Job ID = 6453622 SRX = SRX1300691 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:30:41 prefetch.2.10.7: 1) Downloading 'SRR2548367'... 2020-06-21T08:30:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:38:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:38:25 prefetch.2.10.7: 1) 'SRR2548367' was downloaded successfully Read 25155192 spots for SRR2548367/SRR2548367.sra Written 25155192 spots for SRR2548367/SRR2548367.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: 00:07:04 25155192 reads; of these: 25155192 (100.00%) were unpaired; of these: 1205994 (4.79%) aligned 0 times 16879684 (67.10%) aligned exactly 1 time 7069514 (28.10%) aligned >1 times 95.21% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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 12 files... [bam_rmdupse_core] 3455425 / 23949198 = 0.1443 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 17:53:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.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 17:53:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:15: 1000000 INFO @ Sun, 21 Jun 2020 17:53:22: 2000000 INFO @ Sun, 21 Jun 2020 17:53:28: 3000000 INFO @ Sun, 21 Jun 2020 17:53:35: 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 17:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.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 17:53:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:42: 5000000 INFO @ Sun, 21 Jun 2020 17:53:46: 1000000 INFO @ Sun, 21 Jun 2020 17:53:49: 6000000 INFO @ Sun, 21 Jun 2020 17:53:53: 2000000 INFO @ Sun, 21 Jun 2020 17:53:57: 7000000 INFO @ Sun, 21 Jun 2020 17:54:00: 3000000 INFO @ Sun, 21 Jun 2020 17:54:04: 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 @ Sun, 21 Jun 2020 17:54:08: 4000000 INFO @ Sun, 21 Jun 2020 17:54:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.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 17:54:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:12: 9000000 INFO @ Sun, 21 Jun 2020 17:54:15: 5000000 INFO @ Sun, 21 Jun 2020 17:54:16: 1000000 INFO @ Sun, 21 Jun 2020 17:54:20: 10000000 INFO @ Sun, 21 Jun 2020 17:54:22: 6000000 INFO @ Sun, 21 Jun 2020 17:54:23: 2000000 INFO @ Sun, 21 Jun 2020 17:54:27: 11000000 INFO @ Sun, 21 Jun 2020 17:54:30: 7000000 INFO @ Sun, 21 Jun 2020 17:54:30: 3000000 INFO @ Sun, 21 Jun 2020 17:54:35: 12000000 INFO @ Sun, 21 Jun 2020 17:54:37: 8000000 INFO @ Sun, 21 Jun 2020 17:54:37: 4000000 INFO @ Sun, 21 Jun 2020 17:54:42: 13000000 INFO @ Sun, 21 Jun 2020 17:54:45: 5000000 INFO @ Sun, 21 Jun 2020 17:54:45: 9000000 INFO @ Sun, 21 Jun 2020 17:54:49: 14000000 INFO @ Sun, 21 Jun 2020 17:54:52: 6000000 INFO @ Sun, 21 Jun 2020 17:54:52: 10000000 INFO @ Sun, 21 Jun 2020 17:54:57: 15000000 INFO @ Sun, 21 Jun 2020 17:54:59: 7000000 INFO @ Sun, 21 Jun 2020 17:55:00: 11000000 INFO @ Sun, 21 Jun 2020 17:55:04: 16000000 INFO @ Sun, 21 Jun 2020 17:55:07: 8000000 INFO @ Sun, 21 Jun 2020 17:55:08: 12000000 INFO @ Sun, 21 Jun 2020 17:55:12: 17000000 INFO @ Sun, 21 Jun 2020 17:55:14: 9000000 INFO @ Sun, 21 Jun 2020 17:55:15: 13000000 INFO @ Sun, 21 Jun 2020 17:55:19: 18000000 INFO @ Sun, 21 Jun 2020 17:55:22: 10000000 INFO @ Sun, 21 Jun 2020 17:55:23: 14000000 INFO @ Sun, 21 Jun 2020 17:55:27: 19000000 INFO @ Sun, 21 Jun 2020 17:55:29: 11000000 INFO @ Sun, 21 Jun 2020 17:55:30: 15000000 INFO @ Sun, 21 Jun 2020 17:55:35: 20000000 INFO @ Sun, 21 Jun 2020 17:55:37: 12000000 INFO @ Sun, 21 Jun 2020 17:55:37: 16000000 INFO @ Sun, 21 Jun 2020 17:55:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:55:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:55:38: #1 total tags in treatment: 20493773 INFO @ Sun, 21 Jun 2020 17:55:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:38: #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 17:55:39: #1 tags after filtering in treatment: 20493773 INFO @ Sun, 21 Jun 2020 17:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:41: #2 number of paired peaks: 538 WARNING @ Sun, 21 Jun 2020 17:55:41: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sun, 21 Jun 2020 17:55:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:41: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:55:41: #2 alternative fragment length(s) may be 2,30,584 bps INFO @ Sun, 21 Jun 2020 17:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.05_model.r WARNING @ Sun, 21 Jun 2020 17:55:41: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:55:41: #2 You may need to consider one of the other alternative d(s): 2,30,584 WARNING @ Sun, 21 Jun 2020 17:55:41: #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 17:55:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:44: 13000000 INFO @ Sun, 21 Jun 2020 17:55:45: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:55:51: 14000000 INFO @ Sun, 21 Jun 2020 17:55:53: 18000000 INFO @ Sun, 21 Jun 2020 17:55:59: 15000000 INFO @ Sun, 21 Jun 2020 17:56:00: 19000000 INFO @ Sun, 21 Jun 2020 17:56:06: 16000000 INFO @ Sun, 21 Jun 2020 17:56:08: 20000000 INFO @ Sun, 21 Jun 2020 17:56:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:56:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:56:12: #1 total tags in treatment: 20493773 INFO @ Sun, 21 Jun 2020 17:56:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:12: #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 17:56:13: #1 tags after filtering in treatment: 20493773 INFO @ Sun, 21 Jun 2020 17:56:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:14: 17000000 INFO @ Sun, 21 Jun 2020 17:56:14: #2 number of paired peaks: 538 WARNING @ Sun, 21 Jun 2020 17:56:14: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:14: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:56:14: #2 alternative fragment length(s) may be 2,30,584 bps INFO @ Sun, 21 Jun 2020 17:56:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.10_model.r WARNING @ Sun, 21 Jun 2020 17:56:14: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:56:14: #2 You may need to consider one of the other alternative d(s): 2,30,584 WARNING @ Sun, 21 Jun 2020 17:56:14: #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 17:56:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:21: 18000000 INFO @ Sun, 21 Jun 2020 17:56:28: 19000000 INFO @ Sun, 21 Jun 2020 17:56:35: 20000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.05_summits.bed INFO @ Sun, 21 Jun 2020 17:56:37: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:56:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:56:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:56:39: #1 total tags in treatment: 20493773 INFO @ Sun, 21 Jun 2020 17:56:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:39: #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 17:56:39: #1 tags after filtering in treatment: 20493773 INFO @ Sun, 21 Jun 2020 17:56:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:41: #2 number of paired peaks: 538 WARNING @ Sun, 21 Jun 2020 17:56:41: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:41: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:56:41: #2 alternative fragment length(s) may be 2,30,584 bps INFO @ Sun, 21 Jun 2020 17:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.20_model.r WARNING @ Sun, 21 Jun 2020 17:56:41: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:56:41: #2 You may need to consider one of the other alternative d(s): 2,30,584 WARNING @ Sun, 21 Jun 2020 17:56:41: #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 17:56:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.10_summits.bed INFO @ Sun, 21 Jun 2020 17:57:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:57:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300691/SRX1300691.20_summits.bed INFO @ Sun, 21 Jun 2020 17:57:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling