Job ID = 6453255 SRX = SRX110773 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:44:32 prefetch.2.10.7: 1) Downloading 'SRR388355'... 2020-06-21T08:44:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:54:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:54:08 prefetch.2.10.7: 1) 'SRR388355' was downloaded successfully Read 41597480 spots for SRR388355/SRR388355.sra Written 41597480 spots for SRR388355/SRR388355.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: 00:05:14 41597480 reads; of these: 41597480 (100.00%) were unpaired; of these: 31033541 (74.60%) aligned 0 times 7875368 (18.93%) aligned exactly 1 time 2688571 (6.46%) aligned >1 times 25.40% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 2034461 / 10563939 = 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 18:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.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 18:05:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:26: 1000000 INFO @ Sun, 21 Jun 2020 18:05:33: 2000000 INFO @ Sun, 21 Jun 2020 18:05:39: 3000000 INFO @ Sun, 21 Jun 2020 18:05:45: 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 18:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.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 18:05:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:51: 5000000 INFO @ Sun, 21 Jun 2020 18:05:57: 1000000 INFO @ Sun, 21 Jun 2020 18:05:58: 6000000 INFO @ Sun, 21 Jun 2020 18:06:04: 2000000 INFO @ Sun, 21 Jun 2020 18:06:06: 7000000 INFO @ Sun, 21 Jun 2020 18:06:11: 3000000 INFO @ Sun, 21 Jun 2020 18:06:13: 8000000 INFO @ Sun, 21 Jun 2020 18:06:17: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:06:17: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:06:17: #1 total tags in treatment: 8529478 INFO @ Sun, 21 Jun 2020 18:06:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:06:17: #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 18:06:17: 4000000 INFO @ Sun, 21 Jun 2020 18:06:17: #1 tags after filtering in treatment: 8529463 INFO @ Sun, 21 Jun 2020 18:06:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:06:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:06:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:06:17: #2 looking for paired plus/minus strand peaks... 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 18:06:18: #2 number of paired peaks: 2067 INFO @ Sun, 21 Jun 2020 18:06:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:18: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 18:06:18: #2 alternative fragment length(s) may be 84 bps INFO @ Sun, 21 Jun 2020 18:06:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.05_model.r WARNING @ Sun, 21 Jun 2020 18:06:18: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:06:18: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sun, 21 Jun 2020 18:06:18: #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 18:06:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.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 18:06:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:24: 5000000 INFO @ Sun, 21 Jun 2020 18:06:26: 1000000 INFO @ Sun, 21 Jun 2020 18:06:30: 6000000 INFO @ Sun, 21 Jun 2020 18:06:33: 2000000 INFO @ Sun, 21 Jun 2020 18:06:38: 7000000 INFO @ Sun, 21 Jun 2020 18:06:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:06:39: 3000000 INFO @ Sun, 21 Jun 2020 18:06:45: 8000000 INFO @ Sun, 21 Jun 2020 18:06:45: 4000000 INFO @ Sun, 21 Jun 2020 18:06:49: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:06:49: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:06:49: #1 total tags in treatment: 8529478 INFO @ Sun, 21 Jun 2020 18:06:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:06:49: #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 18:06:49: #1 tags after filtering in treatment: 8529463 INFO @ Sun, 21 Jun 2020 18:06:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:06:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:06:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:06:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:06:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:06:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.05_summits.bed INFO @ Sun, 21 Jun 2020 18:06:49: Done! pass1 - making usageList (434 chroms): 2 millis pass2 - checking and writing primary data (6050 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:06:50: #2 number of paired peaks: 2067 INFO @ Sun, 21 Jun 2020 18:06:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:50: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 18:06:50: #2 alternative fragment length(s) may be 84 bps INFO @ Sun, 21 Jun 2020 18:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.10_model.r WARNING @ Sun, 21 Jun 2020 18:06:50: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:06:50: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sun, 21 Jun 2020 18:06:50: #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 18:06:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:06:51: 5000000 INFO @ Sun, 21 Jun 2020 18:06:57: 6000000 INFO @ Sun, 21 Jun 2020 18:07:04: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:07:10: 8000000 INFO @ Sun, 21 Jun 2020 18:07:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:13: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:07:13: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:07:13: #1 total tags in treatment: 8529478 INFO @ Sun, 21 Jun 2020 18:07:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:13: #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 18:07:14: #1 tags after filtering in treatment: 8529463 INFO @ Sun, 21 Jun 2020 18:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:15: #2 number of paired peaks: 2067 INFO @ Sun, 21 Jun 2020 18:07:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:15: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 18:07:15: #2 alternative fragment length(s) may be 84 bps INFO @ Sun, 21 Jun 2020 18:07:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.20_model.r WARNING @ Sun, 21 Jun 2020 18:07:15: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:07:15: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sun, 21 Jun 2020 18:07:15: #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 18:07:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.10_summits.bed INFO @ Sun, 21 Jun 2020 18:07:20: Done! pass1 - making usageList (206 chroms): 1 millis pass2 - checking and writing primary data (3832 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:07:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110773/SRX110773.20_summits.bed INFO @ Sun, 21 Jun 2020 18:07:43: Done! pass1 - making usageList (114 chroms): 2 millis pass2 - checking and writing primary data (2299 records, 4 fields): 9 millis CompletedMACS2peakCalling