Job ID = 6529141 SRX = SRX013004 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:00:29 3270113 reads; of these: 3270113 (100.00%) were unpaired; of these: 1622639 (49.62%) aligned 0 times 1268054 (38.78%) aligned exactly 1 time 379420 (11.60%) aligned >1 times 50.38% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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] 335719 / 1647474 = 0.2038 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, 30 Jun 2020 01:31:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.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, 30 Jun 2020 01:31:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:31:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:31:28: 1000000 INFO @ Tue, 30 Jun 2020 01:31:31: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:31:31: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:31:31: #1 total tags in treatment: 1311755 INFO @ Tue, 30 Jun 2020 01:31:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:31:31: #1 tags after filtering in treatment: 1311512 INFO @ Tue, 30 Jun 2020 01:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:31:31: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:31:31: #2 number of paired peaks: 844 WARNING @ Tue, 30 Jun 2020 01:31:31: Fewer paired peaks (844) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 844 pairs to build model! INFO @ Tue, 30 Jun 2020 01:31:31: start model_add_line... INFO @ Tue, 30 Jun 2020 01:31:31: start X-correlation... INFO @ Tue, 30 Jun 2020 01:31:31: end of X-cor INFO @ Tue, 30 Jun 2020 01:31:31: #2 finished! INFO @ Tue, 30 Jun 2020 01:31:31: #2 predicted fragment length is 138 bps INFO @ Tue, 30 Jun 2020 01:31:31: #2 alternative fragment length(s) may be 43,138 bps INFO @ Tue, 30 Jun 2020 01:31:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.05_model.r INFO @ Tue, 30 Jun 2020 01:31:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:31:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:31:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:31:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.05_summits.bed INFO @ Tue, 30 Jun 2020 01:31:37: Done! pass1 - making usageList (311 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 11 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, 30 Jun 2020 01:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.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, 30 Jun 2020 01:31:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:31:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:31:59: 1000000 INFO @ Tue, 30 Jun 2020 01:32:02: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:32:02: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:32:02: #1 total tags in treatment: 1311755 INFO @ Tue, 30 Jun 2020 01:32:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:32:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:32:02: #1 tags after filtering in treatment: 1311512 INFO @ Tue, 30 Jun 2020 01:32:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:32:02: #1 finished! INFO @ Tue, 30 Jun 2020 01:32:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:32:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:32:02: #2 number of paired peaks: 844 WARNING @ Tue, 30 Jun 2020 01:32:02: Fewer paired peaks (844) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 844 pairs to build model! INFO @ Tue, 30 Jun 2020 01:32:02: start model_add_line... INFO @ Tue, 30 Jun 2020 01:32:02: start X-correlation... INFO @ Tue, 30 Jun 2020 01:32:02: end of X-cor INFO @ Tue, 30 Jun 2020 01:32:02: #2 finished! INFO @ Tue, 30 Jun 2020 01:32:02: #2 predicted fragment length is 138 bps INFO @ Tue, 30 Jun 2020 01:32:02: #2 alternative fragment length(s) may be 43,138 bps INFO @ Tue, 30 Jun 2020 01:32:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.10_model.r INFO @ Tue, 30 Jun 2020 01:32:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:32:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:32:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:32:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:32:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:32:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.10_summits.bed INFO @ Tue, 30 Jun 2020 01:32:08: Done! pass1 - making usageList (107 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 4 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, 30 Jun 2020 01:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.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, 30 Jun 2020 01:32:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:32:22: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:32:28: 1000000 INFO @ Tue, 30 Jun 2020 01:32:30: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:32:30: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:32:30: #1 total tags in treatment: 1311755 INFO @ Tue, 30 Jun 2020 01:32:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:32:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:32:30: #1 tags after filtering in treatment: 1311512 INFO @ Tue, 30 Jun 2020 01:32:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:32:30: #1 finished! INFO @ Tue, 30 Jun 2020 01:32:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:32:30: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:32:31: #2 number of paired peaks: 844 WARNING @ Tue, 30 Jun 2020 01:32:31: Fewer paired peaks (844) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 844 pairs to build model! INFO @ Tue, 30 Jun 2020 01:32:31: start model_add_line... INFO @ Tue, 30 Jun 2020 01:32:31: start X-correlation... INFO @ Tue, 30 Jun 2020 01:32:31: end of X-cor INFO @ Tue, 30 Jun 2020 01:32:31: #2 finished! INFO @ Tue, 30 Jun 2020 01:32:31: #2 predicted fragment length is 138 bps INFO @ Tue, 30 Jun 2020 01:32:31: #2 alternative fragment length(s) may be 43,138 bps INFO @ Tue, 30 Jun 2020 01:32:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.20_model.r INFO @ Tue, 30 Jun 2020 01:32:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:32:34: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:32:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:32:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:32:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013004/SRX013004.20_summits.bed INFO @ Tue, 30 Jun 2020 01:32:36: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (103 records, 4 fields): 4 millis CompletedMACS2peakCalling