Job ID = 6367256 SRX = SRX323677 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:22:16 prefetch.2.10.7: 1) Downloading 'SRR935751'... 2020-06-15T23:22:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:14 prefetch.2.10.7: 'SRR935751' is valid 2020-06-15T23:23:14 prefetch.2.10.7: 1) 'SRR935751' was downloaded successfully Read 9253546 spots for SRR935751/SRR935751.sra Written 9253546 spots for SRR935751/SRR935751.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: 00:02:03 9253546 reads; of these: 9253546 (100.00%) were unpaired; of these: 2799758 (30.26%) aligned 0 times 5414194 (58.51%) aligned exactly 1 time 1039594 (11.23%) aligned >1 times 69.74% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 2024633 / 6453788 = 0.3137 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 08:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.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 08:27:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:57: 1000000 INFO @ Tue, 16 Jun 2020 08:28:03: 2000000 INFO @ Tue, 16 Jun 2020 08:28:09: 3000000 INFO @ Tue, 16 Jun 2020 08:28:15: 4000000 INFO @ Tue, 16 Jun 2020 08:28:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:18: #1 total tags in treatment: 4429155 INFO @ Tue, 16 Jun 2020 08:28:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:18: #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 08:28:18: #1 tags after filtering in treatment: 4429155 INFO @ Tue, 16 Jun 2020 08:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:18: #2 number of paired peaks: 163 WARNING @ Tue, 16 Jun 2020 08:28:18: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:18: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:28:18: #2 alternative fragment length(s) may be 4,132,151,597 bps INFO @ Tue, 16 Jun 2020 08:28:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.05_model.r INFO @ Tue, 16 Jun 2020 08:28:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:18: #3 Pre-compute pvalue-qvalue table... 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 08:28:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.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 08:28:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:28: 1000000 INFO @ Tue, 16 Jun 2020 08:28:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (293 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:35: 2000000 INFO @ Tue, 16 Jun 2020 08:28:42: 3000000 INFO @ Tue, 16 Jun 2020 08:28:49: 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 08:28:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.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 08:28:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:52: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:52: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:52: #1 total tags in treatment: 4429155 INFO @ Tue, 16 Jun 2020 08:28:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:52: #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 08:28:52: #1 tags after filtering in treatment: 4429155 INFO @ Tue, 16 Jun 2020 08:28:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:53: #2 number of paired peaks: 163 WARNING @ Tue, 16 Jun 2020 08:28:53: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:53: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:28:53: #2 alternative fragment length(s) may be 4,132,151,597 bps INFO @ Tue, 16 Jun 2020 08:28:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.10_model.r INFO @ Tue, 16 Jun 2020 08:28:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:57: 1000000 INFO @ Tue, 16 Jun 2020 08:29:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:04: 2000000 INFO @ Tue, 16 Jun 2020 08:29:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.10_summits.bed INFO @ Tue, 16 Jun 2020 08:29:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (124 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:29:10: 3000000 INFO @ Tue, 16 Jun 2020 08:29:16: 4000000 INFO @ Tue, 16 Jun 2020 08:29:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:29:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:29:18: #1 total tags in treatment: 4429155 INFO @ Tue, 16 Jun 2020 08:29:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:18: #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 08:29:18: #1 tags after filtering in treatment: 4429155 INFO @ Tue, 16 Jun 2020 08:29:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:19: #2 number of paired peaks: 163 WARNING @ Tue, 16 Jun 2020 08:29:19: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:19: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:29:19: #2 alternative fragment length(s) may be 4,132,151,597 bps INFO @ Tue, 16 Jun 2020 08:29:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.20_model.r INFO @ Tue, 16 Jun 2020 08:29:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:29:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323677/SRX323677.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 1 millis CompletedMACS2peakCalling