Job ID = 6453953 SRX = SRX170983 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:43:33 prefetch.2.10.7: 1) Downloading 'SRR527322'... 2020-06-21T08:43:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:57:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:57:22 prefetch.2.10.7: 1) 'SRR527322' was downloaded successfully Read 47460072 spots for SRR527322/SRR527322.sra Written 47460072 spots for SRR527322/SRR527322.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: 00:00:01 Multiseed full-index search: 00:10:18 47460072 reads; of these: 47460072 (100.00%) were unpaired; of these: 26861834 (56.60%) aligned 0 times 15081372 (31.78%) aligned exactly 1 time 5516866 (11.62%) aligned >1 times 43.40% overall alignment rate Time searching: 00:10:19 Overall time: 00:10:19 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 12 files... [bam_rmdupse_core] 12812464 / 20598238 = 0.6220 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 18:15:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.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 18:15:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:33: 1000000 INFO @ Sun, 21 Jun 2020 18:15:40: 2000000 INFO @ Sun, 21 Jun 2020 18:15:46: 3000000 INFO @ Sun, 21 Jun 2020 18:15:52: 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 18:15:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.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 18:15:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:59: 5000000 INFO @ Sun, 21 Jun 2020 18:16:04: 1000000 INFO @ Sun, 21 Jun 2020 18:16:06: 6000000 INFO @ Sun, 21 Jun 2020 18:16:10: 2000000 INFO @ Sun, 21 Jun 2020 18:16:12: 7000000 INFO @ Sun, 21 Jun 2020 18:16:16: 3000000 INFO @ Sun, 21 Jun 2020 18:16:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:16:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:16:18: #1 total tags in treatment: 7785774 INFO @ Sun, 21 Jun 2020 18:16:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:18: #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 18:16:18: #1 tags after filtering in treatment: 7785692 INFO @ Sun, 21 Jun 2020 18:16:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:19: #2 number of paired peaks: 3138 INFO @ Sun, 21 Jun 2020 18:16:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:19: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 18:16:19: #2 alternative fragment length(s) may be 4,64 bps INFO @ Sun, 21 Jun 2020 18:16:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.05_model.r WARNING @ Sun, 21 Jun 2020 18:16:19: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:16:19: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Sun, 21 Jun 2020 18:16:19: #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 18:16:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:16:22: 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 18:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.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 18:16:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:28: 5000000 INFO @ Sun, 21 Jun 2020 18:16:34: 1000000 INFO @ Sun, 21 Jun 2020 18:16:35: 6000000 INFO @ Sun, 21 Jun 2020 18:16:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:40: 2000000 INFO @ Sun, 21 Jun 2020 18:16:41: 7000000 INFO @ Sun, 21 Jun 2020 18:16:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.05_summits.bed INFO @ Sun, 21 Jun 2020 18:16:45: Done! pass1 - making usageList (769 chroms): 3 millis pass2 - checking and writing primary data (5605 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:16:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:16:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:16:46: #1 total tags in treatment: 7785774 INFO @ Sun, 21 Jun 2020 18:16:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:46: #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 18:16:46: 3000000 INFO @ Sun, 21 Jun 2020 18:16:47: #1 tags after filtering in treatment: 7785692 INFO @ Sun, 21 Jun 2020 18:16:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:47: #2 number of paired peaks: 3138 INFO @ Sun, 21 Jun 2020 18:16:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:48: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 18:16:48: #2 alternative fragment length(s) may be 4,64 bps INFO @ Sun, 21 Jun 2020 18:16:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.10_model.r WARNING @ Sun, 21 Jun 2020 18:16:48: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:16:48: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Sun, 21 Jun 2020 18:16:48: #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 18:16:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:16:53: 4000000 INFO @ Sun, 21 Jun 2020 18:16:59: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:17:06: 6000000 INFO @ Sun, 21 Jun 2020 18:17:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:12: 7000000 INFO @ Sun, 21 Jun 2020 18:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.10_summits.bed INFO @ Sun, 21 Jun 2020 18:17:15: Done! pass1 - making usageList (635 chroms): 3 millis pass2 - checking and writing primary data (3225 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:17:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:17:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:17:17: #1 total tags in treatment: 7785774 INFO @ Sun, 21 Jun 2020 18:17:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:17: #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 18:17:17: #1 tags after filtering in treatment: 7785692 INFO @ Sun, 21 Jun 2020 18:17:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:18: #2 number of paired peaks: 3138 INFO @ Sun, 21 Jun 2020 18:17:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:18: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 18:17:18: #2 alternative fragment length(s) may be 4,64 bps INFO @ Sun, 21 Jun 2020 18:17:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.20_model.r WARNING @ Sun, 21 Jun 2020 18:17:18: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:17:18: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Sun, 21 Jun 2020 18:17:18: #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 18:17:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:17:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX170983/SRX170983.20_summits.bed INFO @ Sun, 21 Jun 2020 18:17:44: Done! pass1 - making usageList (379 chroms): 2 millis pass2 - checking and writing primary data (1269 records, 4 fields): 13 millis CompletedMACS2peakCalling