Job ID = 6528522 SRX = SRX969919 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T15:03:39 prefetch.2.10.7: 1) Downloading 'SRR1931635'... 2020-06-29T15:03:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:03:52 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:03:52 prefetch.2.10.7: 'SRR1931635' is valid 2020-06-29T15:03:52 prefetch.2.10.7: 1) 'SRR1931635' was downloaded successfully Read 48165 spots for SRR1931635/SRR1931635.sra Written 48165 spots for SRR1931635/SRR1931635.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: 00:00:01 48165 reads; of these: 48165 (100.00%) were unpaired; of these: 39823 (82.68%) aligned 0 times 6543 (13.58%) aligned exactly 1 time 1799 (3.74%) aligned >1 times 17.32% 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] 6 / 8342 = 0.0007 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 00:04:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.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 00:04:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:04:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:04:26: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:04:26: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:04:26: #1 total tags in treatment: 8336 INFO @ Tue, 30 Jun 2020 00:04:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:04:26: #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 00:04:26: #1 tags after filtering in treatment: 8335 INFO @ Tue, 30 Jun 2020 00:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:04:26: #1 finished! INFO @ Tue, 30 Jun 2020 00:04:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:04:26: #2 number of paired peaks: 133 WARNING @ Tue, 30 Jun 2020 00:04:26: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 30 Jun 2020 00:04:26: start model_add_line... INFO @ Tue, 30 Jun 2020 00:04:26: start X-correlation... INFO @ Tue, 30 Jun 2020 00:04:26: end of X-cor INFO @ Tue, 30 Jun 2020 00:04:26: #2 finished! INFO @ Tue, 30 Jun 2020 00:04:26: #2 predicted fragment length is 297 bps INFO @ Tue, 30 Jun 2020 00:04:26: #2 alternative fragment length(s) may be 124,155,180,208,238,297,323,345,376,396,496,529 bps INFO @ Tue, 30 Jun 2020 00:04:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.05_model.r INFO @ Tue, 30 Jun 2020 00:04:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:04:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:04:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:04:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:04:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:04:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.05_summits.bed INFO @ Tue, 30 Jun 2020 00:04:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) 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 00:04:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.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 00:04:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:04:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:04:56: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:04:56: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:04:56: #1 total tags in treatment: 8336 INFO @ Tue, 30 Jun 2020 00:04:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:04:56: #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 00:04:56: #1 tags after filtering in treatment: 8335 INFO @ Tue, 30 Jun 2020 00:04:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:04:56: #1 finished! INFO @ Tue, 30 Jun 2020 00:04:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:04:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:04:56: #2 number of paired peaks: 133 WARNING @ Tue, 30 Jun 2020 00:04:56: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 30 Jun 2020 00:04:56: start model_add_line... INFO @ Tue, 30 Jun 2020 00:04:56: start X-correlation... INFO @ Tue, 30 Jun 2020 00:04:56: end of X-cor INFO @ Tue, 30 Jun 2020 00:04:56: #2 finished! INFO @ Tue, 30 Jun 2020 00:04:56: #2 predicted fragment length is 297 bps INFO @ Tue, 30 Jun 2020 00:04:56: #2 alternative fragment length(s) may be 124,155,180,208,238,297,323,345,376,396,496,529 bps INFO @ Tue, 30 Jun 2020 00:04:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.10_model.r INFO @ Tue, 30 Jun 2020 00:04:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:04:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:04:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:04:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:04:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:04:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.10_summits.bed INFO @ Tue, 30 Jun 2020 00:04:56: 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/3.5.2/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 @ Tue, 30 Jun 2020 00:05:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.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 00:05:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:05:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:05:26: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:05:26: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:05:26: #1 total tags in treatment: 8336 INFO @ Tue, 30 Jun 2020 00:05:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:05:26: #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 00:05:26: #1 tags after filtering in treatment: 8335 INFO @ Tue, 30 Jun 2020 00:05:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:05:26: #1 finished! INFO @ Tue, 30 Jun 2020 00:05:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:05:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:05:26: #2 number of paired peaks: 133 WARNING @ Tue, 30 Jun 2020 00:05:26: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Tue, 30 Jun 2020 00:05:26: start model_add_line... INFO @ Tue, 30 Jun 2020 00:05:26: start X-correlation... INFO @ Tue, 30 Jun 2020 00:05:26: end of X-cor INFO @ Tue, 30 Jun 2020 00:05:26: #2 finished! INFO @ Tue, 30 Jun 2020 00:05:26: #2 predicted fragment length is 297 bps INFO @ Tue, 30 Jun 2020 00:05:26: #2 alternative fragment length(s) may be 124,155,180,208,238,297,323,345,376,396,496,529 bps INFO @ Tue, 30 Jun 2020 00:05:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.20_model.r INFO @ Tue, 30 Jun 2020 00:05:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:05:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:05:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:05:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX969919/SRX969919.20_summits.bed INFO @ Tue, 30 Jun 2020 00:05:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling