Job ID = 6368217 SRX = SRX494900 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:58:20 prefetch.2.10.7: 1) Downloading 'SRR1198432'... 2020-06-15T23:58:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:56 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:56 prefetch.2.10.7: 1) 'SRR1198432' was downloaded successfully Read 16259739 spots for SRR1198432/SRR1198432.sra Written 16259739 spots for SRR1198432/SRR1198432.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: 00:02:54 16259739 reads; of these: 16259739 (100.00%) were unpaired; of these: 2800009 (17.22%) aligned 0 times 11250422 (69.19%) aligned exactly 1 time 2209308 (13.59%) aligned >1 times 82.78% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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] 4379343 / 13459730 = 0.3254 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 09:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.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 09:08:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:49: 1000000 INFO @ Tue, 16 Jun 2020 09:08:54: 2000000 INFO @ Tue, 16 Jun 2020 09:09:00: 3000000 INFO @ Tue, 16 Jun 2020 09:09:06: 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 09:09:12: 5000000 INFO @ Tue, 16 Jun 2020 09:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.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 09:09:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:18: 6000000 INFO @ Tue, 16 Jun 2020 09:09:19: 1000000 INFO @ Tue, 16 Jun 2020 09:09:25: 7000000 INFO @ Tue, 16 Jun 2020 09:09:25: 2000000 INFO @ Tue, 16 Jun 2020 09:09:31: 8000000 INFO @ Tue, 16 Jun 2020 09:09:31: 3000000 INFO @ Tue, 16 Jun 2020 09:09:37: 9000000 INFO @ Tue, 16 Jun 2020 09:09:37: 4000000 INFO @ Tue, 16 Jun 2020 09:09:37: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:09:37: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:09:37: #1 total tags in treatment: 9080387 INFO @ Tue, 16 Jun 2020 09:09:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:37: #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 09:09:38: #1 tags after filtering in treatment: 9080387 INFO @ Tue, 16 Jun 2020 09:09:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:38: #2 number of paired peaks: 698 WARNING @ Tue, 16 Jun 2020 09:09:38: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:38: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:09:38: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 16 Jun 2020 09:09:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.05_model.r INFO @ Tue, 16 Jun 2020 09:09:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:38: #3 Pre-compute pvalue-qvalue table... 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 09:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.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 09:09:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:43: 5000000 INFO @ Tue, 16 Jun 2020 09:09:49: 1000000 INFO @ Tue, 16 Jun 2020 09:09:49: 6000000 INFO @ Tue, 16 Jun 2020 09:09:55: 2000000 INFO @ Tue, 16 Jun 2020 09:09:55: 7000000 INFO @ Tue, 16 Jun 2020 09:09:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:01: 3000000 INFO @ Tue, 16 Jun 2020 09:10:02: 8000000 INFO @ Tue, 16 Jun 2020 09:10:07: 4000000 INFO @ Tue, 16 Jun 2020 09:10:08: 9000000 INFO @ Tue, 16 Jun 2020 09:10:08: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:10:08: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:10:08: #1 total tags in treatment: 9080387 INFO @ Tue, 16 Jun 2020 09:10:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:08: #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 09:10:08: #1 tags after filtering in treatment: 9080387 INFO @ Tue, 16 Jun 2020 09:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.05_summits.bed INFO @ Tue, 16 Jun 2020 09:10:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2172 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:09: #2 number of paired peaks: 698 WARNING @ Tue, 16 Jun 2020 09:10:09: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:09: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:10:09: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 16 Jun 2020 09:10:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.10_model.r INFO @ Tue, 16 Jun 2020 09:10:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:13: 5000000 INFO @ Tue, 16 Jun 2020 09:10:19: 6000000 INFO @ Tue, 16 Jun 2020 09:10:25: 7000000 INFO @ Tue, 16 Jun 2020 09:10:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:31: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:10:37: 9000000 INFO @ Tue, 16 Jun 2020 09:10:37: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:10:37: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:10:37: #1 total tags in treatment: 9080387 INFO @ Tue, 16 Jun 2020 09:10:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:37: #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 09:10:37: #1 tags after filtering in treatment: 9080387 INFO @ Tue, 16 Jun 2020 09:10:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:38: #2 number of paired peaks: 698 WARNING @ Tue, 16 Jun 2020 09:10:38: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:38: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:10:38: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 16 Jun 2020 09:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.20_model.r INFO @ Tue, 16 Jun 2020 09:10:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.10_summits.bed INFO @ Tue, 16 Jun 2020 09:10:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1332 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:10:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494900/SRX494900.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (738 records, 4 fields): 2 millis CompletedMACS2peakCalling