Job ID = 6455284 SRX = SRX287662 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:05:55 prefetch.2.10.7: 1) Downloading 'SRR869850'... 2020-06-21T10:05:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:11:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:11:17 prefetch.2.10.7: 1) 'SRR869850' was downloaded successfully Read 21425213 spots for SRR869850/SRR869850.sra Written 21425213 spots for SRR869850/SRR869850.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:53 21425213 reads; of these: 21425213 (100.00%) were unpaired; of these: 5522129 (25.77%) aligned 0 times 5814752 (27.14%) aligned exactly 1 time 10088332 (47.09%) aligned >1 times 74.23% overall alignment rate Time searching: 00:09:54 Overall time: 00:09:54 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] 9158830 / 15903084 = 0.5759 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 19:26:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.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 19:26:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:04: 1000000 INFO @ Sun, 21 Jun 2020 19:27:11: 2000000 INFO @ Sun, 21 Jun 2020 19:27:18: 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 19:27:26: 4000000 INFO @ Sun, 21 Jun 2020 19:27:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.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 19:27:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:34: 5000000 INFO @ Sun, 21 Jun 2020 19:27:35: 1000000 INFO @ Sun, 21 Jun 2020 19:27:42: 6000000 INFO @ Sun, 21 Jun 2020 19:27:42: 2000000 INFO @ Sun, 21 Jun 2020 19:27:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:49: #1 total tags in treatment: 6744254 INFO @ Sun, 21 Jun 2020 19:27:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:49: #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 19:27:49: #1 tags after filtering in treatment: 6744252 INFO @ Sun, 21 Jun 2020 19:27:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:50: 3000000 INFO @ Sun, 21 Jun 2020 19:27:50: #2 number of paired peaks: 1517 INFO @ Sun, 21 Jun 2020 19:27:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:50: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:27:50: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 19:27:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.05_model.r WARNING @ Sun, 21 Jun 2020 19:27:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:27:50: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 19:27:50: #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 19:27:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:50: #3 Pre-compute pvalue-qvalue table... 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 19:27:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.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 19:27:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:57: 4000000 INFO @ Sun, 21 Jun 2020 19:28:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:04: 1000000 INFO @ Sun, 21 Jun 2020 19:28:04: 5000000 INFO @ Sun, 21 Jun 2020 19:28:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.05_summits.bed INFO @ Sun, 21 Jun 2020 19:28:10: Done! pass1 - making usageList (758 chroms): 2 millis pass2 - checking and writing primary data (3033 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:12: 2000000 INFO @ Sun, 21 Jun 2020 19:28:13: 6000000 INFO @ Sun, 21 Jun 2020 19:28:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:18: #1 total tags in treatment: 6744254 INFO @ Sun, 21 Jun 2020 19:28:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:18: #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 19:28:19: 3000000 INFO @ Sun, 21 Jun 2020 19:28:19: #1 tags after filtering in treatment: 6744252 INFO @ Sun, 21 Jun 2020 19:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:20: #2 number of paired peaks: 1517 INFO @ Sun, 21 Jun 2020 19:28:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:20: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:28:20: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 19:28:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.10_model.r WARNING @ Sun, 21 Jun 2020 19:28:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:20: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 19:28:20: #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 19:28:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:26: 4000000 INFO @ Sun, 21 Jun 2020 19:28:33: 5000000 INFO @ Sun, 21 Jun 2020 19:28:33: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.10_summits.bed INFO @ Sun, 21 Jun 2020 19:28:40: Done! INFO @ Sun, 21 Jun 2020 19:28:40: 6000000 pass1 - making usageList (586 chroms): 2 millis pass2 - checking and writing primary data (2182 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:46: #1 total tags in treatment: 6744254 INFO @ Sun, 21 Jun 2020 19:28:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:46: #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 19:28:46: #1 tags after filtering in treatment: 6744252 INFO @ Sun, 21 Jun 2020 19:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:47: #2 number of paired peaks: 1517 INFO @ Sun, 21 Jun 2020 19:28:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:47: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:28:47: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 19:28:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.20_model.r WARNING @ Sun, 21 Jun 2020 19:28:47: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:47: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 19:28:47: #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 19:28:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:29:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287662/SRX287662.20_summits.bed INFO @ Sun, 21 Jun 2020 19:29:07: Done! pass1 - making usageList (462 chroms): 2 millis pass2 - checking and writing primary data (1370 records, 4 fields): 26 millis CompletedMACS2peakCalling