Job ID = 6456867 SRX = SRX403435 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:17:39 prefetch.2.10.7: 1) Downloading 'SRR1066650'... 2020-06-21T11:17:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:18:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:18:40 prefetch.2.10.7: 'SRR1066650' is valid 2020-06-21T11:18:40 prefetch.2.10.7: 1) 'SRR1066650' was downloaded successfully Read 5666340 spots for SRR1066650/SRR1066650.sra Written 5666340 spots for SRR1066650/SRR1066650.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: 00:01:33 5666340 reads; of these: 5666340 (100.00%) were unpaired; of these: 1081309 (19.08%) aligned 0 times 2847493 (50.25%) aligned exactly 1 time 1737538 (30.66%) aligned >1 times 80.92% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 883150 / 4585031 = 0.1926 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 20:21:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.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 20:21:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:21:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:21:59: 1000000 INFO @ Sun, 21 Jun 2020 20:22:04: 2000000 INFO @ Sun, 21 Jun 2020 20:22:09: 3000000 INFO @ Sun, 21 Jun 2020 20:22:13: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:22:13: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:22:13: #1 total tags in treatment: 3701881 INFO @ Sun, 21 Jun 2020 20:22:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:22:13: #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 20:22:13: #1 tags after filtering in treatment: 3701876 INFO @ Sun, 21 Jun 2020 20:22:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:22:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:22:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:22:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:22:14: #2 number of paired peaks: 1062 INFO @ Sun, 21 Jun 2020 20:22:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:22:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:22:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:22:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:22:14: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 20:22:14: #2 alternative fragment length(s) may be 4,42,592 bps INFO @ Sun, 21 Jun 2020 20:22:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.05_model.r WARNING @ Sun, 21 Jun 2020 20:22:14: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:22:14: #2 You may need to consider one of the other alternative d(s): 4,42,592 WARNING @ Sun, 21 Jun 2020 20:22:14: #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 20:22:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:22:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:22:22: #3 Call peaks for each chromosome... 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 20:22:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.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 20:22:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:22:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:22:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.05_summits.bed INFO @ Sun, 21 Jun 2020 20:22:26: Done! pass1 - making usageList (521 chroms): 1 millis pass2 - checking and writing primary data (1576 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:22:30: 1000000 INFO @ Sun, 21 Jun 2020 20:22:35: 2000000 INFO @ Sun, 21 Jun 2020 20:22:41: 3000000 INFO @ Sun, 21 Jun 2020 20:22:46: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:22:46: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:22:46: #1 total tags in treatment: 3701881 INFO @ Sun, 21 Jun 2020 20:22:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:22:46: #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 20:22:46: #1 tags after filtering in treatment: 3701876 INFO @ Sun, 21 Jun 2020 20:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:22:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:22:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:22:46: #2 number of paired peaks: 1062 INFO @ Sun, 21 Jun 2020 20:22:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:22:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:22:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:22:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:22:46: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 20:22:46: #2 alternative fragment length(s) may be 4,42,592 bps INFO @ Sun, 21 Jun 2020 20:22:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.10_model.r WARNING @ Sun, 21 Jun 2020 20:22:46: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:22:46: #2 You may need to consider one of the other alternative d(s): 4,42,592 WARNING @ Sun, 21 Jun 2020 20:22:46: #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 20:22:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:22:46: #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 20:22:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.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 20:22:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:22:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:22:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:22:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.10_summits.bed INFO @ Sun, 21 Jun 2020 20:22:59: Done! INFO @ Sun, 21 Jun 2020 20:22:59: 1000000 pass1 - making usageList (219 chroms): 2 millis pass2 - checking and writing primary data (418 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:23:04: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:23:09: 3000000 INFO @ Sun, 21 Jun 2020 20:23:13: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:23:13: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:23:13: #1 total tags in treatment: 3701881 INFO @ Sun, 21 Jun 2020 20:23:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:13: #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 20:23:13: #1 tags after filtering in treatment: 3701876 INFO @ Sun, 21 Jun 2020 20:23:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:14: #2 number of paired peaks: 1062 INFO @ Sun, 21 Jun 2020 20:23:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:14: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 20:23:14: #2 alternative fragment length(s) may be 4,42,592 bps INFO @ Sun, 21 Jun 2020 20:23:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.20_model.r WARNING @ Sun, 21 Jun 2020 20:23:14: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:23:14: #2 You may need to consider one of the other alternative d(s): 4,42,592 WARNING @ Sun, 21 Jun 2020 20:23:14: #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 20:23:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:23:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX403435/SRX403435.20_summits.bed INFO @ Sun, 21 Jun 2020 20:23:26: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 3 millis CompletedMACS2peakCalling