Job ID = 6457979 SRX = SRX4933886 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:08:51 prefetch.2.10.7: 1) Downloading 'SRR8107276'... 2020-06-21T12:08:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:10:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:10:14 prefetch.2.10.7: 'SRR8107276' is valid 2020-06-21T12:10:14 prefetch.2.10.7: 1) 'SRR8107276' was downloaded successfully 2020-06-21T12:10:14 prefetch.2.10.7: 'SRR8107276' has 0 unresolved dependencies Read 9792526 spots for SRR8107276/SRR8107276.sra Written 9792526 spots for SRR8107276/SRR8107276.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: 00:02:49 9792526 reads; of these: 9792526 (100.00%) were unpaired; of these: 611441 (6.24%) aligned 0 times 6748757 (68.92%) aligned exactly 1 time 2432328 (24.84%) aligned >1 times 93.76% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 3984175 / 9181085 = 0.4340 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 21:16:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.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 21:16:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:16:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:16:55: 1000000 INFO @ Sun, 21 Jun 2020 21:17:03: 2000000 INFO @ Sun, 21 Jun 2020 21:17:10: 3000000 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 21:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.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 21:17:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:17:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:17:19: 4000000 INFO @ Sun, 21 Jun 2020 21:17:24: 1000000 INFO @ Sun, 21 Jun 2020 21:17:27: 5000000 INFO @ Sun, 21 Jun 2020 21:17:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:17:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:17:29: #1 total tags in treatment: 5196910 INFO @ Sun, 21 Jun 2020 21:17:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:29: #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 21:17:30: #1 tags after filtering in treatment: 5196894 INFO @ Sun, 21 Jun 2020 21:17:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:30: #2 number of paired peaks: 1060 INFO @ Sun, 21 Jun 2020 21:17:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:30: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:17:30: #2 alternative fragment length(s) may be 4,72,89,113,142 bps INFO @ Sun, 21 Jun 2020 21:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.05_model.r WARNING @ Sun, 21 Jun 2020 21:17:30: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:17:30: #2 You may need to consider one of the other alternative d(s): 4,72,89,113,142 WARNING @ Sun, 21 Jun 2020 21:17:30: #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 21:17:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:17:32: 2000000 INFO @ Sun, 21 Jun 2020 21:17:40: 3000000 INFO @ Sun, 21 Jun 2020 21:17:41: #3 Call peaks for each chromosome... 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 21:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.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 21:17:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:17:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:17:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.05_summits.bed INFO @ Sun, 21 Jun 2020 21:17:47: Done! INFO @ Sun, 21 Jun 2020 21:17:48: 4000000 pass1 - making usageList (602 chroms): 2 millis pass2 - checking and writing primary data (2089 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:17:54: 1000000 INFO @ Sun, 21 Jun 2020 21:17:56: 5000000 INFO @ Sun, 21 Jun 2020 21:17:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:17:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:17:57: #1 total tags in treatment: 5196910 INFO @ Sun, 21 Jun 2020 21:17:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:57: #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 21:17:58: #1 tags after filtering in treatment: 5196894 INFO @ Sun, 21 Jun 2020 21:17:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:59: #2 number of paired peaks: 1060 INFO @ Sun, 21 Jun 2020 21:17:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:59: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:17:59: #2 alternative fragment length(s) may be 4,72,89,113,142 bps INFO @ Sun, 21 Jun 2020 21:17:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.10_model.r WARNING @ Sun, 21 Jun 2020 21:17:59: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:17:59: #2 You may need to consider one of the other alternative d(s): 4,72,89,113,142 WARNING @ Sun, 21 Jun 2020 21:17:59: #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 21:17:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:18:01: 2000000 INFO @ Sun, 21 Jun 2020 21:18:09: 3000000 INFO @ Sun, 21 Jun 2020 21:18:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.10_summits.bed INFO @ Sun, 21 Jun 2020 21:18:16: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (432 chroms): 1 millis pass2 - checking and writing primary data (943 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:18:16: 4000000 INFO @ Sun, 21 Jun 2020 21:18:24: 5000000 INFO @ Sun, 21 Jun 2020 21:18:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:18:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:18:26: #1 total tags in treatment: 5196910 INFO @ Sun, 21 Jun 2020 21:18:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:18:26: #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 21:18:26: #1 tags after filtering in treatment: 5196894 INFO @ Sun, 21 Jun 2020 21:18:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:18:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:18:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:18:27: #2 number of paired peaks: 1060 INFO @ Sun, 21 Jun 2020 21:18:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:18:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:18:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:18:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:18:27: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:18:27: #2 alternative fragment length(s) may be 4,72,89,113,142 bps INFO @ Sun, 21 Jun 2020 21:18:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.20_model.r WARNING @ Sun, 21 Jun 2020 21:18:27: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:18:27: #2 You may need to consider one of the other alternative d(s): 4,72,89,113,142 WARNING @ Sun, 21 Jun 2020 21:18:27: #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 21:18:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:18:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:18:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933886/SRX4933886.20_summits.bed INFO @ Sun, 21 Jun 2020 21:18:44: Done! pass1 - making usageList (131 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 11 millis CompletedMACS2peakCalling