Job ID = 6456212 SRX = SRX331369 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:33:52 prefetch.2.10.7: 1) Downloading 'SRR947606'... 2020-06-21T10:33:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:36:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:36:36 prefetch.2.10.7: 1) 'SRR947606' was downloaded successfully Read 18493128 spots for SRR947606/SRR947606.sra Written 18493128 spots for SRR947606/SRR947606.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: 00:04:58 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1283993 (6.94%) aligned 0 times 13226996 (71.52%) aligned exactly 1 time 3982139 (21.53%) aligned >1 times 93.06% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 1868489 / 17209135 = 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 19:47:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.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 19:47:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:20: 1000000 INFO @ Sun, 21 Jun 2020 19:47:26: 2000000 INFO @ Sun, 21 Jun 2020 19:47:31: 3000000 INFO @ Sun, 21 Jun 2020 19:47:36: 4000000 INFO @ Sun, 21 Jun 2020 19:47:42: 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 @ Sun, 21 Jun 2020 19:47:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.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 19:47:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:47: 6000000 INFO @ Sun, 21 Jun 2020 19:47:51: 1000000 INFO @ Sun, 21 Jun 2020 19:47:53: 7000000 INFO @ Sun, 21 Jun 2020 19:47:57: 2000000 INFO @ Sun, 21 Jun 2020 19:47:59: 8000000 INFO @ Sun, 21 Jun 2020 19:48:03: 3000000 INFO @ Sun, 21 Jun 2020 19:48:05: 9000000 INFO @ Sun, 21 Jun 2020 19:48:09: 4000000 INFO @ Sun, 21 Jun 2020 19:48:11: 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 @ Sun, 21 Jun 2020 19:48:15: 5000000 INFO @ Sun, 21 Jun 2020 19:48:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.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 19:48:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:17: 11000000 INFO @ Sun, 21 Jun 2020 19:48:21: 6000000 INFO @ Sun, 21 Jun 2020 19:48:21: 1000000 INFO @ Sun, 21 Jun 2020 19:48:23: 12000000 INFO @ Sun, 21 Jun 2020 19:48:27: 7000000 INFO @ Sun, 21 Jun 2020 19:48:28: 2000000 INFO @ Sun, 21 Jun 2020 19:48:29: 13000000 INFO @ Sun, 21 Jun 2020 19:48:33: 8000000 INFO @ Sun, 21 Jun 2020 19:48:34: 3000000 INFO @ Sun, 21 Jun 2020 19:48:36: 14000000 INFO @ Sun, 21 Jun 2020 19:48:40: 9000000 INFO @ Sun, 21 Jun 2020 19:48:40: 4000000 INFO @ Sun, 21 Jun 2020 19:48:42: 15000000 INFO @ Sun, 21 Jun 2020 19:48:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:48:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:48:44: #1 total tags in treatment: 15340646 INFO @ Sun, 21 Jun 2020 19:48:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:44: #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 19:48:45: #1 tags after filtering in treatment: 15340644 INFO @ Sun, 21 Jun 2020 19:48:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:46: 10000000 INFO @ Sun, 21 Jun 2020 19:48:46: #2 number of paired peaks: 296 WARNING @ Sun, 21 Jun 2020 19:48:46: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 21 Jun 2020 19:48:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:46: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:48:46: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.05_model.r WARNING @ Sun, 21 Jun 2020 19:48:46: #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 19:48:46: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:48:46: #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 19:48:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:48:46: 5000000 INFO @ Sun, 21 Jun 2020 19:48:52: 11000000 INFO @ Sun, 21 Jun 2020 19:48:52: 6000000 INFO @ Sun, 21 Jun 2020 19:48:58: 12000000 INFO @ Sun, 21 Jun 2020 19:48:58: 7000000 INFO @ Sun, 21 Jun 2020 19:49:04: 8000000 INFO @ Sun, 21 Jun 2020 19:49:04: 13000000 INFO @ Sun, 21 Jun 2020 19:49:10: 9000000 INFO @ Sun, 21 Jun 2020 19:49:10: 14000000 INFO @ Sun, 21 Jun 2020 19:49:16: 10000000 INFO @ Sun, 21 Jun 2020 19:49:17: 15000000 INFO @ Sun, 21 Jun 2020 19:49:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:49:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:49:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:49:19: #1 total tags in treatment: 15340646 INFO @ Sun, 21 Jun 2020 19:49:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:19: #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 19:49:19: #1 tags after filtering in treatment: 15340644 INFO @ Sun, 21 Jun 2020 19:49:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:20: #2 number of paired peaks: 296 WARNING @ Sun, 21 Jun 2020 19:49:20: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 21 Jun 2020 19:49:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:21: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:49:21: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.10_model.r WARNING @ Sun, 21 Jun 2020 19:49:21: #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 19:49:21: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:49:21: #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 19:49:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:22: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:49:28: 12000000 INFO @ Sun, 21 Jun 2020 19:49:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:49:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:49:34: 13000000 INFO @ Sun, 21 Jun 2020 19:49:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.05_summits.bed INFO @ Sun, 21 Jun 2020 19:49:34: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (2156 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:49:39: 14000000 INFO @ Sun, 21 Jun 2020 19:49:45: 15000000 INFO @ Sun, 21 Jun 2020 19:49:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:49:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:49:47: #1 total tags in treatment: 15340646 INFO @ Sun, 21 Jun 2020 19:49:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:47: #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 19:49:48: #1 tags after filtering in treatment: 15340644 INFO @ Sun, 21 Jun 2020 19:49:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:49: #2 number of paired peaks: 296 WARNING @ Sun, 21 Jun 2020 19:49:49: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 21 Jun 2020 19:49:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:49: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:49:49: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:49:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.20_model.r WARNING @ Sun, 21 Jun 2020 19:49:49: #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 19:49:49: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:49:49: #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 19:49:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:50:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.10_summits.bed INFO @ Sun, 21 Jun 2020 19:50:06: Done! pass1 - making usageList (415 chroms): 1 millis pass2 - checking and writing primary data (1263 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:50:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331369/SRX331369.20_summits.bed INFO @ Sun, 21 Jun 2020 19:50:34: Done! pass1 - making usageList (211 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 8 millis CompletedMACS2peakCalling