Job ID = 6455054 SRX = SRX2642401 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:44:40 prefetch.2.10.7: 1) Downloading 'SRR5345741'... 2020-06-21T09:44:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:45:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:45:15 prefetch.2.10.7: 'SRR5345741' is valid 2020-06-21T09:45:15 prefetch.2.10.7: 1) 'SRR5345741' was downloaded successfully 2020-06-21T09:45:15 prefetch.2.10.7: 'SRR5345741' has 0 unresolved dependencies Read 2599526 spots for SRR5345741/SRR5345741.sra Written 2599526 spots for SRR5345741/SRR5345741.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: 00:01:07 2599526 reads; of these: 2599526 (100.00%) were unpaired; of these: 223313 (8.59%) aligned 0 times 1893727 (72.85%) aligned exactly 1 time 482486 (18.56%) aligned >1 times 91.41% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 45410 / 2376213 = 0.0191 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 18:47:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.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 18:47:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:05: 1000000 INFO @ Sun, 21 Jun 2020 18:48:12: 2000000 INFO @ Sun, 21 Jun 2020 18:48:14: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:48:14: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:48:14: #1 total tags in treatment: 2330803 INFO @ Sun, 21 Jun 2020 18:48:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:14: #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 18:48:15: #1 tags after filtering in treatment: 2330702 INFO @ Sun, 21 Jun 2020 18:48:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:15: #2 number of paired peaks: 1976 INFO @ Sun, 21 Jun 2020 18:48:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:15: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 18:48:15: #2 alternative fragment length(s) may be 155,173,175 bps INFO @ Sun, 21 Jun 2020 18:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.05_model.r WARNING @ Sun, 21 Jun 2020 18:48:15: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:48:15: #2 You may need to consider one of the other alternative d(s): 155,173,175 WARNING @ Sun, 21 Jun 2020 18:48:15: #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 18:48:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.05_summits.bed INFO @ Sun, 21 Jun 2020 18:48:24: Done! pass1 - making usageList (167 chroms): 0 millis pass2 - checking and writing primary data (294 records, 4 fields): 6 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 18:48:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.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 18:48:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:35: 1000000 INFO @ Sun, 21 Jun 2020 18:48:42: 2000000 INFO @ Sun, 21 Jun 2020 18:48:44: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:48:44: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:48:44: #1 total tags in treatment: 2330803 INFO @ Sun, 21 Jun 2020 18:48:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:44: #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 18:48:45: #1 tags after filtering in treatment: 2330702 INFO @ Sun, 21 Jun 2020 18:48:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:45: #2 number of paired peaks: 1976 INFO @ Sun, 21 Jun 2020 18:48:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:45: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:45: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:45: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:45: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 18:48:45: #2 alternative fragment length(s) may be 155,173,175 bps INFO @ Sun, 21 Jun 2020 18:48:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.10_model.r WARNING @ Sun, 21 Jun 2020 18:48:45: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:48:45: #2 You may need to consider one of the other alternative d(s): 155,173,175 WARNING @ Sun, 21 Jun 2020 18:48:45: #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 18:48:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.10_summits.bed INFO @ Sun, 21 Jun 2020 18:48:54: Done! pass1 - making usageList (110 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 5 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 18:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.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 18:48:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:05: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:49:12: 2000000 INFO @ Sun, 21 Jun 2020 18:49:15: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:49:15: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:49:15: #1 total tags in treatment: 2330803 INFO @ Sun, 21 Jun 2020 18:49:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:15: #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 18:49:15: #1 tags after filtering in treatment: 2330702 INFO @ Sun, 21 Jun 2020 18:49:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:16: #2 number of paired peaks: 1976 INFO @ Sun, 21 Jun 2020 18:49:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:16: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 18:49:16: #2 alternative fragment length(s) may be 155,173,175 bps INFO @ Sun, 21 Jun 2020 18:49:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.20_model.r WARNING @ Sun, 21 Jun 2020 18:49:16: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:16: #2 You may need to consider one of the other alternative d(s): 155,173,175 WARNING @ Sun, 21 Jun 2020 18:49:16: #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 18:49:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:49:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642401/SRX2642401.20_summits.bed INFO @ Sun, 21 Jun 2020 18:49:24: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 3 millis CompletedMACS2peakCalling