Job ID = 6454596 SRX = SRX2385059 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:25:59 prefetch.2.10.7: 1) Downloading 'SRR5064690'... 2020-06-21T09:25:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:27:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:27:58 prefetch.2.10.7: 'SRR5064690' is valid 2020-06-21T09:27:58 prefetch.2.10.7: 1) 'SRR5064690' was downloaded successfully 2020-06-21T09:27:58 prefetch.2.10.7: 'SRR5064690' has 0 unresolved dependencies Read 20501669 spots for SRR5064690/SRR5064690.sra Written 20501669 spots for SRR5064690/SRR5064690.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: 00:05:25 20501669 reads; of these: 20501669 (100.00%) were unpaired; of these: 778919 (3.80%) aligned 0 times 14415866 (70.32%) aligned exactly 1 time 5306884 (25.89%) aligned >1 times 96.20% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 3288634 / 19722750 = 0.1667 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 18:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.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 18:38:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:32: 1000000 INFO @ Sun, 21 Jun 2020 18:38:38: 2000000 INFO @ Sun, 21 Jun 2020 18:38:44: 3000000 INFO @ Sun, 21 Jun 2020 18:38:49: 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 18:38:55: 5000000 INFO @ Sun, 21 Jun 2020 18:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.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 18:38:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:02: 6000000 INFO @ Sun, 21 Jun 2020 18:39:03: 1000000 INFO @ Sun, 21 Jun 2020 18:39:09: 7000000 INFO @ Sun, 21 Jun 2020 18:39:10: 2000000 INFO @ Sun, 21 Jun 2020 18:39:15: 8000000 INFO @ Sun, 21 Jun 2020 18:39:16: 3000000 INFO @ Sun, 21 Jun 2020 18:39:22: 9000000 INFO @ Sun, 21 Jun 2020 18:39:23: 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 18:39:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.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 18:39:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:29: 10000000 INFO @ Sun, 21 Jun 2020 18:39:30: 5000000 INFO @ Sun, 21 Jun 2020 18:39:33: 1000000 INFO @ Sun, 21 Jun 2020 18:39:36: 11000000 INFO @ Sun, 21 Jun 2020 18:39:37: 6000000 INFO @ Sun, 21 Jun 2020 18:39:40: 2000000 INFO @ Sun, 21 Jun 2020 18:39:43: 12000000 INFO @ Sun, 21 Jun 2020 18:39:44: 7000000 INFO @ Sun, 21 Jun 2020 18:39:47: 3000000 INFO @ Sun, 21 Jun 2020 18:39:50: 13000000 INFO @ Sun, 21 Jun 2020 18:39:51: 8000000 INFO @ Sun, 21 Jun 2020 18:39:53: 4000000 INFO @ Sun, 21 Jun 2020 18:39:57: 14000000 INFO @ Sun, 21 Jun 2020 18:39:57: 9000000 INFO @ Sun, 21 Jun 2020 18:40:00: 5000000 INFO @ Sun, 21 Jun 2020 18:40:04: 15000000 INFO @ Sun, 21 Jun 2020 18:40:04: 10000000 INFO @ Sun, 21 Jun 2020 18:40:07: 6000000 INFO @ Sun, 21 Jun 2020 18:40:11: 16000000 INFO @ Sun, 21 Jun 2020 18:40:11: 11000000 INFO @ Sun, 21 Jun 2020 18:40:14: 7000000 INFO @ Sun, 21 Jun 2020 18:40:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:14: #1 total tags in treatment: 16434116 INFO @ Sun, 21 Jun 2020 18:40:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:14: #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 18:40:14: #1 tags after filtering in treatment: 16434116 INFO @ Sun, 21 Jun 2020 18:40:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:15: #2 number of paired peaks: 190 WARNING @ Sun, 21 Jun 2020 18:40:15: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sun, 21 Jun 2020 18:40:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:16: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:40:16: #2 alternative fragment length(s) may be 2,45,546,569 bps INFO @ Sun, 21 Jun 2020 18:40:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.05_model.r WARNING @ Sun, 21 Jun 2020 18:40:16: #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 18:40:16: #2 You may need to consider one of the other alternative d(s): 2,45,546,569 WARNING @ Sun, 21 Jun 2020 18:40:16: #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 18:40:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:18: 12000000 INFO @ Sun, 21 Jun 2020 18:40:20: 8000000 INFO @ Sun, 21 Jun 2020 18:40:24: 13000000 INFO @ Sun, 21 Jun 2020 18:40:27: 9000000 INFO @ Sun, 21 Jun 2020 18:40:32: 14000000 INFO @ Sun, 21 Jun 2020 18:40:34: 10000000 INFO @ Sun, 21 Jun 2020 18:40:38: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:40:40: 11000000 INFO @ Sun, 21 Jun 2020 18:40:45: 16000000 INFO @ Sun, 21 Jun 2020 18:40:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:47: 12000000 INFO @ Sun, 21 Jun 2020 18:40:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:48: #1 total tags in treatment: 16434116 INFO @ Sun, 21 Jun 2020 18:40:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:48: #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 18:40:49: #1 tags after filtering in treatment: 16434116 INFO @ Sun, 21 Jun 2020 18:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:50: #2 number of paired peaks: 190 WARNING @ Sun, 21 Jun 2020 18:40:50: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sun, 21 Jun 2020 18:40:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:50: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:40:50: #2 alternative fragment length(s) may be 2,45,546,569 bps INFO @ Sun, 21 Jun 2020 18:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.10_model.r WARNING @ Sun, 21 Jun 2020 18:40:50: #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 18:40:50: #2 You may need to consider one of the other alternative d(s): 2,45,546,569 WARNING @ Sun, 21 Jun 2020 18:40:50: #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 18:40:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:53: 13000000 INFO @ Sun, 21 Jun 2020 18:40:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.05_summits.bed INFO @ Sun, 21 Jun 2020 18:40:59: Done! INFO @ Sun, 21 Jun 2020 18:40:59: 14000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:41:05: 15000000 INFO @ Sun, 21 Jun 2020 18:41:11: 16000000 INFO @ Sun, 21 Jun 2020 18:41:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:41:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:41:14: #1 total tags in treatment: 16434116 INFO @ Sun, 21 Jun 2020 18:41:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:14: #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 18:41:14: #1 tags after filtering in treatment: 16434116 INFO @ Sun, 21 Jun 2020 18:41:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:15: #2 number of paired peaks: 190 WARNING @ Sun, 21 Jun 2020 18:41:15: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sun, 21 Jun 2020 18:41:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:16: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:41:16: #2 alternative fragment length(s) may be 2,45,546,569 bps INFO @ Sun, 21 Jun 2020 18:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.20_model.r WARNING @ Sun, 21 Jun 2020 18:41:16: #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 18:41:16: #2 You may need to consider one of the other alternative d(s): 2,45,546,569 WARNING @ Sun, 21 Jun 2020 18:41:16: #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 18:41:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:41:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.10_summits.bed INFO @ Sun, 21 Jun 2020 18:41:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:41:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2385059/SRX2385059.20_summits.bed INFO @ Sun, 21 Jun 2020 18:41:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling