Job ID = 12264962 SRX = SRX3088407 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13438 spots for SRR5928085/SRR5928085.sra Written 13438 spots for SRR5928085/SRR5928085.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265117 ("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: 00:00:00 13438 reads; of these: 13438 (100.00%) were unpaired; of these: 4983 (37.08%) aligned 0 times 6535 (48.63%) aligned exactly 1 time 1920 (14.29%) aligned >1 times 62.92% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 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] 2794 / 8455 = 0.3305 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:02:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.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 @ Sat, 03 Apr 2021 06:02:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:45: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:02:45: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:02:45: #1 total tags in treatment: 5661 INFO @ Sat, 03 Apr 2021 06:02:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:02:45: #1 tags after filtering in treatment: 5660 INFO @ Sat, 03 Apr 2021 06:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:45: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:45: #2 number of paired peaks: 193 WARNING @ Sat, 03 Apr 2021 06:02:45: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 03 Apr 2021 06:02:45: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:45: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:45: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:45: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:45: #2 predicted fragment length is 224 bps INFO @ Sat, 03 Apr 2021 06:02:45: #2 alternative fragment length(s) may be 9,37,74,105,149,171,224,257,284,320,437,466,579 bps INFO @ Sat, 03 Apr 2021 06:02:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.05_model.r INFO @ Sat, 03 Apr 2021 06:02:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:02:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.05_summits.bed INFO @ Sat, 03 Apr 2021 06:02:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:03:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.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 @ Sat, 03 Apr 2021 06:03:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:03:15: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:03:15: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:03:15: #1 total tags in treatment: 5661 INFO @ Sat, 03 Apr 2021 06:03:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:03:15: #1 tags after filtering in treatment: 5660 INFO @ Sat, 03 Apr 2021 06:03:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:15: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:15: #2 number of paired peaks: 193 WARNING @ Sat, 03 Apr 2021 06:03:15: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 03 Apr 2021 06:03:15: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:15: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:15: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:15: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:15: #2 predicted fragment length is 224 bps INFO @ Sat, 03 Apr 2021 06:03:15: #2 alternative fragment length(s) may be 9,37,74,105,149,171,224,257,284,320,437,466,579 bps INFO @ Sat, 03 Apr 2021 06:03:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.10_model.r INFO @ Sat, 03 Apr 2021 06:03:15: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:03:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:03:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:03:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.10_summits.bed INFO @ Sat, 03 Apr 2021 06:03:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:03:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.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 @ Sat, 03 Apr 2021 06:03:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:03:45: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:03:45: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:03:45: #1 total tags in treatment: 5661 INFO @ Sat, 03 Apr 2021 06:03:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:03:45: #1 tags after filtering in treatment: 5660 INFO @ Sat, 03 Apr 2021 06:03:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:45: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:45: #2 number of paired peaks: 193 WARNING @ Sat, 03 Apr 2021 06:03:45: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 03 Apr 2021 06:03:45: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:45: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:45: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:45: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:45: #2 predicted fragment length is 224 bps INFO @ Sat, 03 Apr 2021 06:03:45: #2 alternative fragment length(s) may be 9,37,74,105,149,171,224,257,284,320,437,466,579 bps INFO @ Sat, 03 Apr 2021 06:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.20_model.r INFO @ Sat, 03 Apr 2021 06:03:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:03:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088407/SRX3088407.20_summits.bed INFO @ Sat, 03 Apr 2021 06:03:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling