Job ID = 6456231 SRX = SRX331385 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:58:46 prefetch.2.10.7: 1) Downloading 'SRR947622'... 2020-06-21T10:58:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:01:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:01:57 prefetch.2.10.7: 1) 'SRR947622' was downloaded successfully Read 18493128 spots for SRR947622/SRR947622.sra Written 18493128 spots for SRR947622/SRR947622.sra 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: 00:05:17 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1283963 (6.94%) aligned 0 times 13226982 (71.52%) aligned exactly 1 time 3982183 (21.53%) aligned >1 times 93.06% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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 8 files... [bam_rmdupse_core] 1868849 / 17209165 = 0.1086 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 @ Sun, 21 Jun 2020 20:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.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 @ Sun, 21 Jun 2020 20:14:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:22: 1000000 INFO @ Sun, 21 Jun 2020 20:14:28: 2000000 INFO @ Sun, 21 Jun 2020 20:14:35: 3000000 INFO @ Sun, 21 Jun 2020 20:14:41: 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 @ Sun, 21 Jun 2020 20:14:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.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 @ Sun, 21 Jun 2020 20:14:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:47: 5000000 INFO @ Sun, 21 Jun 2020 20:14:52: 1000000 INFO @ Sun, 21 Jun 2020 20:14:54: 6000000 INFO @ Sun, 21 Jun 2020 20:14:58: 2000000 INFO @ Sun, 21 Jun 2020 20:15:00: 7000000 INFO @ Sun, 21 Jun 2020 20:15:04: 3000000 INFO @ Sun, 21 Jun 2020 20:15:07: 8000000 INFO @ Sun, 21 Jun 2020 20:15:10: 4000000 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 @ Sun, 21 Jun 2020 20:15:13: 9000000 INFO @ Sun, 21 Jun 2020 20:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.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 @ Sun, 21 Jun 2020 20:15:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:16: 5000000 INFO @ Sun, 21 Jun 2020 20:15:20: 10000000 INFO @ Sun, 21 Jun 2020 20:15:22: 6000000 INFO @ Sun, 21 Jun 2020 20:15:23: 1000000 INFO @ Sun, 21 Jun 2020 20:15:27: 11000000 INFO @ Sun, 21 Jun 2020 20:15:28: 7000000 INFO @ Sun, 21 Jun 2020 20:15:30: 2000000 INFO @ Sun, 21 Jun 2020 20:15:34: 8000000 INFO @ Sun, 21 Jun 2020 20:15:34: 12000000 INFO @ Sun, 21 Jun 2020 20:15:37: 3000000 INFO @ Sun, 21 Jun 2020 20:15:40: 9000000 INFO @ Sun, 21 Jun 2020 20:15:42: 13000000 INFO @ Sun, 21 Jun 2020 20:15:44: 4000000 INFO @ Sun, 21 Jun 2020 20:15:46: 10000000 INFO @ Sun, 21 Jun 2020 20:15:49: 14000000 INFO @ Sun, 21 Jun 2020 20:15:51: 5000000 INFO @ Sun, 21 Jun 2020 20:15:52: 11000000 INFO @ Sun, 21 Jun 2020 20:15:56: 15000000 INFO @ Sun, 21 Jun 2020 20:15:58: 6000000 INFO @ Sun, 21 Jun 2020 20:15:58: 12000000 INFO @ Sun, 21 Jun 2020 20:16:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:16:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:16:00: #1 total tags in treatment: 15340316 INFO @ Sun, 21 Jun 2020 20:16:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:16:01: #1 tags after filtering in treatment: 15340315 INFO @ Sun, 21 Jun 2020 20:16:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:02: #2 number of paired peaks: 298 WARNING @ Sun, 21 Jun 2020 20:16:02: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sun, 21 Jun 2020 20:16:02: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:02: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:02: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:02: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:02: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 20:16:02: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 20:16:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.05_model.r WARNING @ Sun, 21 Jun 2020 20:16:02: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:16:02: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 20:16:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:16:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:04: 7000000 INFO @ Sun, 21 Jun 2020 20:16:05: 13000000 INFO @ Sun, 21 Jun 2020 20:16:10: 8000000 INFO @ Sun, 21 Jun 2020 20:16:11: 14000000 INFO @ Sun, 21 Jun 2020 20:16:17: 9000000 INFO @ Sun, 21 Jun 2020 20:16:17: 15000000 INFO @ Sun, 21 Jun 2020 20:16:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:16:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:16:20: #1 total tags in treatment: 15340316 INFO @ Sun, 21 Jun 2020 20:16:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:16:20: #1 tags after filtering in treatment: 15340315 INFO @ Sun, 21 Jun 2020 20:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:20: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:22: #2 number of paired peaks: 298 WARNING @ Sun, 21 Jun 2020 20:16:22: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sun, 21 Jun 2020 20:16:22: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:22: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:22: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:22: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:22: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 20:16:22: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 20:16:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.10_model.r WARNING @ Sun, 21 Jun 2020 20:16:22: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:16:22: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 20:16:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:16:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:23: 10000000 INFO @ Sun, 21 Jun 2020 20:16:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:16:30: 11000000 INFO @ Sun, 21 Jun 2020 20:16:36: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:16:43: 13000000 INFO @ Sun, 21 Jun 2020 20:16:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:16:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:16:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.05_summits.bed INFO @ Sun, 21 Jun 2020 20:16:44: Done! pass1 - making usageList (507 chroms): 2 millis pass2 - checking and writing primary data (2147 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:16:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:16:50: 14000000 INFO @ Sun, 21 Jun 2020 20:16:56: 15000000 INFO @ Sun, 21 Jun 2020 20:16:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:16:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:16:59: #1 total tags in treatment: 15340316 INFO @ Sun, 21 Jun 2020 20:16:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:16:59: #1 tags after filtering in treatment: 15340315 INFO @ Sun, 21 Jun 2020 20:16:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:59: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:17:00: #2 number of paired peaks: 298 WARNING @ Sun, 21 Jun 2020 20:17:00: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sun, 21 Jun 2020 20:17:00: start model_add_line... INFO @ Sun, 21 Jun 2020 20:17:01: start X-correlation... INFO @ Sun, 21 Jun 2020 20:17:01: end of X-cor INFO @ Sun, 21 Jun 2020 20:17:01: #2 finished! INFO @ Sun, 21 Jun 2020 20:17:01: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 20:17:01: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 20:17:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.20_model.r WARNING @ Sun, 21 Jun 2020 20:17:01: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:17:01: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 20:17:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:17:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:17:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:17:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.10_summits.bed INFO @ Sun, 21 Jun 2020 20:17:02: Done! pass1 - making usageList (414 chroms): 1 millis pass2 - checking and writing primary data (1266 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:17:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331385/SRX331385.20_summits.bed INFO @ Sun, 21 Jun 2020 20:17:42: Done! pass1 - making usageList (207 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 13 millis CompletedMACS2peakCalling