Job ID = 6366793 SRX = SRX233458 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:56:14 prefetch.2.10.7: 1) Downloading 'SRR701514'... 2020-06-15T22:56:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:58 prefetch.2.10.7: 'SRR701514' is valid 2020-06-15T22:56:58 prefetch.2.10.7: 1) 'SRR701514' was downloaded successfully Read 9036519 spots for SRR701514/SRR701514.sra Written 9036519 spots for SRR701514/SRR701514.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: 00:01:17 9036519 reads; of these: 9036519 (100.00%) were unpaired; of these: 1239009 (13.71%) aligned 0 times 6564411 (72.64%) aligned exactly 1 time 1233099 (13.65%) aligned >1 times 86.29% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 749077 / 7797510 = 0.0961 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 08:00:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.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 08:00:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:34: 1000000 INFO @ Tue, 16 Jun 2020 08:00:40: 2000000 INFO @ Tue, 16 Jun 2020 08:00:45: 3000000 INFO @ Tue, 16 Jun 2020 08:00:51: 4000000 INFO @ Tue, 16 Jun 2020 08:00:56: 5000000 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 08:00:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.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 08:00:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:02: 6000000 INFO @ Tue, 16 Jun 2020 08:01:04: 1000000 INFO @ Tue, 16 Jun 2020 08:01:08: 7000000 INFO @ Tue, 16 Jun 2020 08:01:08: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:01:08: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:01:08: #1 total tags in treatment: 7048433 INFO @ Tue, 16 Jun 2020 08:01:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:08: #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 08:01:08: #1 tags after filtering in treatment: 7048433 INFO @ Tue, 16 Jun 2020 08:01:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:09: #2 number of paired peaks: 432 WARNING @ Tue, 16 Jun 2020 08:01:09: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:09: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 08:01:09: #2 alternative fragment length(s) may be 4,41,92,565,573,579 bps INFO @ Tue, 16 Jun 2020 08:01:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.05_model.r INFO @ Tue, 16 Jun 2020 08:01:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:09: 2000000 INFO @ Tue, 16 Jun 2020 08:01:14: 3000000 INFO @ Tue, 16 Jun 2020 08:01:20: 4000000 INFO @ Tue, 16 Jun 2020 08:01:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:25: 5000000 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 08:01:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.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 08:01:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:30: 6000000 INFO @ Tue, 16 Jun 2020 08:01:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.05_summits.bed INFO @ Tue, 16 Jun 2020 08:01:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1622 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:34: 1000000 INFO @ Tue, 16 Jun 2020 08:01:35: 7000000 INFO @ Tue, 16 Jun 2020 08:01:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:01:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:01:35: #1 total tags in treatment: 7048433 INFO @ Tue, 16 Jun 2020 08:01:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:35: #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 08:01:35: #1 tags after filtering in treatment: 7048433 INFO @ Tue, 16 Jun 2020 08:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:36: #2 number of paired peaks: 432 WARNING @ Tue, 16 Jun 2020 08:01:36: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:36: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 08:01:36: #2 alternative fragment length(s) may be 4,41,92,565,573,579 bps INFO @ Tue, 16 Jun 2020 08:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.10_model.r INFO @ Tue, 16 Jun 2020 08:01:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:39: 2000000 INFO @ Tue, 16 Jun 2020 08:01:44: 3000000 INFO @ Tue, 16 Jun 2020 08:01:49: 4000000 INFO @ Tue, 16 Jun 2020 08:01:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:54: 5000000 INFO @ Tue, 16 Jun 2020 08:01:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.10_summits.bed INFO @ Tue, 16 Jun 2020 08:01:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (827 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:59: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:02:05: 7000000 INFO @ Tue, 16 Jun 2020 08:02:05: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:02:05: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:02:05: #1 total tags in treatment: 7048433 INFO @ Tue, 16 Jun 2020 08:02:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:05: #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 08:02:05: #1 tags after filtering in treatment: 7048433 INFO @ Tue, 16 Jun 2020 08:02:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:05: #2 number of paired peaks: 432 WARNING @ Tue, 16 Jun 2020 08:02:05: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:05: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 08:02:05: #2 alternative fragment length(s) may be 4,41,92,565,573,579 bps INFO @ Tue, 16 Jun 2020 08:02:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.20_model.r INFO @ Tue, 16 Jun 2020 08:02:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:02:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233458/SRX233458.20_summits.bed INFO @ Tue, 16 Jun 2020 08:02:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (279 records, 4 fields): 1 millis CompletedMACS2peakCalling