Job ID = 6366897 SRX = SRX257642 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:04:53 prefetch.2.10.7: 1) Downloading 'SRR800653'... 2020-06-15T23:04:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:17 prefetch.2.10.7: 'SRR800653' is valid 2020-06-15T23:05:17 prefetch.2.10.7: 1) 'SRR800653' was downloaded successfully Read 6511216 spots for SRR800653/SRR800653.sra Written 6511216 spots for SRR800653/SRR800653.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: 00:00:54 6511216 reads; of these: 6511216 (100.00%) were unpaired; of these: 200395 (3.08%) aligned 0 times 5321445 (81.73%) aligned exactly 1 time 989376 (15.19%) aligned >1 times 96.92% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 2834779 / 6310821 = 0.4492 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 08:07:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.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 08:07:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:57: 1000000 INFO @ Tue, 16 Jun 2020 08:08:01: 2000000 INFO @ Tue, 16 Jun 2020 08:08:06: 3000000 INFO @ Tue, 16 Jun 2020 08:08:08: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:08:08: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:08:08: #1 total tags in treatment: 3476042 INFO @ Tue, 16 Jun 2020 08:08:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:08: #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 08:08:08: #1 tags after filtering in treatment: 3476042 INFO @ Tue, 16 Jun 2020 08:08:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:08: #2 number of paired peaks: 789 WARNING @ Tue, 16 Jun 2020 08:08:08: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:08: #2 predicted fragment length is 196 bps INFO @ Tue, 16 Jun 2020 08:08:08: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 16 Jun 2020 08:08:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.05_model.r INFO @ Tue, 16 Jun 2020 08:08:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:17: #3 Call peaks for each chromosome... 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 08:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (728 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.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 08:08:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:27: 1000000 INFO @ Tue, 16 Jun 2020 08:08:32: 2000000 INFO @ Tue, 16 Jun 2020 08:08:37: 3000000 INFO @ Tue, 16 Jun 2020 08:08:39: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:08:39: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:08:39: #1 total tags in treatment: 3476042 INFO @ Tue, 16 Jun 2020 08:08:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:39: #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 08:08:39: #1 tags after filtering in treatment: 3476042 INFO @ Tue, 16 Jun 2020 08:08:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:40: #2 number of paired peaks: 789 WARNING @ Tue, 16 Jun 2020 08:08:40: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:40: #2 predicted fragment length is 196 bps INFO @ Tue, 16 Jun 2020 08:08:40: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 16 Jun 2020 08:08:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.10_model.r INFO @ Tue, 16 Jun 2020 08:08:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:48: #3 Call peaks for each chromosome... 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 08:08:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (413 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.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 08:08:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:57: 1000000 INFO @ Tue, 16 Jun 2020 08:09:02: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:09:08: 3000000 INFO @ Tue, 16 Jun 2020 08:09:10: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:09:10: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:09:10: #1 total tags in treatment: 3476042 INFO @ Tue, 16 Jun 2020 08:09:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:10: #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 08:09:10: #1 tags after filtering in treatment: 3476042 INFO @ Tue, 16 Jun 2020 08:09:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:10: #2 number of paired peaks: 789 WARNING @ Tue, 16 Jun 2020 08:09:10: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:10: #2 predicted fragment length is 196 bps INFO @ Tue, 16 Jun 2020 08:09:10: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 16 Jun 2020 08:09:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.20_model.r INFO @ Tue, 16 Jun 2020 08:09:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257642/SRX257642.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 1 millis CompletedMACS2peakCalling