Job ID = 6457902 SRX = SRX485208 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:03:04 prefetch.2.10.7: 1) Downloading 'SRR1187966'... 2020-06-21T12:03:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:06:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:06:13 prefetch.2.10.7: 1) 'SRR1187966' was downloaded successfully 2020-06-21T12:06:13 prefetch.2.10.7: 'SRR1187966' has 0 unresolved dependencies Read 19281031 spots for SRR1187966/SRR1187966.sra Written 19281031 spots for SRR1187966/SRR1187966.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: 00:03:35 19281031 reads; of these: 19281031 (100.00%) were unpaired; of these: 10602239 (54.99%) aligned 0 times 6011903 (31.18%) aligned exactly 1 time 2666889 (13.83%) aligned >1 times 45.01% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 4828672 / 8678792 = 0.5564 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 21:13:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.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 21:13:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:13:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:13:27: 1000000 INFO @ Sun, 21 Jun 2020 21:13:34: 2000000 INFO @ Sun, 21 Jun 2020 21:13:40: 3000000 INFO @ Sun, 21 Jun 2020 21:13:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:13:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:13:46: #1 total tags in treatment: 3850120 INFO @ Sun, 21 Jun 2020 21:13:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:46: #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 21:13:46: #1 tags after filtering in treatment: 3849980 INFO @ Sun, 21 Jun 2020 21:13:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:47: #2 number of paired peaks: 2916 INFO @ Sun, 21 Jun 2020 21:13:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:47: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 21:13:47: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 21:13:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.05_model.r WARNING @ Sun, 21 Jun 2020 21:13:47: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:13:47: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 21:13:47: #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 21:13:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:47: #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 21:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.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 21:13:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:13:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:13:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:13:58: 1000000 INFO @ Sun, 21 Jun 2020 21:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.05_summits.bed INFO @ Sun, 21 Jun 2020 21:14:02: Done! pass1 - making usageList (667 chroms): 1 millis pass2 - checking and writing primary data (3170 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:14:04: 2000000 INFO @ Sun, 21 Jun 2020 21:14:10: 3000000 INFO @ Sun, 21 Jun 2020 21:14:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:14:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:14:16: #1 total tags in treatment: 3850120 INFO @ Sun, 21 Jun 2020 21:14:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:14:16: #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 21:14:16: #1 tags after filtering in treatment: 3849980 INFO @ Sun, 21 Jun 2020 21:14:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:14:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:14:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:14:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:14:17: #2 number of paired peaks: 2916 INFO @ Sun, 21 Jun 2020 21:14:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:14:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:14:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:14:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:14:17: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 21:14:17: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 21:14:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.10_model.r WARNING @ Sun, 21 Jun 2020 21:14:17: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:14:17: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 21:14:17: #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 21:14:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:14:17: #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 21:14:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.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 21:14:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:28: 1000000 INFO @ Sun, 21 Jun 2020 21:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.10_summits.bed INFO @ Sun, 21 Jun 2020 21:14:33: Done! pass1 - making usageList (400 chroms): 2 millis pass2 - checking and writing primary data (1189 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:14:34: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:14:40: 3000000 INFO @ Sun, 21 Jun 2020 21:14:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:14:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:14:46: #1 total tags in treatment: 3850120 INFO @ Sun, 21 Jun 2020 21:14:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:14:46: #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 21:14:46: #1 tags after filtering in treatment: 3849980 INFO @ Sun, 21 Jun 2020 21:14:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:14:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:14:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:14:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:14:47: #2 number of paired peaks: 2916 INFO @ Sun, 21 Jun 2020 21:14:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:14:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:14:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:14:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:14:47: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 21:14:47: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 21:14:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.20_model.r WARNING @ Sun, 21 Jun 2020 21:14:47: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:14:47: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 21:14:47: #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 21:14:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:14:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:14:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:15:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:15:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:15:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485208/SRX485208.20_summits.bed INFO @ Sun, 21 Jun 2020 21:15:02: Done! pass1 - making usageList (176 chroms): 1 millis pass2 - checking and writing primary data (360 records, 4 fields): 13 millis CompletedMACS2peakCalling