Job ID = 6458897 SRX = SRX5775906 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:51:40 prefetch.2.10.7: 1) Downloading 'SRR8997109'... 2020-06-21T12:51:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:57:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:57:12 prefetch.2.10.7: 1) 'SRR8997109' was downloaded successfully Read 20215194 spots for SRR8997109/SRR8997109.sra Written 20215194 spots for SRR8997109/SRR8997109.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: 00:04:56 20215194 reads; of these: 20215194 (100.00%) were unpaired; of these: 11011699 (54.47%) aligned 0 times 6556655 (32.43%) aligned exactly 1 time 2646840 (13.09%) aligned >1 times 45.53% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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] 5672382 / 9203495 = 0.6163 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 22:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.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 22:05:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:05:57: 1000000 INFO @ Sun, 21 Jun 2020 22:06:04: 2000000 INFO @ Sun, 21 Jun 2020 22:06:11: 3000000 INFO @ Sun, 21 Jun 2020 22:06:15: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:06:15: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:06:15: #1 total tags in treatment: 3531113 INFO @ Sun, 21 Jun 2020 22:06:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:15: #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 22:06:15: #1 tags after filtering in treatment: 3531096 INFO @ Sun, 21 Jun 2020 22:06:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:15: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:16: #2 number of paired peaks: 1383 INFO @ Sun, 21 Jun 2020 22:06:16: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:16: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:16: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:16: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:16: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 22:06:16: #2 alternative fragment length(s) may be 75 bps INFO @ Sun, 21 Jun 2020 22:06:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.05_model.r WARNING @ Sun, 21 Jun 2020 22:06:16: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:06:16: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sun, 21 Jun 2020 22:06:16: #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 22:06:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:16: #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 22:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.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 22:06:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:27: 1000000 INFO @ Sun, 21 Jun 2020 22:06:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.05_summits.bed INFO @ Sun, 21 Jun 2020 22:06:28: Done! pass1 - making usageList (646 chroms): 2 millis pass2 - checking and writing primary data (1970 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:34: 2000000 INFO @ Sun, 21 Jun 2020 22:06:42: 3000000 INFO @ Sun, 21 Jun 2020 22:06:45: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:06:45: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:06:45: #1 total tags in treatment: 3531113 INFO @ Sun, 21 Jun 2020 22:06:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:45: #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 22:06:46: #1 tags after filtering in treatment: 3531096 INFO @ Sun, 21 Jun 2020 22:06:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:46: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:46: #2 number of paired peaks: 1383 INFO @ Sun, 21 Jun 2020 22:06:46: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:46: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:46: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:46: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:46: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 22:06:46: #2 alternative fragment length(s) may be 75 bps INFO @ Sun, 21 Jun 2020 22:06:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.10_model.r WARNING @ Sun, 21 Jun 2020 22:06:46: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:06:46: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sun, 21 Jun 2020 22:06:46: #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 22:06:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:46: #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 22:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.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 22:06:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:57: 1000000 INFO @ Sun, 21 Jun 2020 22:06:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.10_summits.bed INFO @ Sun, 21 Jun 2020 22:06:59: Done! pass1 - making usageList (519 chroms): 1 millis pass2 - checking and writing primary data (1414 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:07:04: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:07:11: 3000000 INFO @ Sun, 21 Jun 2020 22:07:15: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:07:15: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:07:15: #1 total tags in treatment: 3531113 INFO @ Sun, 21 Jun 2020 22:07:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:15: #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 22:07:16: #1 tags after filtering in treatment: 3531096 INFO @ Sun, 21 Jun 2020 22:07:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:16: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:16: #2 number of paired peaks: 1383 INFO @ Sun, 21 Jun 2020 22:07:16: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:16: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:16: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:16: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:16: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 22:07:16: #2 alternative fragment length(s) may be 75 bps INFO @ Sun, 21 Jun 2020 22:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.20_model.r WARNING @ Sun, 21 Jun 2020 22:07:16: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:07:16: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sun, 21 Jun 2020 22:07:16: #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 22:07:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:07:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:07:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775906/SRX5775906.20_summits.bed INFO @ Sun, 21 Jun 2020 22:07:29: Done! pass1 - making usageList (388 chroms): 1 millis pass2 - checking and writing primary data (842 records, 4 fields): 12 millis CompletedMACS2peakCalling