Job ID = 6453857 SRX = SRX1531761 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:35:39 prefetch.2.10.7: 1) Downloading 'SRR3102819'... 2020-06-21T08:35:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:41:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:41:14 prefetch.2.10.7: 1) 'SRR3102819' was downloaded successfully Read 28924023 spots for SRR3102819/SRR3102819.sra Written 28924023 spots for SRR3102819/SRR3102819.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:20 28924023 reads; of these: 28924023 (100.00%) were unpaired; of these: 13489313 (46.64%) aligned 0 times 10017601 (34.63%) aligned exactly 1 time 5417109 (18.73%) aligned >1 times 53.36% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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] 4433038 / 15434710 = 0.2872 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 17:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.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 17:54:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:53: 1000000 INFO @ Sun, 21 Jun 2020 17:54:59: 2000000 INFO @ Sun, 21 Jun 2020 17:55:04: 3000000 INFO @ Sun, 21 Jun 2020 17:55:09: 4000000 INFO @ Sun, 21 Jun 2020 17:55:14: 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 17:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.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 17:55:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:19: 6000000 INFO @ Sun, 21 Jun 2020 17:55:24: 1000000 INFO @ Sun, 21 Jun 2020 17:55:25: 7000000 INFO @ Sun, 21 Jun 2020 17:55:29: 2000000 INFO @ Sun, 21 Jun 2020 17:55:31: 8000000 INFO @ Sun, 21 Jun 2020 17:55:34: 3000000 INFO @ Sun, 21 Jun 2020 17:55:37: 9000000 INFO @ Sun, 21 Jun 2020 17:55:40: 4000000 INFO @ Sun, 21 Jun 2020 17:55:42: 10000000 INFO @ Sun, 21 Jun 2020 17:55:45: 5000000 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 17:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.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 17:55:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:48: 11000000 INFO @ Sun, 21 Jun 2020 17:55:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:55:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:55:48: #1 total tags in treatment: 11001672 INFO @ Sun, 21 Jun 2020 17:55:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:48: #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 17:55:49: #1 tags after filtering in treatment: 11001672 INFO @ Sun, 21 Jun 2020 17:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:50: #2 number of paired peaks: 857 WARNING @ Sun, 21 Jun 2020 17:55:50: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Sun, 21 Jun 2020 17:55:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:50: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 17:55:50: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 17:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.05_model.r WARNING @ Sun, 21 Jun 2020 17:55:50: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:55:50: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 17:55:50: #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 17:55:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:50: 6000000 INFO @ Sun, 21 Jun 2020 17:55:53: 1000000 INFO @ Sun, 21 Jun 2020 17:55:55: 7000000 INFO @ Sun, 21 Jun 2020 17:55:58: 2000000 INFO @ Sun, 21 Jun 2020 17:56:00: 8000000 INFO @ Sun, 21 Jun 2020 17:56:03: 3000000 INFO @ Sun, 21 Jun 2020 17:56:06: 9000000 INFO @ Sun, 21 Jun 2020 17:56:08: 4000000 INFO @ Sun, 21 Jun 2020 17:56:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:12: 10000000 INFO @ Sun, 21 Jun 2020 17:56:13: 5000000 INFO @ Sun, 21 Jun 2020 17:56:18: 11000000 INFO @ Sun, 21 Jun 2020 17:56:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:56:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:56:18: #1 total tags in treatment: 11001672 INFO @ Sun, 21 Jun 2020 17:56:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:18: #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 17:56:18: 6000000 INFO @ Sun, 21 Jun 2020 17:56:19: #1 tags after filtering in treatment: 11001672 INFO @ Sun, 21 Jun 2020 17:56:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:19: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:20: #2 number of paired peaks: 857 WARNING @ Sun, 21 Jun 2020 17:56:20: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:20: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.05_summits.bed INFO @ Sun, 21 Jun 2020 17:56:20: Done! INFO @ Sun, 21 Jun 2020 17:56:20: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:20: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:20: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:20: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 17:56:20: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 17:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.10_model.r WARNING @ Sun, 21 Jun 2020 17:56:20: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:56:20: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 17:56:20: #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 17:56:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:20: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (585 chroms): 2 millis pass2 - checking and writing primary data (2120 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:56:23: 7000000 INFO @ Sun, 21 Jun 2020 17:56:28: 8000000 INFO @ Sun, 21 Jun 2020 17:56:34: 9000000 INFO @ Sun, 21 Jun 2020 17:56:39: 10000000 INFO @ Sun, 21 Jun 2020 17:56:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:45: 11000000 INFO @ Sun, 21 Jun 2020 17:56:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:56:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:56:45: #1 total tags in treatment: 11001672 INFO @ Sun, 21 Jun 2020 17:56:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:45: #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 17:56:46: #1 tags after filtering in treatment: 11001672 INFO @ Sun, 21 Jun 2020 17:56:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:46: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:46: #2 number of paired peaks: 857 WARNING @ Sun, 21 Jun 2020 17:56:46: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:46: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:47: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:47: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:47: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:47: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 17:56:47: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 17:56:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.20_model.r WARNING @ Sun, 21 Jun 2020 17:56:47: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:56:47: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 17:56:47: #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 17:56:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.10_summits.bed INFO @ Sun, 21 Jun 2020 17:56:50: Done! pass1 - making usageList (518 chroms): 1 millis pass2 - checking and writing primary data (1867 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:57:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531761/SRX1531761.20_summits.bed INFO @ Sun, 21 Jun 2020 17:57:16: Done! pass1 - making usageList (407 chroms): 1 millis pass2 - checking and writing primary data (1003 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。