Job ID = 6365969 SRX = SRX043980 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:43:07 prefetch.2.10.7: 1) Downloading 'SRR107555'... 2020-06-15T22:43:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:28 prefetch.2.10.7: 'SRR107555' is valid 2020-06-15T22:43:28 prefetch.2.10.7: 1) 'SRR107555' was downloaded successfully Read 2422483 spots for SRR107555/SRR107555.sra Written 2422483 spots for SRR107555/SRR107555.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: 00:00:15 2422483 reads; of these: 2422483 (100.00%) were unpaired; of these: 1701437 (70.24%) aligned 0 times 611403 (25.24%) aligned exactly 1 time 109643 (4.53%) aligned >1 times 29.76% overall alignment rate Time searching: 00:00:15 Overall time: 00:00:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 42643 / 721046 = 0.0591 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, 16 Jun 2020 07:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 07:44:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:37: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:44:37: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:44:37: #1 total tags in treatment: 678403 INFO @ Tue, 16 Jun 2020 07:44:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:44:37: #1 tags after filtering in treatment: 678403 INFO @ Tue, 16 Jun 2020 07:44:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:37: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:37: #2 number of paired peaks: 781 WARNING @ Tue, 16 Jun 2020 07:44:37: Fewer paired peaks (781) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 781 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:37: #2 predicted fragment length is 183 bps INFO @ Tue, 16 Jun 2020 07:44:37: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 16 Jun 2020 07:44:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.05_model.r INFO @ Tue, 16 Jun 2020 07:44:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.05_summits.bed INFO @ Tue, 16 Jun 2020 07:44:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (307 records, 4 fields): 1 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, 16 Jun 2020 07:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 07:45:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:06: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:45:06: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:45:06: #1 total tags in treatment: 678403 INFO @ Tue, 16 Jun 2020 07:45:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:45:06: #1 tags after filtering in treatment: 678403 INFO @ Tue, 16 Jun 2020 07:45:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:06: #2 number of paired peaks: 781 WARNING @ Tue, 16 Jun 2020 07:45:06: Fewer paired peaks (781) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 781 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:06: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:06: #2 predicted fragment length is 183 bps INFO @ Tue, 16 Jun 2020 07:45:06: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 16 Jun 2020 07:45:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.10_model.r INFO @ Tue, 16 Jun 2020 07:45:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.10_summits.bed INFO @ Tue, 16 Jun 2020 07:45:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 1 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, 16 Jun 2020 07:45:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 07:45:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:32: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:45:36: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:45:36: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:45:36: #1 total tags in treatment: 678403 INFO @ Tue, 16 Jun 2020 07:45:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:45:36: #1 tags after filtering in treatment: 678403 INFO @ Tue, 16 Jun 2020 07:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:36: #2 number of paired peaks: 781 WARNING @ Tue, 16 Jun 2020 07:45:36: Fewer paired peaks (781) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 781 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:36: #2 predicted fragment length is 183 bps INFO @ Tue, 16 Jun 2020 07:45:36: #2 alternative fragment length(s) may be 183 bps INFO @ Tue, 16 Jun 2020 07:45:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.20_model.r INFO @ Tue, 16 Jun 2020 07:45:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043980/SRX043980.20_summits.bed INFO @ Tue, 16 Jun 2020 07:45:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling