Job ID = 12264951 SRX = SRX3088400 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14483 spots for SRR5928078/SRR5928078.sra Written 14483 spots for SRR5928078/SRR5928078.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265107 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:00 14483 reads; of these: 14483 (100.00%) were unpaired; of these: 6038 (41.69%) aligned 0 times 6309 (43.56%) aligned exactly 1 time 2136 (14.75%) aligned >1 times 58.31% 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] 2643 / 8445 = 0.3130 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 06:02:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.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 06:02:14: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:14: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:14: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:02:14: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:02:14: #1 total tags in treatment: 5802 INFO @ Sat, 03 Apr 2021 06:02:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:14: #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 06:02:14: #1 tags after filtering in treatment: 5802 INFO @ Sat, 03 Apr 2021 06:02:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:14: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:14: #2 number of paired peaks: 180 WARNING @ Sat, 03 Apr 2021 06:02:14: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 03 Apr 2021 06:02:14: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:14: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:14: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:14: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:14: #2 predicted fragment length is 221 bps INFO @ Sat, 03 Apr 2021 06:02:14: #2 alternative fragment length(s) may be 9,44,82,115,152,169,194,221,267,291,357 bps INFO @ Sat, 03 Apr 2021 06:02:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.05_model.r INFO @ Sat, 03 Apr 2021 06:02:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:02:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:02:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.05_summits.bed INFO @ Sat, 03 Apr 2021 06:02:14: 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 06:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.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 06:02:44: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:44: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:44: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:02:44: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:02:44: #1 total tags in treatment: 5802 INFO @ Sat, 03 Apr 2021 06:02:44: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:44: #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 06:02:44: #1 tags after filtering in treatment: 5802 INFO @ Sat, 03 Apr 2021 06:02:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:44: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:44: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:44: #2 number of paired peaks: 180 WARNING @ Sat, 03 Apr 2021 06:02:44: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 03 Apr 2021 06:02:44: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:44: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:44: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:44: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:44: #2 predicted fragment length is 221 bps INFO @ Sat, 03 Apr 2021 06:02:44: #2 alternative fragment length(s) may be 9,44,82,115,152,169,194,221,267,291,357 bps INFO @ Sat, 03 Apr 2021 06:02:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.10_model.r INFO @ Sat, 03 Apr 2021 06:02:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:02:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:02:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.10_summits.bed INFO @ Sat, 03 Apr 2021 06:02:44: 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 06:03:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.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 06:03:14: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:14: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:03:14: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:03:14: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:03:14: #1 total tags in treatment: 5802 INFO @ Sat, 03 Apr 2021 06:03:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:14: #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 06:03:14: #1 tags after filtering in treatment: 5802 INFO @ Sat, 03 Apr 2021 06:03:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:14: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:14: #2 number of paired peaks: 180 WARNING @ Sat, 03 Apr 2021 06:03:14: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 03 Apr 2021 06:03:14: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:14: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:14: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:14: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:14: #2 predicted fragment length is 221 bps INFO @ Sat, 03 Apr 2021 06:03:14: #2 alternative fragment length(s) may be 9,44,82,115,152,169,194,221,267,291,357 bps INFO @ Sat, 03 Apr 2021 06:03:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.20_model.r INFO @ Sat, 03 Apr 2021 06:03:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:03:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:03:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:03:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088400/SRX3088400.20_summits.bed INFO @ Sat, 03 Apr 2021 06:03:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling