Job ID = 6367399 SRX = SRX331158 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:51 prefetch.2.10.7: 1) Downloading 'SRR947389'... 2020-06-15T23:27:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:28:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:28:23 prefetch.2.10.7: 'SRR947389' is valid 2020-06-15T23:28:23 prefetch.2.10.7: 1) 'SRR947389' was downloaded successfully Read 2506637 spots for SRR947389/SRR947389.sra Written 2506637 spots for SRR947389/SRR947389.sra 2020-06-15T23:28:40 prefetch.2.10.7: 1) Downloading 'SRR947390'... 2020-06-15T23:28:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:02 prefetch.2.10.7: 'SRR947390' is valid 2020-06-15T23:29:02 prefetch.2.10.7: 1) 'SRR947390' was downloaded successfully Read 1020157 spots for SRR947390/SRR947390.sra Written 1020157 spots for SRR947390/SRR947390.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: 00:00:21 3526794 reads; of these: 3526794 (100.00%) were unpaired; of these: 2153547 (61.06%) aligned 0 times 1173876 (33.28%) aligned exactly 1 time 199371 (5.65%) aligned >1 times 38.94% overall alignment rate Time searching: 00:00:21 Overall time: 00:00:21 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] 297889 / 1373247 = 0.2169 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 08:30:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.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 08:30:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:19: 1000000 INFO @ Tue, 16 Jun 2020 08:30:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:20: #1 total tags in treatment: 1075358 INFO @ Tue, 16 Jun 2020 08:30:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:20: #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 08:30:20: #1 tags after filtering in treatment: 1075358 INFO @ Tue, 16 Jun 2020 08:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:20: #2 number of paired peaks: 736 WARNING @ Tue, 16 Jun 2020 08:30:20: Fewer paired peaks (736) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 736 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:20: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 08:30:20: #2 alternative fragment length(s) may be 120 bps INFO @ Tue, 16 Jun 2020 08:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.05_model.r INFO @ Tue, 16 Jun 2020 08:30:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.05_summits.bed INFO @ Tue, 16 Jun 2020 08:30:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 1 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 08:30:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.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 08:30:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:49: 1000000 INFO @ Tue, 16 Jun 2020 08:30:50: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:50: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:50: #1 total tags in treatment: 1075358 INFO @ Tue, 16 Jun 2020 08:30:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:50: #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 08:30:50: #1 tags after filtering in treatment: 1075358 INFO @ Tue, 16 Jun 2020 08:30:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:50: #2 number of paired peaks: 736 WARNING @ Tue, 16 Jun 2020 08:30:50: Fewer paired peaks (736) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 736 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:50: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 08:30:50: #2 alternative fragment length(s) may be 120 bps INFO @ Tue, 16 Jun 2020 08:30:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.10_model.r INFO @ Tue, 16 Jun 2020 08:30:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.10_summits.bed INFO @ Tue, 16 Jun 2020 08:30:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (199 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 08:31:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.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 08:31:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:14: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:20: 1000000 INFO @ Tue, 16 Jun 2020 08:31:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:20: #1 total tags in treatment: 1075358 INFO @ Tue, 16 Jun 2020 08:31:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:20: #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 08:31:20: #1 tags after filtering in treatment: 1075358 INFO @ Tue, 16 Jun 2020 08:31:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:20: #2 number of paired peaks: 736 WARNING @ Tue, 16 Jun 2020 08:31:20: Fewer paired peaks (736) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 736 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:20: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 08:31:20: #2 alternative fragment length(s) may be 120 bps INFO @ Tue, 16 Jun 2020 08:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.20_model.r INFO @ Tue, 16 Jun 2020 08:31:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:31:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331158/SRX331158.20_summits.bed INFO @ Tue, 16 Jun 2020 08:31:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (46 records, 4 fields): 1 millis CompletedMACS2peakCalling