000 INFO @ Tue, 30 Jun 2020 03:43:55: 25000000 INFO @ Tue, 30 Jun 2020 03:43:57: 29000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:44:02: 26000000 INFO @ Tue, 30 Jun 2020 03:44:02: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:44:02: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:44:02: #1 total tags in treatment: 29656173 INFO @ Tue, 30 Jun 2020 03:44:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:44:02: #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 03:44:03: #1 tags after filtering in treatment: 29656169 INFO @ Tue, 30 Jun 2020 03:44:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:44:03: #1 finished! INFO @ Tue, 30 Jun 2020 03:44:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:44:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:44:05: #2 number of paired peaks: 173 WARNING @ Tue, 30 Jun 2020 03:44:05: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 30 Jun 2020 03:44:05: start model_add_line... INFO @ Tue, 30 Jun 2020 03:44:05: start X-correlation... INFO @ Tue, 30 Jun 2020 03:44:05: end of X-cor INFO @ Tue, 30 Jun 2020 03:44:05: #2 finished! INFO @ Tue, 30 Jun 2020 03:44:05: #2 predicted fragment length is 78 bps INFO @ Tue, 30 Jun 2020 03:44:05: #2 alternative fragment length(s) may be 3,78,592 bps INFO @ Tue, 30 Jun 2020 03:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.10_model.r WARNING @ Tue, 30 Jun 2020 03:44:05: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:44:05: #2 You may need to consider one of the other alternative d(s): 3,78,592 WARNING @ Tue, 30 Jun 2020 03:44:05: #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 03:44:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:44:09: 27000000 INFO @ Tue, 30 Jun 2020 03:44:16: 28000000 INFO @ Tue, 30 Jun 2020 03:44:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:44:23: 29000000 INFO @ Tue, 30 Jun 2020 03:44:28: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:44:28: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:44:28: #1 total tags in treatment: 29656173 INFO @ Tue, 30 Jun 2020 03:44:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:44:28: #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 03:44:29: #1 tags after filtering in treatment: 29656169 INFO @ Tue, 30 Jun 2020 03:44:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:44:29: #1 finished! INFO @ Tue, 30 Jun 2020 03:44:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:44:31: #2 number of paired peaks: 173 WARNING @ Tue, 30 Jun 2020 03:44:31: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 30 Jun 2020 03:44:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:44:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:44:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:44:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:44:31: #2 predicted fragment length is 78 bps INFO @ Tue, 30 Jun 2020 03:44:31: #2 alternative fragment length(s) may be 3,78,592 bps INFO @ Tue, 30 Jun 2020 03:44:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.20_model.r WARNING @ Tue, 30 Jun 2020 03:44:31: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:44:31: #2 You may need to consider one of the other alternative d(s): 3,78,592 WARNING @ Tue, 30 Jun 2020 03:44:31: #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 03:44:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:44:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:44:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:44:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:44:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.05_summits.bed INFO @ Tue, 30 Jun 2020 03:44:44: Done! pass1 - making usageList (826 chroms): 1 millis pass2 - checking and writing primary data (4350 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:44:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:45:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:45:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:45:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.10_summits.bed INFO @ Tue, 30 Jun 2020 03:45:14: Done! pass1 - making usageList (605 chroms): 2 millis pass2 - checking and writing primary data (2153 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:45:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:45:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:45:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:45:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6962951/SRX6962951.20_summits.bed INFO @ Tue, 30 Jun 2020 03:45:40: Done! pass1 - making usageList (350 chroms): 1 millis pass2 - checking and writing primary data (916 records, 4 fields): 11 millis CompletedMACS2peakCalling