Job ID = 6367318 SRX = SRX331080 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:23:46 prefetch.2.10.7: 1) Downloading 'SRR947306'... 2020-06-15T23:23:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:06 prefetch.2.10.7: 'SRR947306' is valid 2020-06-15T23:24:06 prefetch.2.10.7: 1) 'SRR947306' was downloaded successfully Read 4779497 spots for SRR947306/SRR947306.sra Written 4779497 spots for SRR947306/SRR947306.sra 2020-06-15T23:24:29 prefetch.2.10.7: 1) Downloading 'SRR947307'... 2020-06-15T23:24:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:54 prefetch.2.10.7: 'SRR947307' is valid 2020-06-15T23:24:54 prefetch.2.10.7: 1) 'SRR947307' was downloaded successfully Read 3456980 spots for SRR947307/SRR947307.sra Written 3456980 spots for SRR947307/SRR947307.sra 2020-06-15T23:25:14 prefetch.2.10.7: 1) Downloading 'SRR947308'... 2020-06-15T23:25:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:25:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:25:31 prefetch.2.10.7: 'SRR947308' is valid 2020-06-15T23:25:31 prefetch.2.10.7: 1) 'SRR947308' was downloaded successfully Read 3515168 spots for SRR947308/SRR947308.sra Written 3515168 spots for SRR947308/SRR947308.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: 00:00:35 11751645 reads; of these: 11751645 (100.00%) were unpaired; of these: 10425211 (88.71%) aligned 0 times 1122655 (9.55%) aligned exactly 1 time 203779 (1.73%) aligned >1 times 11.29% overall alignment rate Time searching: 00:00:35 Overall time: 00:00:35 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] 133468 / 1326434 = 0.1006 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 08:27:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.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 08:27:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:12: 1000000 INFO @ Tue, 16 Jun 2020 08:27:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:13: #1 total tags in treatment: 1192966 INFO @ Tue, 16 Jun 2020 08:27:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:13: #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 08:27:13: #1 tags after filtering in treatment: 1192966 INFO @ Tue, 16 Jun 2020 08:27:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:13: #2 number of paired peaks: 784 WARNING @ Tue, 16 Jun 2020 08:27:13: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:13: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 08:27:13: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 16 Jun 2020 08:27:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.05_model.r INFO @ Tue, 16 Jun 2020 08:27:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (965 records, 4 fields): 8 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 08:27:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.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 08:27:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:42: 1000000 INFO @ Tue, 16 Jun 2020 08:27:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:43: #1 total tags in treatment: 1192966 INFO @ Tue, 16 Jun 2020 08:27:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:43: #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 08:27:43: #1 tags after filtering in treatment: 1192966 INFO @ Tue, 16 Jun 2020 08:27:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:43: #2 number of paired peaks: 784 WARNING @ Tue, 16 Jun 2020 08:27:43: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:43: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 08:27:43: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 16 Jun 2020 08:27:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.10_model.r INFO @ Tue, 16 Jun 2020 08:27:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (291 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 08:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.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 08:28:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:07: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:12: 1000000 INFO @ Tue, 16 Jun 2020 08:28:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:13: #1 total tags in treatment: 1192966 INFO @ Tue, 16 Jun 2020 08:28:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:13: #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 08:28:13: #1 tags after filtering in treatment: 1192966 INFO @ Tue, 16 Jun 2020 08:28:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:13: #2 number of paired peaks: 784 WARNING @ Tue, 16 Jun 2020 08:28:13: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:13: start X-correlation... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:13: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 08:28:13: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 16 Jun 2020 08:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.20_model.r INFO @ Tue, 16 Jun 2020 08:28:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331080/SRX331080.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling