Job ID = 6366898 SRX = SRX257643 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:23 prefetch.2.10.7: 1) Downloading 'SRR800654'... 2020-06-15T23:05:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:53 prefetch.2.10.7: 'SRR800654' is valid 2020-06-15T23:05:53 prefetch.2.10.7: 1) 'SRR800654' was downloaded successfully Read 8060704 spots for SRR800654/SRR800654.sra Written 8060704 spots for SRR800654/SRR800654.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: 00:01:32 8060704 reads; of these: 8060704 (100.00%) were unpaired; of these: 270987 (3.36%) aligned 0 times 6321759 (78.43%) aligned exactly 1 time 1467958 (18.21%) aligned >1 times 96.64% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 2325168 / 7789717 = 0.2985 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 08:09:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.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 08:09:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:01: 1000000 INFO @ Tue, 16 Jun 2020 08:10:07: 2000000 INFO @ Tue, 16 Jun 2020 08:10:12: 3000000 INFO @ Tue, 16 Jun 2020 08:10:18: 4000000 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 08:10:24: 5000000 INFO @ Tue, 16 Jun 2020 08:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.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 08:10:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:27: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:10:27: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:10:27: #1 total tags in treatment: 5464549 INFO @ Tue, 16 Jun 2020 08:10:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:27: #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 08:10:27: #1 tags after filtering in treatment: 5464549 INFO @ Tue, 16 Jun 2020 08:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:27: #2 number of paired peaks: 843 WARNING @ Tue, 16 Jun 2020 08:10:27: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:27: #2 predicted fragment length is 190 bps INFO @ Tue, 16 Jun 2020 08:10:27: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 16 Jun 2020 08:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.05_model.r INFO @ Tue, 16 Jun 2020 08:10:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:31: 1000000 INFO @ Tue, 16 Jun 2020 08:10:38: 2000000 INFO @ Tue, 16 Jun 2020 08:10:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:45: 3000000 INFO @ Tue, 16 Jun 2020 08:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.05_summits.bed INFO @ Tue, 16 Jun 2020 08:10:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3317 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:10:51: 4000000 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 08:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.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 08:10:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:58: 5000000 INFO @ Tue, 16 Jun 2020 08:11:01: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:11:01: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:11:01: #1 total tags in treatment: 5464549 INFO @ Tue, 16 Jun 2020 08:11:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:01: #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 08:11:01: #1 tags after filtering in treatment: 5464549 INFO @ Tue, 16 Jun 2020 08:11:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:01: 1000000 INFO @ Tue, 16 Jun 2020 08:11:01: #2 number of paired peaks: 843 WARNING @ Tue, 16 Jun 2020 08:11:01: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:02: #2 predicted fragment length is 190 bps INFO @ Tue, 16 Jun 2020 08:11:02: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 16 Jun 2020 08:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.10_model.r INFO @ Tue, 16 Jun 2020 08:11:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:07: 2000000 INFO @ Tue, 16 Jun 2020 08:11:13: 3000000 INFO @ Tue, 16 Jun 2020 08:11:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:19: 4000000 INFO @ Tue, 16 Jun 2020 08:11:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.10_summits.bed INFO @ Tue, 16 Jun 2020 08:11:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1386 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:25: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:11:27: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:11:27: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:11:27: #1 total tags in treatment: 5464549 INFO @ Tue, 16 Jun 2020 08:11:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:27: #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 08:11:27: #1 tags after filtering in treatment: 5464549 INFO @ Tue, 16 Jun 2020 08:11:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:28: #2 number of paired peaks: 843 WARNING @ Tue, 16 Jun 2020 08:11:28: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:28: #2 predicted fragment length is 190 bps INFO @ Tue, 16 Jun 2020 08:11:28: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 16 Jun 2020 08:11:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.20_model.r INFO @ Tue, 16 Jun 2020 08:11:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257643/SRX257643.20_summits.bed INFO @ Tue, 16 Jun 2020 08:11:50: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (577 records, 4 fields): 2 millis CompletedMACS2peakCalling