Job ID = 6626545 SRX = SRX6813083 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8439690 spots for SRR10080059/SRR10080059.sra Written 8439690 spots for SRR10080059/SRR10080059.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626667 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:32 8439690 reads; of these: 8439690 (100.00%) were unpaired; of these: 5450939 (64.59%) aligned 0 times 2120804 (25.13%) aligned exactly 1 time 867947 (10.28%) aligned >1 times 35.41% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 518138 / 2988751 = 0.1734 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 @ Tue, 14 Jul 2020 07:29:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.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 @ Tue, 14 Jul 2020 07:29:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:29:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:29:24: 1000000 INFO @ Tue, 14 Jul 2020 07:29:29: 2000000 INFO @ Tue, 14 Jul 2020 07:29:32: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:29:32: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:29:32: #1 total tags in treatment: 2470613 INFO @ Tue, 14 Jul 2020 07:29:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:29:32: #1 tags after filtering in treatment: 2470613 INFO @ Tue, 14 Jul 2020 07:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:29:32: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:32: #2 number of paired peaks: 940 WARNING @ Tue, 14 Jul 2020 07:29:32: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Tue, 14 Jul 2020 07:29:32: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:32: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:32: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:32: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:32: #2 predicted fragment length is 132 bps INFO @ Tue, 14 Jul 2020 07:29:32: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 14 Jul 2020 07:29:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.05_model.r INFO @ Tue, 14 Jul 2020 07:29:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:29:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:29:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.05_summits.bed INFO @ Tue, 14 Jul 2020 07:29:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1825 records, 4 fields): 24 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 @ Tue, 14 Jul 2020 07:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.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 @ Tue, 14 Jul 2020 07:29:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:29:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:29:54: 1000000 INFO @ Tue, 14 Jul 2020 07:29:59: 2000000 INFO @ Tue, 14 Jul 2020 07:30:01: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:30:01: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:30:01: #1 total tags in treatment: 2470613 INFO @ Tue, 14 Jul 2020 07:30:01: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:30:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:30:01: #1 tags after filtering in treatment: 2470613 INFO @ Tue, 14 Jul 2020 07:30:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:30:01: #1 finished! INFO @ Tue, 14 Jul 2020 07:30:01: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:30:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:30:01: #2 number of paired peaks: 940 WARNING @ Tue, 14 Jul 2020 07:30:01: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Tue, 14 Jul 2020 07:30:01: start model_add_line... INFO @ Tue, 14 Jul 2020 07:30:01: start X-correlation... INFO @ Tue, 14 Jul 2020 07:30:01: end of X-cor INFO @ Tue, 14 Jul 2020 07:30:01: #2 finished! INFO @ Tue, 14 Jul 2020 07:30:01: #2 predicted fragment length is 132 bps INFO @ Tue, 14 Jul 2020 07:30:01: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 14 Jul 2020 07:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.10_model.r INFO @ Tue, 14 Jul 2020 07:30:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:30:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:30:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:30:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.10_summits.bed INFO @ Tue, 14 Jul 2020 07:30:10: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1149 records, 4 fields): 2 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 @ Tue, 14 Jul 2020 07:30:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.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 @ Tue, 14 Jul 2020 07:30:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:30:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:30:24: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:30:29: 2000000 INFO @ Tue, 14 Jul 2020 07:30:31: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:30:31: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:30:31: #1 total tags in treatment: 2470613 INFO @ Tue, 14 Jul 2020 07:30:31: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:30:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:30:31: #1 tags after filtering in treatment: 2470613 INFO @ Tue, 14 Jul 2020 07:30:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:30:31: #1 finished! INFO @ Tue, 14 Jul 2020 07:30:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:30:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:30:31: #2 number of paired peaks: 940 WARNING @ Tue, 14 Jul 2020 07:30:31: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Tue, 14 Jul 2020 07:30:31: start model_add_line... INFO @ Tue, 14 Jul 2020 07:30:31: start X-correlation... INFO @ Tue, 14 Jul 2020 07:30:31: end of X-cor INFO @ Tue, 14 Jul 2020 07:30:31: #2 finished! INFO @ Tue, 14 Jul 2020 07:30:31: #2 predicted fragment length is 132 bps INFO @ Tue, 14 Jul 2020 07:30:31: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 14 Jul 2020 07:30:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.20_model.r INFO @ Tue, 14 Jul 2020 07:30:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:30:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:30:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:30:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813083/SRX6813083.20_summits.bed INFO @ Tue, 14 Jul 2020 07:30:40: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (725 records, 4 fields): 17 millis CompletedMACS2peakCalling