Job ID = 6508826 SRX = SRX495195 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:18:58 prefetch.2.10.7: 1) Downloading 'SRR1198700'... 2020-06-26T15:18:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:20:47 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:20:47 prefetch.2.10.7: 1) 'SRR1198700' was downloaded successfully Read 19141145 spots for SRR1198700/SRR1198700.sra Written 19141145 spots for SRR1198700/SRR1198700.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: 00:03:40 19141145 reads; of these: 19141145 (100.00%) were unpaired; of these: 2487340 (12.99%) aligned 0 times 14907493 (77.88%) aligned exactly 1 time 1746312 (9.12%) aligned >1 times 87.01% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 3109662 / 16653805 = 0.1867 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 @ Sat, 27 Jun 2020 00:29:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.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 @ Sat, 27 Jun 2020 00:29:48: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:29:48: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:29:55: 1000000 INFO @ Sat, 27 Jun 2020 00:30:02: 2000000 INFO @ Sat, 27 Jun 2020 00:30:09: 3000000 INFO @ Sat, 27 Jun 2020 00:30:16: 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 @ Sat, 27 Jun 2020 00:30:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.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 @ Sat, 27 Jun 2020 00:30:18: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:30:18: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:30:24: 5000000 INFO @ Sat, 27 Jun 2020 00:30:26: 1000000 INFO @ Sat, 27 Jun 2020 00:30:31: 6000000 INFO @ Sat, 27 Jun 2020 00:30:33: 2000000 INFO @ Sat, 27 Jun 2020 00:30:38: 7000000 INFO @ Sat, 27 Jun 2020 00:30:40: 3000000 INFO @ Sat, 27 Jun 2020 00:30:46: 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 @ Sat, 27 Jun 2020 00:30:47: 4000000 INFO @ Sat, 27 Jun 2020 00:30:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.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 @ Sat, 27 Jun 2020 00:30:48: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:30:48: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:30:54: 9000000 INFO @ Sat, 27 Jun 2020 00:30:54: 5000000 INFO @ Sat, 27 Jun 2020 00:30:56: 1000000 INFO @ Sat, 27 Jun 2020 00:31:02: 10000000 INFO @ Sat, 27 Jun 2020 00:31:02: 6000000 INFO @ Sat, 27 Jun 2020 00:31:04: 2000000 INFO @ Sat, 27 Jun 2020 00:31:09: 7000000 INFO @ Sat, 27 Jun 2020 00:31:10: 11000000 INFO @ Sat, 27 Jun 2020 00:31:12: 3000000 INFO @ Sat, 27 Jun 2020 00:31:16: 8000000 INFO @ Sat, 27 Jun 2020 00:31:18: 12000000 INFO @ Sat, 27 Jun 2020 00:31:20: 4000000 INFO @ Sat, 27 Jun 2020 00:31:24: 9000000 INFO @ Sat, 27 Jun 2020 00:31:26: 13000000 INFO @ Sat, 27 Jun 2020 00:31:28: 5000000 INFO @ Sat, 27 Jun 2020 00:31:30: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:31:30: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:31:30: #1 total tags in treatment: 13544143 INFO @ Sat, 27 Jun 2020 00:31:30: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:31:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:31:31: 10000000 INFO @ Sat, 27 Jun 2020 00:31:31: #1 tags after filtering in treatment: 13544071 INFO @ Sat, 27 Jun 2020 00:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:31:31: #1 finished! INFO @ Sat, 27 Jun 2020 00:31:31: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:31:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:31:32: #2 number of paired peaks: 121 WARNING @ Sat, 27 Jun 2020 00:31:32: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 27 Jun 2020 00:31:32: start model_add_line... INFO @ Sat, 27 Jun 2020 00:31:32: start X-correlation... INFO @ Sat, 27 Jun 2020 00:31:32: end of X-cor INFO @ Sat, 27 Jun 2020 00:31:32: #2 finished! INFO @ Sat, 27 Jun 2020 00:31:32: #2 predicted fragment length is 9 bps INFO @ Sat, 27 Jun 2020 00:31:32: #2 alternative fragment length(s) may be 4,9,36,66 bps INFO @ Sat, 27 Jun 2020 00:31:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.05_model.r WARNING @ Sat, 27 Jun 2020 00:31:32: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:31:32: #2 You may need to consider one of the other alternative d(s): 4,9,36,66 WARNING @ Sat, 27 Jun 2020 00:31:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:31:32: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:31:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:31:35: 