Job ID = 6455231 SRX = SRX287576 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:56:10 prefetch.2.10.7: 1) Downloading 'SRR869719'... 2020-06-21T09:56:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:59:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:59:11 prefetch.2.10.7: 'SRR869719' is valid 2020-06-21T09:59:11 prefetch.2.10.7: 1) 'SRR869719' was downloaded successfully Read 13358141 spots for SRR869719/SRR869719.sra Written 13358141 spots for SRR869719/SRR869719.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: 00:04:46 13358141 reads; of these: 13358141 (100.00%) were unpaired; of these: 838015 (6.27%) aligned 0 times 5844034 (43.75%) aligned exactly 1 time 6676092 (49.98%) aligned >1 times 93.73% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 2601071 / 12520126 = 0.2078 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 19:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.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 19:08:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:05: 1000000 INFO @ Sun, 21 Jun 2020 19:08:10: 2000000 INFO @ Sun, 21 Jun 2020 19:08:15: 3000000 INFO @ Sun, 21 Jun 2020 19:08:20: 4000000 INFO @ Sun, 21 Jun 2020 19:08:25: 5000000 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 19:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.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 19:08:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:30: 6000000 INFO @ Sun, 21 Jun 2020 19:08:36: 1000000 INFO @ Sun, 21 Jun 2020 19:08:36: 7000000 INFO @ Sun, 21 Jun 2020 19:08:41: 2000000 INFO @ Sun, 21 Jun 2020 19:08:41: 8000000 INFO @ Sun, 21 Jun 2020 19:08:46: 3000000 INFO @ Sun, 21 Jun 2020 19:08:47: 9000000 INFO @ Sun, 21 Jun 2020 19:08:52: 4000000 INFO @ Sun, 21 Jun 2020 19:08:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:08:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:08:52: #1 total tags in treatment: 9919055 INFO @ Sun, 21 Jun 2020 19:08:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:52: #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 19:08:52: #1 tags after filtering in treatment: 9919052 INFO @ Sun, 21 Jun 2020 19:08:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:53: #2 number of paired peaks: 2101 INFO @ Sun, 21 Jun 2020 19:08:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:53: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 19:08:53: #2 alternative fragment length(s) may be 4,55,591 bps INFO @ Sun, 21 Jun 2020 19:08:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.05_model.r WARNING @ Sun, 21 Jun 2020 19:08:53: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:08:53: #2 You may need to consider one of the other alternative d(s): 4,55,591 WARNING @ Sun, 21 Jun 2020 19:08:53: #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 19:08:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:57: 5000000 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 19:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.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 19:09:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:02: 6000000 INFO @ Sun, 21 Jun 2020 19:09:06: 1000000 INFO @ Sun, 21 Jun 2020 19:09:07: 7000000 INFO @ Sun, 21 Jun 2020 19:09:11: 2000000 INFO @ Sun, 21 Jun 2020 19:09:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:13: 8000000 INFO @ Sun, 21 Jun 2020 19:09:16: 3000000 INFO @ Sun, 21 Jun 2020 19:09:19: 9000000 INFO @ Sun, 21 Jun 2020 19:09:22: 4000000 INFO @ Sun, 21 Jun 2020 19:09:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.05_summits.bed INFO @ Sun, 21 Jun 2020 19:09:22: Done! pass1 - making usageList (1076 chroms): 1 millis pass2 - checking and writing primary data (5646 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:24: #1 total tags in treatment: 9919055 INFO @ Sun, 21 Jun 2020 19:09:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:24: #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 19:09:24: #1 tags after filtering in treatment: 9919052 INFO @ Sun, 21 Jun 2020 19:09:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:25: #2 number of paired peaks: 2101 INFO @ Sun, 21 Jun 2020 19:09:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:25: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 19:09:25: #2 alternative fragment length(s) may be 4,55,591 bps INFO @ Sun, 21 Jun 2020 19:09:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.10_model.r WARNING @ Sun, 21 Jun 2020 19:09:25: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:25: #2 You may need to consider one of the other alternative d(s): 4,55,591 WARNING @ Sun, 21 Jun 2020 19:09:25: #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 19:09:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:27: 5000000 INFO @ Sun, 21 Jun 2020 19:09:32: 6000000 INFO @ Sun, 21 Jun 2020 19:09:38: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:09:43: 8000000 INFO @ Sun, 21 Jun 2020 19:09:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:48: 9000000 INFO @ Sun, 21 Jun 2020 19:09:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:53: #1 total tags in treatment: 9919055 INFO @ Sun, 21 Jun 2020 19:09:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:53: #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 19:09:54: #1 tags after filtering in treatment: 9919052 INFO @ Sun, 21 Jun 2020 19:09:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:54: #2 number of paired peaks: 2101 INFO @ Sun, 21 Jun 2020 19:09:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:54: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 19:09:54: #2 alternative fragment length(s) may be 4,55,591 bps INFO @ Sun, 21 Jun 2020 19:09:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.20_model.r WARNING @ Sun, 21 Jun 2020 19:09:54: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:54: #2 You may need to consider one of the other alternative d(s): 4,55,591 WARNING @ Sun, 21 Jun 2020 19:09:54: #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 19:09:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.10_summits.bed INFO @ Sun, 21 Jun 2020 19:09:56: Done! pass1 - making usageList (802 chroms): 1 millis pass2 - checking and writing primary data (3225 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287576/SRX287576.20_summits.bed INFO @ Sun, 21 Jun 2020 19:10:24: Done! pass1 - making usageList (471 chroms): 1 millis pass2 - checking and writing primary data (1169 records, 4 fields): 13 millis CompletedMACS2peakCalling