Job ID = 6459826 SRX = SRX864533 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:42:17 prefetch.2.10.7: 1) Downloading 'SRR1785673'... 2020-06-21T13:42:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:45:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:45:14 prefetch.2.10.7: 'SRR1785673' is valid 2020-06-21T13:45:14 prefetch.2.10.7: 1) 'SRR1785673' was downloaded successfully 2020-06-21T13:45:14 prefetch.2.10.7: 'SRR1785673' has 0 unresolved dependencies Read 6446090 spots for SRR1785673/SRR1785673.sra Written 6446090 spots for SRR1785673/SRR1785673.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: 00:04:14 6446090 reads; of these: 6446090 (100.00%) were unpaired; of these: 156052 (2.42%) aligned 0 times 5484110 (85.08%) aligned exactly 1 time 805928 (12.50%) aligned >1 times 97.58% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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_sort_core] merging from 8 files... [bam_rmdupse_core] 625848 / 6290038 = 0.0995 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 22:53:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.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 22:53:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:53:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:53:45: 1000000 INFO @ Sun, 21 Jun 2020 22:53:52: 2000000 INFO @ Sun, 21 Jun 2020 22:54:00: 3000000 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 22:54:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.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 22:54:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:54:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:54:08: 4000000 INFO @ Sun, 21 Jun 2020 22:54:15: 1000000 INFO @ Sun, 21 Jun 2020 22:54:18: 5000000 INFO @ Sun, 21 Jun 2020 22:54:24: 2000000 INFO @ Sun, 21 Jun 2020 22:54:24: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 22:54:24: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 22:54:24: #1 total tags in treatment: 5664190 INFO @ Sun, 21 Jun 2020 22:54:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:54:24: #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 22:54:24: #1 tags after filtering in treatment: 5663966 INFO @ Sun, 21 Jun 2020 22:54:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:54:24: #1 finished! INFO @ Sun, 21 Jun 2020 22:54:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:54:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:54:25: #2 number of paired peaks: 2429 INFO @ Sun, 21 Jun 2020 22:54:25: start model_add_line... INFO @ Sun, 21 Jun 2020 22:54:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:54:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:54:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:54:25: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 22:54:25: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 22:54:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.05_model.r WARNING @ Sun, 21 Jun 2020 22:54:25: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:54:25: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Sun, 21 Jun 2020 22:54:25: #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 22:54:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:54:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:54:32: 3000000 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 22:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.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 22:54:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:54:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:54:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:54:41: 4000000 INFO @ Sun, 21 Jun 2020 22:54:46: 1000000 INFO @ Sun, 21 Jun 2020 22:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.05_summits.bed INFO @ Sun, 21 Jun 2020 22:54:49: Done! pass1 - making usageList (232 chroms): 2 millis pass2 - checking and writing primary data (7209 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:54:51: 5000000 INFO @ Sun, 21 Jun 2020 22:54:56: 2000000 INFO @ Sun, 21 Jun 2020 22:54:57: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 22:54:57: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 22:54:57: #1 total tags in treatment: 5664190 INFO @ Sun, 21 Jun 2020 22:54:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:54:57: #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 22:54:57: #1 tags after filtering in treatment: 5663966 INFO @ Sun, 21 Jun 2020 22:54:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:54:57: #1 finished! INFO @ Sun, 21 Jun 2020 22:54:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:54:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:54:58: #2 number of paired peaks: 2429 INFO @ Sun, 21 Jun 2020 22:54:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:54:58: start X-correlation... INFO @ Sun, 21 Jun 2020 22:54:58: end of X-cor INFO @ Sun, 21 Jun 2020 22:54:58: #2 finished! INFO @ Sun, 21 Jun 2020 22:54:58: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 22:54:58: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 22:54:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.10_model.r WARNING @ Sun, 21 Jun 2020 22:54:58: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:54:58: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Sun, 21 Jun 2020 22:54:58: #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 22:54:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:54:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:55:06: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:55:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:55:15: 4000000 INFO @ Sun, 21 Jun 2020 22:55:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:55:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:55:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.10_summits.bed INFO @ Sun, 21 Jun 2020 22:55:20: Done! pass1 - making usageList (161 chroms): 2 millis pass2 - checking and writing primary data (4181 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:55:25: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:55:32: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 22:55:32: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 22:55:32: #1 total tags in treatment: 5664190 INFO @ Sun, 21 Jun 2020 22:55:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:55:32: #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 22:55:32: #1 tags after filtering in treatment: 5663966 INFO @ Sun, 21 Jun 2020 22:55:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:55:32: #1 finished! INFO @ Sun, 21 Jun 2020 22:55:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:55:33: #2 number of paired peaks: 2429 INFO @ Sun, 21 Jun 2020 22:55:33: start model_add_line... INFO @ Sun, 21 Jun 2020 22:55:33: start X-correlation... INFO @ Sun, 21 Jun 2020 22:55:33: end of X-cor INFO @ Sun, 21 Jun 2020 22:55:33: #2 finished! INFO @ Sun, 21 Jun 2020 22:55:33: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 22:55:33: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 22:55:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.20_model.r WARNING @ Sun, 21 Jun 2020 22:55:33: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:55:33: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Sun, 21 Jun 2020 22:55:33: #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 22:55:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:55:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:55:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:55:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:55:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:55:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX864533/SRX864533.20_summits.bed INFO @ Sun, 21 Jun 2020 22:55:54: Done! pass1 - making usageList (90 chroms): 1 millis pass2 - checking and writing primary data (1959 records, 4 fields): 6 millis CompletedMACS2peakCalling