6000000 INFO @ Sat, 27 Jun 2020 00:31:39: 11000000 INFO @ Sat, 27 Jun 2020 00:31:43: 7000000 INFO @ Sat, 27 Jun 2020 00:31:46: 12000000 INFO @ Sat, 27 Jun 2020 00:31:51: 8000000 INFO @ Sat, 27 Jun 2020 00:31:53: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:31:57: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:31:57: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:31:57: #1 total tags in treatment: 13544143 INFO @ Sat, 27 Jun 2020 00:31:57: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:31:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:31:58: #1 tags after filtering in treatment: 13544071 INFO @ Sat, 27 Jun 2020 00:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:31:58: #1 finished! INFO @ Sat, 27 Jun 2020 00:31:58: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:31:59: 9000000 INFO @ Sat, 27 Jun 2020 00:31:59: #2 number of paired peaks: 121 WARNING @ Sat, 27 Jun 2020 00:31:59: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 27 Jun 2020 00:31:59: start model_add_line... INFO @ Sat, 27 Jun 2020 00:31:59: start X-correlation... INFO @ Sat, 27 Jun 2020 00:31:59: end of X-cor INFO @ Sat, 27 Jun 2020 00:31:59: #2 finished! INFO @ Sat, 27 Jun 2020 00:31:59: #2 predicted fragment length is 9 bps INFO @ Sat, 27 Jun 2020 00:31:59: #2 alternative fragment length(s) may be 4,9,36,66 bps INFO @ Sat, 27 Jun 2020 00:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.10_model.r WARNING @ Sat, 27 Jun 2020 00:31:59: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:31:59: #2 You may need to consider one of the other alternative d(s): 4,9,36,66 WARNING @ Sat, 27 Jun 2020 00:31:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:31:59: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:32:00: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:32:06: 10000000 INFO @ Sat, 27 Jun 2020 00:32:14: 11000000 INFO @ Sat, 27 Jun 2020 00:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.05_summits.bed INFO @ Sat, 27 Jun 2020 00:32:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:32:21: 12000000 INFO @ Sat, 27 Jun 2020 00:32:27: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:32:29: 13000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:32:33: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:32:33: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:32:33: #1 total tags in treatment: 13544143 INFO @ Sat, 27 Jun 2020 00:32:33: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:32:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:32:33: #1 tags after filtering in treatment: 13544071 INFO @ Sat, 27 Jun 2020 00:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:32:33: #1 finished! INFO @ Sat, 27 Jun 2020 00:32:33: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:32:34: #2 number of paired peaks: 121 WARNING @ Sat, 27 Jun 2020 00:32:34: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 27 Jun 2020 00:32:34: start model_add_line... INFO @ Sat, 27 Jun 2020 00:32:34: start X-correlation... INFO @ Sat, 27 Jun 2020 00:32:34: end of X-cor INFO @ Sat, 27 Jun 2020 00:32:34: #2 finished! INFO @ Sat, 27 Jun 2020 00:32:34: #2 predicted fragment length is 9 bps INFO @ Sat, 27 Jun 2020 00:32:34: #2 alternative fragment length(s) may be 4,9,36,66 bps INFO @ Sat, 27 Jun 2020 00:32:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.20_model.r WARNING @ Sat, 27 Jun 2020 00:32:34: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:32:34: #2 You may need to consider one of the other alternative d(s): 4,9,36,66 WARNING @ Sat, 27 Jun 2020 00:32:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:32:34: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:32:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:32:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:32:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:32:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.10_summits.bed INFO @ Sat, 27 Jun 2020 00:32:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:33:04: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:33:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:33:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:33:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495195/SRX495195.20_summits.bed INFO @ Sat, 27 Jun 2020 00:33:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling