Job ID = 6453999 SRX = SRX1760703 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:53:49 prefetch.2.10.7: 1) Downloading 'SRR3503063'... 2020-06-21T08:53:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:56:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:56:05 prefetch.2.10.7: 'SRR3503063' is valid 2020-06-21T08:56:05 prefetch.2.10.7: 1) 'SRR3503063' was downloaded successfully 2020-06-21T08:56:05 prefetch.2.10.7: 'SRR3503063' has 0 unresolved dependencies Read 3874955 spots for SRR3503063/SRR3503063.sra Written 3874955 spots for SRR3503063/SRR3503063.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: 00:04:24 3874955 reads; of these: 3874955 (100.00%) were unpaired; of these: 939054 (24.23%) aligned 0 times 1629627 (42.06%) aligned exactly 1 time 1306274 (33.71%) aligned >1 times 75.77% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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] 194226 / 2935901 = 0.0662 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 18:02:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.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 18:02:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:03:03: 1000000 INFO @ Sun, 21 Jun 2020 18:03:12: 2000000 INFO @ Sun, 21 Jun 2020 18:03:19: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:03:19: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:03:19: #1 total tags in treatment: 2741675 INFO @ Sun, 21 Jun 2020 18:03:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:03:19: #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 18:03:19: #1 tags after filtering in treatment: 2741461 INFO @ Sun, 21 Jun 2020 18:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:03:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:03:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:03:19: #2 number of paired peaks: 2371 INFO @ Sun, 21 Jun 2020 18:03:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:03:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:03:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:03:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:03:19: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 18:03:19: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 18:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.05_model.r WARNING @ Sun, 21 Jun 2020 18:03:19: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:03:19: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Sun, 21 Jun 2020 18:03:19: #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 18:03:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:03:19: #3 Pre-compute pvalue-qvalue table... 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 18:03:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.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 18:03:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:03:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:03:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.05_summits.bed INFO @ Sun, 21 Jun 2020 18:03:30: Done! pass1 - making usageList (693 chroms): 1 millis pass2 - checking and writing primary data (1804 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:03:31: 1000000 INFO @ Sun, 21 Jun 2020 18:03:40: 2000000 INFO @ Sun, 21 Jun 2020 18:03:46: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:03:46: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:03:46: #1 total tags in treatment: 2741675 INFO @ Sun, 21 Jun 2020 18:03:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:03:46: #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 18:03:46: #1 tags after filtering in treatment: 2741461 INFO @ Sun, 21 Jun 2020 18:03:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:03:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:03:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:03:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:03:47: #2 number of paired peaks: 2371 INFO @ Sun, 21 Jun 2020 18:03:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:03:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:03:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:03:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:03:47: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 18:03:47: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 18:03:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.10_model.r WARNING @ Sun, 21 Jun 2020 18:03:47: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:03:47: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Sun, 21 Jun 2020 18:03:47: #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 18:03:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:03:47: #3 Pre-compute pvalue-qvalue table... 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 18:03:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.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 18:03:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:03:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:03:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:03:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.10_summits.bed INFO @ Sun, 21 Jun 2020 18:03:57: Done! pass1 - making usageList (625 chroms): 1 millis pass2 - checking and writing primary data (1341 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:04:01: 1000000 INFO @ Sun, 21 Jun 2020 18:04:10: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:04:16: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:04:16: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:04:16: #1 total tags in treatment: 2741675 INFO @ Sun, 21 Jun 2020 18:04:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:04:16: #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 18:04:16: #1 tags after filtering in treatment: 2741461 INFO @ Sun, 21 Jun 2020 18:04:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:04:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:04:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:04:17: #2 number of paired peaks: 2371 INFO @ Sun, 21 Jun 2020 18:04:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:04:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:04:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:04:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:04:17: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 18:04:17: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 18:04:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.20_model.r WARNING @ Sun, 21 Jun 2020 18:04:17: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:04:17: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Sun, 21 Jun 2020 18:04:17: #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 18:04:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:04:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:04:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:04:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:04:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760703/SRX1760703.20_summits.bed INFO @ Sun, 21 Jun 2020 18:04:27: Done! pass1 - making usageList (502 chroms): 1 millis pass2 - checking and writing primary data (829 records, 4 fields): 14 millis CompletedMACS2peakCalling