Job ID = 6455046 SRX = SRX2642393 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:50:40 prefetch.2.10.7: 1) Downloading 'SRR5345733'... 2020-06-21T09:50:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:51:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:51:22 prefetch.2.10.7: 'SRR5345733' is valid 2020-06-21T09:51:22 prefetch.2.10.7: 1) 'SRR5345733' was downloaded successfully 2020-06-21T09:51:22 prefetch.2.10.7: 'SRR5345733' has 0 unresolved dependencies Read 2399647 spots for SRR5345733/SRR5345733.sra Written 2399647 spots for SRR5345733/SRR5345733.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: 00:01:07 2399647 reads; of these: 2399647 (100.00%) were unpaired; of these: 232280 (9.68%) aligned 0 times 1721316 (71.73%) aligned exactly 1 time 446051 (18.59%) aligned >1 times 90.32% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 40877 / 2167367 = 0.0189 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 18:54:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.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 18:54:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:10: 1000000 INFO @ Sun, 21 Jun 2020 18:54:18: 2000000 INFO @ Sun, 21 Jun 2020 18:54:19: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:54:19: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:54:19: #1 total tags in treatment: 2126490 INFO @ Sun, 21 Jun 2020 18:54:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:19: #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 18:54:20: #1 tags after filtering in treatment: 2126379 INFO @ Sun, 21 Jun 2020 18:54:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:20: #2 number of paired peaks: 1969 INFO @ Sun, 21 Jun 2020 18:54:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:20: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 18:54:20: #2 alternative fragment length(s) may be 144,158,161 bps INFO @ Sun, 21 Jun 2020 18:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.05_model.r WARNING @ Sun, 21 Jun 2020 18:54:20: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:20: #2 You may need to consider one of the other alternative d(s): 144,158,161 WARNING @ Sun, 21 Jun 2020 18:54:20: #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 18:54:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.05_summits.bed INFO @ Sun, 21 Jun 2020 18:54:28: Done! pass1 - making usageList (183 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 7 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 18:54:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.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 18:54:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:39: 1000000 INFO @ Sun, 21 Jun 2020 18:54:46: 2000000 INFO @ Sun, 21 Jun 2020 18:54:47: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:54:47: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:54:47: #1 total tags in treatment: 2126490 INFO @ Sun, 21 Jun 2020 18:54:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:47: #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 18:54:47: #1 tags after filtering in treatment: 2126379 INFO @ Sun, 21 Jun 2020 18:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:48: #2 number of paired peaks: 1969 INFO @ Sun, 21 Jun 2020 18:54:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:48: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 18:54:48: #2 alternative fragment length(s) may be 144,158,161 bps INFO @ Sun, 21 Jun 2020 18:54:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.10_model.r WARNING @ Sun, 21 Jun 2020 18:54:48: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:48: #2 You may need to consider one of the other alternative d(s): 144,158,161 WARNING @ Sun, 21 Jun 2020 18:54:48: #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 18:54:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.10_summits.bed INFO @ Sun, 21 Jun 2020 18:54:55: Done! pass1 - making usageList (113 chroms): 3 millis pass2 - checking and writing primary data (164 records, 4 fields): 5 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 18:55:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.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 18:55:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:09: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:55:16: 2000000 INFO @ Sun, 21 Jun 2020 18:55:17: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 18:55:17: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 18:55:17: #1 total tags in treatment: 2126490 INFO @ Sun, 21 Jun 2020 18:55:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:17: #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 18:55:17: #1 tags after filtering in treatment: 2126379 INFO @ Sun, 21 Jun 2020 18:55:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:17: #2 number of paired peaks: 1969 INFO @ Sun, 21 Jun 2020 18:55:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:17: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 18:55:17: #2 alternative fragment length(s) may be 144,158,161 bps INFO @ Sun, 21 Jun 2020 18:55:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.20_model.r WARNING @ Sun, 21 Jun 2020 18:55:17: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:55:17: #2 You may need to consider one of the other alternative d(s): 144,158,161 WARNING @ Sun, 21 Jun 2020 18:55:17: #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 18:55:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:55:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642393/SRX2642393.20_summits.bed INFO @ Sun, 21 Jun 2020 18:55:25: Done! pass1 - making usageList (57 chroms): 0 millis pass2 - checking and writing primary data (72 records, 4 fields): 4 millis CompletedMACS2peakCalling