Job ID = 6367703 SRX = SRX395527 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:05 prefetch.2.10.7: 1) Downloading 'SRR1054254'... 2020-06-15T23:34:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:40 prefetch.2.10.7: 'SRR1054254' is valid 2020-06-15T23:34:40 prefetch.2.10.7: 1) 'SRR1054254' was downloaded successfully Read 4889143 spots for SRR1054254/SRR1054254.sra Written 4889143 spots for SRR1054254/SRR1054254.sra 2020-06-15T23:35:04 prefetch.2.10.7: 1) Downloading 'SRR1054255'... 2020-06-15T23:35:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:44 prefetch.2.10.7: 'SRR1054255' is valid 2020-06-15T23:35:44 prefetch.2.10.7: 1) 'SRR1054255' was downloaded successfully Read 5689358 spots for SRR1054255/SRR1054255.sra Written 5689358 spots for SRR1054255/SRR1054255.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: 00:01:04 10578501 reads; of these: 10578501 (100.00%) were unpaired; of these: 5603363 (52.97%) aligned 0 times 4047702 (38.26%) aligned exactly 1 time 927436 (8.77%) aligned >1 times 47.03% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 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] 2131902 / 4975138 = 0.4285 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 08:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.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 08:38:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:31: 1000000 INFO @ Tue, 16 Jun 2020 08:38:37: 2000000 INFO @ Tue, 16 Jun 2020 08:38:42: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:38:42: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:38:42: #1 total tags in treatment: 2843236 INFO @ Tue, 16 Jun 2020 08:38:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:42: #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 08:38:42: #1 tags after filtering in treatment: 2843236 INFO @ Tue, 16 Jun 2020 08:38:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:42: #2 number of paired peaks: 950 WARNING @ Tue, 16 Jun 2020 08:38:42: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:42: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 08:38:42: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 16 Jun 2020 08:38:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.05_model.r INFO @ Tue, 16 Jun 2020 08:38:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:38:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.05_summits.bed INFO @ Tue, 16 Jun 2020 08:38:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2008 records, 4 fields): 3 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 08:38:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.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 08:38:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:01: 1000000 INFO @ Tue, 16 Jun 2020 08:39:07: 2000000 INFO @ Tue, 16 Jun 2020 08:39:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:39:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:39:12: #1 total tags in treatment: 2843236 INFO @ Tue, 16 Jun 2020 08:39:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:12: #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 08:39:12: #1 tags after filtering in treatment: 2843236 INFO @ Tue, 16 Jun 2020 08:39:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:12: #2 number of paired peaks: 950 WARNING @ Tue, 16 Jun 2020 08:39:12: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:13: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 08:39:13: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 16 Jun 2020 08:39:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.10_model.r INFO @ Tue, 16 Jun 2020 08:39:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:20: #3 Call peaks for each chromosome... BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:39:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.10_summits.bed 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 08:39:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1102 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.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 08:39:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:31: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:39:37: 2000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:39:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:39:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:39:43: #1 total tags in treatment: 2843236 INFO @ Tue, 16 Jun 2020 08:39:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:43: #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 08:39:43: #1 tags after filtering in treatment: 2843236 INFO @ Tue, 16 Jun 2020 08:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:43: #2 number of paired peaks: 950 WARNING @ Tue, 16 Jun 2020 08:39:43: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:43: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 08:39:43: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 16 Jun 2020 08:39:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.20_model.r INFO @ Tue, 16 Jun 2020 08:39:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395527/SRX395527.20_summits.bed INFO @ Tue, 16 Jun 2020 08:39:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (483 records, 4 fields): 2 millis CompletedMACS2peakCalling