Job ID = 6456093 SRX = SRX3170975 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:30:06 prefetch.2.10.7: 1) Downloading 'SRR6019822'... 2020-06-21T10:30:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:31:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:31:15 prefetch.2.10.7: 'SRR6019822' is valid 2020-06-21T10:31:15 prefetch.2.10.7: 1) 'SRR6019822' was downloaded successfully 2020-06-21T10:31:15 prefetch.2.10.7: 'SRR6019822' has 0 unresolved dependencies Read 8678734 spots for SRR6019822/SRR6019822.sra Written 8678734 spots for SRR6019822/SRR6019822.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: 00:02:02 8678734 reads; of these: 8678734 (100.00%) were unpaired; of these: 266454 (3.07%) aligned 0 times 6703960 (77.25%) aligned exactly 1 time 1708320 (19.68%) aligned >1 times 96.93% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 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] 1948966 / 8412280 = 0.2317 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 19:35:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.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 19:35:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:54: 1000000 INFO @ Sun, 21 Jun 2020 19:35:59: 2000000 INFO @ Sun, 21 Jun 2020 19:36:05: 3000000 INFO @ Sun, 21 Jun 2020 19:36:10: 4000000 INFO @ Sun, 21 Jun 2020 19:36:16: 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 19:36:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.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 19:36:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:22: 6000000 INFO @ Sun, 21 Jun 2020 19:36:24: 1000000 INFO @ Sun, 21 Jun 2020 19:36:25: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:36:25: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:36:25: #1 total tags in treatment: 6463314 INFO @ Sun, 21 Jun 2020 19:36:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:25: #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 19:36:25: #1 tags after filtering in treatment: 6463133 INFO @ Sun, 21 Jun 2020 19:36:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:26: #2 number of paired peaks: 821 WARNING @ Sun, 21 Jun 2020 19:36:26: Fewer paired peaks (821) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 821 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:26: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 19:36:26: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 19:36:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.05_model.r INFO @ Sun, 21 Jun 2020 19:36:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:30: 2000000 INFO @ Sun, 21 Jun 2020 19:36:35: 3000000 INFO @ Sun, 21 Jun 2020 19:36:41: 4000000 INFO @ Sun, 21 Jun 2020 19:36:42: #3 Call peaks for each chromosome... 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 19:36:46: 5000000 INFO @ Sun, 21 Jun 2020 19:36:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.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 19:36:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.05_summits.bed INFO @ Sun, 21 Jun 2020 19:36:50: Done! pass1 - making usageList (228 chroms): 2 millis pass2 - checking and writing primary data (2190 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:52: 6000000 INFO @ Sun, 21 Jun 2020 19:36:54: 1000000 INFO @ Sun, 21 Jun 2020 19:36:55: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:36:55: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:36:55: #1 total tags in treatment: 6463314 INFO @ Sun, 21 Jun 2020 19:36:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:55: #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 19:36:56: #1 tags after filtering in treatment: 6463133 INFO @ Sun, 21 Jun 2020 19:36:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:56: #2 number of paired peaks: 821 WARNING @ Sun, 21 Jun 2020 19:36:56: Fewer paired peaks (821) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 821 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:56: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 19:36:56: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 19:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.10_model.r INFO @ Sun, 21 Jun 2020 19:36:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:00: 2000000 INFO @ Sun, 21 Jun 2020 19:37:05: 3000000 INFO @ Sun, 21 Jun 2020 19:37:11: 4000000 INFO @ Sun, 21 Jun 2020 19:37:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:16: 5000000 INFO @ Sun, 21 Jun 2020 19:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.10_summits.bed INFO @ Sun, 21 Jun 2020 19:37:20: Done! pass1 - making usageList (143 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:21: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:37:24: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:37:24: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:37:24: #1 total tags in treatment: 6463314 INFO @ Sun, 21 Jun 2020 19:37:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:24: #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 19:37:24: #1 tags after filtering in treatment: 6463133 INFO @ Sun, 21 Jun 2020 19:37:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:25: #2 number of paired peaks: 821 WARNING @ Sun, 21 Jun 2020 19:37:25: Fewer paired peaks (821) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 821 pairs to build model! INFO @ Sun, 21 Jun 2020 19:37:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:25: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 19:37:25: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 19:37:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.20_model.r INFO @ Sun, 21 Jun 2020 19:37:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:37:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3170975/SRX3170975.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:48: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 3 millis CompletedMACS2peakCalling