Job ID = 6458427 SRX = SRX5226986 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:28:22 prefetch.2.10.7: 1) Downloading 'SRR8417901'... 2020-06-21T12:28:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:29:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:29:11 prefetch.2.10.7: 'SRR8417901' is valid 2020-06-21T12:29:11 prefetch.2.10.7: 1) 'SRR8417901' was downloaded successfully 2020-06-21T12:29:11 prefetch.2.10.7: 'SRR8417901' has 0 unresolved dependencies Read 3461881 spots for SRR8417901/SRR8417901.sra Written 3461881 spots for SRR8417901/SRR8417901.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: 00:01:30 3461881 reads; of these: 3461881 (100.00%) were unpaired; of these: 682965 (19.73%) aligned 0 times 1517677 (43.84%) aligned exactly 1 time 1261239 (36.43%) aligned >1 times 80.27% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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] 468129 / 2778916 = 0.1685 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 21:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.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 21:32:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:27: 1000000 INFO @ Sun, 21 Jun 2020 21:32:34: 2000000 INFO @ Sun, 21 Jun 2020 21:32:36: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:32:36: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:32:36: #1 total tags in treatment: 2310787 INFO @ Sun, 21 Jun 2020 21:32:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:36: #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 21:32:36: #1 tags after filtering in treatment: 2310504 INFO @ Sun, 21 Jun 2020 21:32:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:37: #2 number of paired peaks: 2782 INFO @ Sun, 21 Jun 2020 21:32:37: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:37: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:37: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 21:32:37: #2 alternative fragment length(s) may be 111,551 bps INFO @ Sun, 21 Jun 2020 21:32:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.05_model.r WARNING @ Sun, 21 Jun 2020 21:32:37: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:32:37: #2 You may need to consider one of the other alternative d(s): 111,551 WARNING @ Sun, 21 Jun 2020 21:32:37: #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 21:32:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.05_summits.bed INFO @ Sun, 21 Jun 2020 21:32:46: Done! pass1 - making usageList (583 chroms): 2 millis pass2 - checking and writing primary data (2043 records, 4 fields): 16 millis CompletedMACS2peakCalling 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 21:32:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.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 21:32:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:57: 1000000 INFO @ Sun, 21 Jun 2020 21:33:03: 2000000 INFO @ Sun, 21 Jun 2020 21:33:05: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:33:05: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:33:05: #1 total tags in treatment: 2310787 INFO @ Sun, 21 Jun 2020 21:33:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:05: #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 21:33:06: #1 tags after filtering in treatment: 2310504 INFO @ Sun, 21 Jun 2020 21:33:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:06: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:06: #2 number of paired peaks: 2782 INFO @ Sun, 21 Jun 2020 21:33:06: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:06: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:06: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:06: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:06: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 21:33:06: #2 alternative fragment length(s) may be 111,551 bps INFO @ Sun, 21 Jun 2020 21:33:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.10_model.r WARNING @ Sun, 21 Jun 2020 21:33:06: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:06: #2 You may need to consider one of the other alternative d(s): 111,551 WARNING @ Sun, 21 Jun 2020 21:33:06: #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 21:33:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.10_summits.bed INFO @ Sun, 21 Jun 2020 21:33:14: Done! pass1 - making usageList (357 chroms): 1 millis pass2 - checking and writing primary data (921 records, 4 fields): 11 millis CompletedMACS2peakCalling 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 21:33:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.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 21:33:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:26: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:33:31: 2000000 INFO @ Sun, 21 Jun 2020 21:33:33: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:33:33: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:33:33: #1 total tags in treatment: 2310787 INFO @ Sun, 21 Jun 2020 21:33:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:33: #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 21:33:33: #1 tags after filtering in treatment: 2310504 INFO @ Sun, 21 Jun 2020 21:33:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:34: #2 number of paired peaks: 2782 INFO @ Sun, 21 Jun 2020 21:33:34: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:34: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:34: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:34: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:34: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 21:33:34: #2 alternative fragment length(s) may be 111,551 bps INFO @ Sun, 21 Jun 2020 21:33:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.20_model.r WARNING @ Sun, 21 Jun 2020 21:33:34: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:34: #2 You may need to consider one of the other alternative d(s): 111,551 WARNING @ Sun, 21 Jun 2020 21:33:34: #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 21:33:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:33:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226986/SRX5226986.20_summits.bed INFO @ Sun, 21 Jun 2020 21:33:42: Done! pass1 - making usageList (153 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 5 millis CompletedMACS2peakCalling