Job ID = 6459053 SRX = SRX6386734 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:52:10 prefetch.2.10.7: 1) Downloading 'SRR9624466'... 2020-06-21T12:52:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:54:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:54:18 prefetch.2.10.7: 'SRR9624466' is valid 2020-06-21T12:54:18 prefetch.2.10.7: 1) 'SRR9624466' was downloaded successfully Read 12576928 spots for SRR9624466/SRR9624466.sra Written 12576928 spots for SRR9624466/SRR9624466.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: 00:01:36 12576928 reads; of these: 12576928 (100.00%) were unpaired; of these: 9572894 (76.11%) aligned 0 times 2185432 (17.38%) aligned exactly 1 time 818602 (6.51%) aligned >1 times 23.89% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 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_rmdupse_core] 1103250 / 3004034 = 0.3673 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 21:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.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 21:57:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:47: 1000000 INFO @ Sun, 21 Jun 2020 21:57:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:57:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:57:53: #1 total tags in treatment: 1900784 INFO @ Sun, 21 Jun 2020 21:57:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:57:53: #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 21:57:53: #1 tags after filtering in treatment: 1900616 INFO @ Sun, 21 Jun 2020 21:57:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:57:53: #1 finished! INFO @ Sun, 21 Jun 2020 21:57:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:57:53: #2 number of paired peaks: 1263 INFO @ Sun, 21 Jun 2020 21:57:53: start model_add_line... INFO @ Sun, 21 Jun 2020 21:57:53: start X-correlation... INFO @ Sun, 21 Jun 2020 21:57:53: end of X-cor INFO @ Sun, 21 Jun 2020 21:57:53: #2 finished! INFO @ Sun, 21 Jun 2020 21:57:53: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 21:57:53: #2 alternative fragment length(s) may be 64 bps INFO @ Sun, 21 Jun 2020 21:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.05_model.r WARNING @ Sun, 21 Jun 2020 21:57:53: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:57:53: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sun, 21 Jun 2020 21:57:53: #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 21:57:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:57:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.05_summits.bed INFO @ Sun, 21 Jun 2020 21:58:00: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (1439 records, 4 fields): 14 millis CompletedMACS2peakCalling 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 21:58:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.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 21:58:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:17: 1000000 INFO @ Sun, 21 Jun 2020 21:58:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:58:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:58:23: #1 total tags in treatment: 1900784 INFO @ Sun, 21 Jun 2020 21:58:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:23: #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 21:58:23: #1 tags after filtering in treatment: 1900616 INFO @ Sun, 21 Jun 2020 21:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:23: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:23: #2 number of paired peaks: 1263 INFO @ Sun, 21 Jun 2020 21:58:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:23: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:23: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:23: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 21:58:23: #2 alternative fragment length(s) may be 64 bps INFO @ Sun, 21 Jun 2020 21:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.10_model.r WARNING @ Sun, 21 Jun 2020 21:58:23: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:23: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sun, 21 Jun 2020 21:58:23: #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 21:58:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.10_summits.bed INFO @ Sun, 21 Jun 2020 21:58:30: Done! pass1 - making usageList (296 chroms): 1 millis pass2 - checking and writing primary data (542 records, 4 fields): 8 millis CompletedMACS2peakCalling 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 21:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.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 21:58:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:47: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:58:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:58:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:58:53: #1 total tags in treatment: 1900784 INFO @ Sun, 21 Jun 2020 21:58:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:53: #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 21:58:53: #1 tags after filtering in treatment: 1900616 INFO @ Sun, 21 Jun 2020 21:58:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:53: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:53: #2 number of paired peaks: 1263 INFO @ Sun, 21 Jun 2020 21:58:53: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:53: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:53: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:53: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:53: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 21:58:53: #2 alternative fragment length(s) may be 64 bps INFO @ Sun, 21 Jun 2020 21:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.20_model.r WARNING @ Sun, 21 Jun 2020 21:58:53: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:53: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sun, 21 Jun 2020 21:58:53: #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 21:58:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386734/SRX6386734.20_summits.bed INFO @ Sun, 21 Jun 2020 21:59:00: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 4 millis CompletedMACS2peakCalling