Job ID = 6454298 SRX = SRX197570 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:01:05 prefetch.2.10.7: 1) Downloading 'SRR596998'... 2020-06-21T09:01:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:02:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:03:00 prefetch.2.10.7: 'SRR596998' is valid 2020-06-21T09:03:00 prefetch.2.10.7: 1) 'SRR596998' was downloaded successfully Read 20339444 spots for SRR596998/SRR596998.sra Written 20339444 spots for SRR596998/SRR596998.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: 00:04:11 20339444 reads; of these: 20339444 (100.00%) were unpaired; of these: 6483474 (31.88%) aligned 0 times 9956286 (48.95%) aligned exactly 1 time 3899684 (19.17%) aligned >1 times 68.12% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 4737456 / 13855970 = 0.3419 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 18:11:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.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 18:11:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:28: 1000000 INFO @ Sun, 21 Jun 2020 18:11:34: 2000000 INFO @ Sun, 21 Jun 2020 18:11:39: 3000000 INFO @ Sun, 21 Jun 2020 18:11:45: 4000000 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 18:11:50: 5000000 INFO @ Sun, 21 Jun 2020 18:11:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.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 18:11:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:56: 6000000 INFO @ Sun, 21 Jun 2020 18:11:59: 1000000 INFO @ Sun, 21 Jun 2020 18:12:02: 7000000 INFO @ Sun, 21 Jun 2020 18:12:05: 2000000 INFO @ Sun, 21 Jun 2020 18:12:08: 8000000 INFO @ Sun, 21 Jun 2020 18:12:12: 3000000 INFO @ Sun, 21 Jun 2020 18:12:14: 9000000 INFO @ Sun, 21 Jun 2020 18:12:15: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:12:15: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:12:15: #1 total tags in treatment: 9118514 INFO @ Sun, 21 Jun 2020 18:12:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:15: #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 18:12:15: #1 tags after filtering in treatment: 9118514 INFO @ Sun, 21 Jun 2020 18:12:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:12:16: #2 number of paired peaks: 1133 INFO @ Sun, 21 Jun 2020 18:12:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:12:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:16: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 18:12:16: #2 alternative fragment length(s) may be 3,48,88 bps INFO @ Sun, 21 Jun 2020 18:12:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.05_model.r WARNING @ Sun, 21 Jun 2020 18:12:16: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:12:16: #2 You may need to consider one of the other alternative d(s): 3,48,88 WARNING @ Sun, 21 Jun 2020 18:12:16: #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 18:12:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:12:18: 4000000 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 18:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.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 18:12:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:12:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:12:24: 5000000 INFO @ Sun, 21 Jun 2020 18:12:28: 1000000 INFO @ Sun, 21 Jun 2020 18:12:30: 6000000 INFO @ Sun, 21 Jun 2020 18:12:34: 2000000 INFO @ Sun, 21 Jun 2020 18:12:36: 7000000 INFO @ Sun, 21 Jun 2020 18:12:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:12:40: 3000000 INFO @ Sun, 21 Jun 2020 18:12:43: 8000000 INFO @ Sun, 21 Jun 2020 18:12:46: 4000000 INFO @ Sun, 21 Jun 2020 18:12:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:12:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:12:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.05_summits.bed INFO @ Sun, 21 Jun 2020 18:12:48: Done! pass1 - making usageList (642 chroms): 1 millis pass2 - checking and writing primary data (2979 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:12:50: 9000000 INFO @ Sun, 21 Jun 2020 18:12:51: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:12:51: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:12:51: #1 total tags in treatment: 9118514 INFO @ Sun, 21 Jun 2020 18:12:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:51: #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 18:12:52: #1 tags after filtering in treatment: 9118514 INFO @ Sun, 21 Jun 2020 18:12:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:52: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:12:52: 5000000 INFO @ Sun, 21 Jun 2020 18:12:52: #2 number of paired peaks: 1133 INFO @ Sun, 21 Jun 2020 18:12:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:12:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:52: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 18:12:52: #2 alternative fragment length(s) may be 3,48,88 bps INFO @ Sun, 21 Jun 2020 18:12:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.10_model.r WARNING @ Sun, 21 Jun 2020 18:12:52: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:12:52: #2 You may need to consider one of the other alternative d(s): 3,48,88 WARNING @ Sun, 21 Jun 2020 18:12:52: #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 18:12:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:12:57: 6000000 INFO @ Sun, 21 Jun 2020 18:13:03: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:13:09: 8000000 INFO @ Sun, 21 Jun 2020 18:13:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:15: 9000000 INFO @ Sun, 21 Jun 2020 18:13:16: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:13:16: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:13:16: #1 total tags in treatment: 9118514 INFO @ Sun, 21 Jun 2020 18:13:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:13:16: #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 18:13:16: #1 tags after filtering in treatment: 9118514 INFO @ Sun, 21 Jun 2020 18:13:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:13:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:13:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:13:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:13:17: #2 number of paired peaks: 1133 INFO @ Sun, 21 Jun 2020 18:13:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:13:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:13:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:13:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:13:17: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 18:13:17: #2 alternative fragment length(s) may be 3,48,88 bps INFO @ Sun, 21 Jun 2020 18:13:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.20_model.r WARNING @ Sun, 21 Jun 2020 18:13:17: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:13:17: #2 You may need to consider one of the other alternative d(s): 3,48,88 WARNING @ Sun, 21 Jun 2020 18:13:17: #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 18:13:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:13:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:13:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:13:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:13:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.10_summits.bed INFO @ Sun, 21 Jun 2020 18:13:24: Done! pass1 - making usageList (520 chroms): 2 millis pass2 - checking and writing primary data (2187 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:13:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:13:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:13:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197570/SRX197570.20_summits.bed INFO @ Sun, 21 Jun 2020 18:13:49: Done! pass1 - making usageList (346 chroms): 1 millis pass2 - checking and writing primary data (914 records, 4 fields): 13 millis CompletedMACS2peakCalling