Job ID = 6452417 SRX = SRX013045 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:32:57 prefetch.2.10.7: 1) Downloading 'SRR030311'... 2020-06-21T07:32:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:34:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:34:31 prefetch.2.10.7: 'SRR030311' is valid 2020-06-21T07:34:31 prefetch.2.10.7: 1) 'SRR030311' was downloaded successfully Read 6504449 spots for SRR030311/SRR030311.sra Written 6504449 spots for SRR030311/SRR030311.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: 00:01:04 6504449 reads; of these: 6504449 (100.00%) were unpaired; of these: 1130394 (17.38%) aligned 0 times 4786082 (73.58%) aligned exactly 1 time 587973 (9.04%) aligned >1 times 82.62% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 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] 221826 / 5374055 = 0.0413 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 16:37:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.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 16:37:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:37:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:37:35: 1000000 INFO @ Sun, 21 Jun 2020 16:37:39: 2000000 INFO @ Sun, 21 Jun 2020 16:37:44: 3000000 INFO @ Sun, 21 Jun 2020 16:37:48: 4000000 INFO @ Sun, 21 Jun 2020 16:37:53: 5000000 INFO @ Sun, 21 Jun 2020 16:37:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:37:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:37:54: #1 total tags in treatment: 5152229 INFO @ Sun, 21 Jun 2020 16:37:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:37:54: #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 16:37:54: #1 tags after filtering in treatment: 5152087 INFO @ Sun, 21 Jun 2020 16:37:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:37:54: #1 finished! INFO @ Sun, 21 Jun 2020 16:37:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:37:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:37:55: #2 number of paired peaks: 886 WARNING @ Sun, 21 Jun 2020 16:37:55: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Sun, 21 Jun 2020 16:37:55: start model_add_line... INFO @ Sun, 21 Jun 2020 16:37:55: start X-correlation... INFO @ Sun, 21 Jun 2020 16:37:55: end of X-cor INFO @ Sun, 21 Jun 2020 16:37:55: #2 finished! INFO @ Sun, 21 Jun 2020 16:37:55: #2 predicted fragment length is 170 bps INFO @ Sun, 21 Jun 2020 16:37:55: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 21 Jun 2020 16:37:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.05_model.r INFO @ Sun, 21 Jun 2020 16:37:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:37:55: #3 Pre-compute pvalue-qvalue table... 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 16:38:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.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 16:38:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:38:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:38:05: 1000000 INFO @ Sun, 21 Jun 2020 16:38:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:38:10: 2000000 INFO @ Sun, 21 Jun 2020 16:38:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:38:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:38:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.05_summits.bed INFO @ Sun, 21 Jun 2020 16:38:13: Done! pass1 - making usageList (73 chroms): 1 millis pass2 - checking and writing primary data (3707 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:38:14: 3000000 INFO @ Sun, 21 Jun 2020 16:38:19: 4000000 INFO @ Sun, 21 Jun 2020 16:38:24: 5000000 INFO @ Sun, 21 Jun 2020 16:38:25: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:38:25: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:38:25: #1 total tags in treatment: 5152229 INFO @ Sun, 21 Jun 2020 16:38:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:38:25: #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 16:38:25: #1 tags after filtering in treatment: 5152087 INFO @ Sun, 21 Jun 2020 16:38:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:38:25: #1 finished! INFO @ Sun, 21 Jun 2020 16:38:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:38:25: #2 number of paired peaks: 886 WARNING @ Sun, 21 Jun 2020 16:38:25: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Sun, 21 Jun 2020 16:38:25: start model_add_line... INFO @ Sun, 21 Jun 2020 16:38:25: start X-correlation... INFO @ Sun, 21 Jun 2020 16:38:25: end of X-cor INFO @ Sun, 21 Jun 2020 16:38:25: #2 finished! INFO @ Sun, 21 Jun 2020 16:38:25: #2 predicted fragment length is 170 bps INFO @ Sun, 21 Jun 2020 16:38:25: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 21 Jun 2020 16:38:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.10_model.r INFO @ Sun, 21 Jun 2020 16:38:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:38:25: #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 16:38:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.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 16:38:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:38:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:38:35: 1000000 INFO @ Sun, 21 Jun 2020 16:38:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:38:39: 2000000 INFO @ Sun, 21 Jun 2020 16:38:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:38:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:38:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.10_summits.bed INFO @ Sun, 21 Jun 2020 16:38:43: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (1552 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:38:44: 3000000 INFO @ Sun, 21 Jun 2020 16:38:48: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:38:53: 5000000 INFO @ Sun, 21 Jun 2020 16:38:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:38:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:38:54: #1 total tags in treatment: 5152229 INFO @ Sun, 21 Jun 2020 16:38:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:38:54: #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 16:38:54: #1 tags after filtering in treatment: 5152087 INFO @ Sun, 21 Jun 2020 16:38:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:38:54: #1 finished! INFO @ Sun, 21 Jun 2020 16:38:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:38:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:38:55: #2 number of paired peaks: 886 WARNING @ Sun, 21 Jun 2020 16:38:55: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Sun, 21 Jun 2020 16:38:55: start model_add_line... INFO @ Sun, 21 Jun 2020 16:38:55: start X-correlation... INFO @ Sun, 21 Jun 2020 16:38:55: end of X-cor INFO @ Sun, 21 Jun 2020 16:38:55: #2 finished! INFO @ Sun, 21 Jun 2020 16:38:55: #2 predicted fragment length is 170 bps INFO @ Sun, 21 Jun 2020 16:38:55: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 21 Jun 2020 16:38:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.20_model.r INFO @ Sun, 21 Jun 2020 16:38:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:38:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:39:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:39:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013045/SRX013045.20_summits.bed INFO @ Sun, 21 Jun 2020 16:39:12: Done! pass1 - making usageList (38 chroms): 0 millis pass2 - checking and writing primary data (375 records, 4 fields): 3 millis CompletedMACS2peakCalling