Job ID = 6455406 SRX = SRX287762 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:56:56 prefetch.2.10.7: 1) Downloading 'SRR869951'... 2020-06-21T09:56:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:59:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:59:08 prefetch.2.10.7: 'SRR869951' is valid 2020-06-21T09:59:08 prefetch.2.10.7: 1) 'SRR869951' was downloaded successfully Read 11457191 spots for SRR869951/SRR869951.sra Written 11457191 spots for SRR869951/SRR869951.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: 00:02:39 11457191 reads; of these: 11457191 (100.00%) were unpaired; of these: 1734007 (15.13%) aligned 0 times 7623173 (66.54%) aligned exactly 1 time 2100011 (18.33%) aligned >1 times 84.87% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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] 624214 / 9723184 = 0.0642 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 19:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.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 19:05:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:31: 1000000 INFO @ Sun, 21 Jun 2020 19:05:37: 2000000 INFO @ Sun, 21 Jun 2020 19:05:43: 3000000 INFO @ Sun, 21 Jun 2020 19:05:49: 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 19:05:55: 5000000 INFO @ Sun, 21 Jun 2020 19:05:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.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 19:05:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:06:01: 6000000 INFO @ Sun, 21 Jun 2020 19:06:01: 1000000 INFO @ Sun, 21 Jun 2020 19:06:07: 7000000 INFO @ Sun, 21 Jun 2020 19:06:08: 2000000 INFO @ Sun, 21 Jun 2020 19:06:14: 8000000 INFO @ Sun, 21 Jun 2020 19:06:15: 3000000 INFO @ Sun, 21 Jun 2020 19:06:21: 9000000 INFO @ Sun, 21 Jun 2020 19:06:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:22: #1 total tags in treatment: 9098970 INFO @ Sun, 21 Jun 2020 19:06:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:22: #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 19:06:22: 4000000 INFO @ Sun, 21 Jun 2020 19:06:22: #1 tags after filtering in treatment: 9098966 INFO @ Sun, 21 Jun 2020 19:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:22: #2 looking for paired plus/minus strand peaks... 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 19:06:23: #2 number of paired peaks: 547 WARNING @ Sun, 21 Jun 2020 19:06:23: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:23: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 19:06:23: #2 alternative fragment length(s) may be 139 bps INFO @ Sun, 21 Jun 2020 19:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.05_model.r INFO @ Sun, 21 Jun 2020 19:06:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.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 19:06:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:06:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:06:28: 5000000 INFO @ Sun, 21 Jun 2020 19:06:31: 1000000 INFO @ Sun, 21 Jun 2020 19:06:35: 6000000 INFO @ Sun, 21 Jun 2020 19:06:37: 2000000 INFO @ Sun, 21 Jun 2020 19:06:41: 7000000 INFO @ Sun, 21 Jun 2020 19:06:43: 3000000 INFO @ Sun, 21 Jun 2020 19:06:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:48: 8000000 INFO @ Sun, 21 Jun 2020 19:06:50: 4000000 INFO @ Sun, 21 Jun 2020 19:06:55: 9000000 INFO @ Sun, 21 Jun 2020 19:06:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:56: #1 total tags in treatment: 9098970 INFO @ Sun, 21 Jun 2020 19:06:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:56: #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 19:06:56: 5000000 INFO @ Sun, 21 Jun 2020 19:06:56: #1 tags after filtering in treatment: 9098966 INFO @ Sun, 21 Jun 2020 19:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:57: #2 number of paired peaks: 547 WARNING @ Sun, 21 Jun 2020 19:06:57: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:57: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 19:06:57: #2 alternative fragment length(s) may be 139 bps INFO @ Sun, 21 Jun 2020 19:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.10_model.r INFO @ Sun, 21 Jun 2020 19:06:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.05_summits.bed INFO @ Sun, 21 Jun 2020 19:06:57: Done! pass1 - making usageList (350 chroms): 2 millis pass2 - checking and writing primary data (4417 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:02: 6000000 INFO @ Sun, 21 Jun 2020 19:07:07: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:07:14: 8000000 INFO @ Sun, 21 Jun 2020 19:07:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:19: 9000000 INFO @ Sun, 21 Jun 2020 19:07:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:07:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:07:20: #1 total tags in treatment: 9098970 INFO @ Sun, 21 Jun 2020 19:07:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:20: #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 19:07:21: #1 tags after filtering in treatment: 9098966 INFO @ Sun, 21 Jun 2020 19:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:21: #2 number of paired peaks: 547 WARNING @ Sun, 21 Jun 2020 19:07:21: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Sun, 21 Jun 2020 19:07:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:21: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 19:07:21: #2 alternative fragment length(s) may be 139 bps INFO @ Sun, 21 Jun 2020 19:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.20_model.r INFO @ Sun, 21 Jun 2020 19:07:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.10_summits.bed INFO @ Sun, 21 Jun 2020 19:07:30: Done! pass1 - making usageList (176 chroms): 1 millis pass2 - checking and writing primary data (1265 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:07:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287762/SRX287762.20_summits.bed INFO @ Sun, 21 Jun 2020 19:07:55: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 4 millis CompletedMACS2peakCalling