Job ID = 6367430 SRX = SRX331188 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:35:50 prefetch.2.10.7: 1) Downloading 'SRR947420'... 2020-06-15T23:35:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:29 prefetch.2.10.7: 'SRR947420' is valid 2020-06-15T23:36:29 prefetch.2.10.7: 1) 'SRR947420' was downloaded successfully Read 7928979 spots for SRR947420/SRR947420.sra Written 7928979 spots for SRR947420/SRR947420.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: 00:01:08 7928979 reads; of these: 7928979 (100.00%) were unpaired; of these: 1110932 (14.01%) aligned 0 times 5726566 (72.22%) aligned exactly 1 time 1091481 (13.77%) aligned >1 times 85.99% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 1604917 / 6818047 = 0.2354 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 08:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.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 08:39:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:03: 1000000 INFO @ Tue, 16 Jun 2020 08:40:08: 2000000 INFO @ Tue, 16 Jun 2020 08:40:13: 3000000 INFO @ Tue, 16 Jun 2020 08:40:18: 4000000 INFO @ Tue, 16 Jun 2020 08:40:24: 5000000 INFO @ Tue, 16 Jun 2020 08:40:25: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:25: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:25: #1 total tags in treatment: 5213130 INFO @ Tue, 16 Jun 2020 08:40:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:25: #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 08:40:25: #1 tags after filtering in treatment: 5213130 INFO @ Tue, 16 Jun 2020 08:40:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:25: #2 number of paired peaks: 525 WARNING @ Tue, 16 Jun 2020 08:40:25: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:25: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 08:40:25: #2 alternative fragment length(s) may be 4,48,53,55,62,91 bps INFO @ Tue, 16 Jun 2020 08:40:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.05_model.r INFO @ Tue, 16 Jun 2020 08:40:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:25: #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 08:40:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.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 08:40:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:35: 1000000 INFO @ Tue, 16 Jun 2020 08:40:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:41: 2000000 INFO @ Tue, 16 Jun 2020 08:40:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1337 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:47: 3000000 INFO @ Tue, 16 Jun 2020 08:40:53: 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 08:40:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.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 08:40:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:00: 5000000 INFO @ Tue, 16 Jun 2020 08:41:01: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:41:01: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:41:01: #1 total tags in treatment: 5213130 INFO @ Tue, 16 Jun 2020 08:41:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:01: #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 08:41:01: #1 tags after filtering in treatment: 5213130 INFO @ Tue, 16 Jun 2020 08:41:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:01: #2 number of paired peaks: 525 WARNING @ Tue, 16 Jun 2020 08:41:01: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:01: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 08:41:01: #2 alternative fragment length(s) may be 4,48,53,55,62,91 bps INFO @ Tue, 16 Jun 2020 08:41:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.10_model.r INFO @ Tue, 16 Jun 2020 08:41:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:05: 1000000 INFO @ Tue, 16 Jun 2020 08:41:11: 2000000 INFO @ Tue, 16 Jun 2020 08:41:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:17: 3000000 INFO @ Tue, 16 Jun 2020 08:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.10_summits.bed INFO @ Tue, 16 Jun 2020 08:41:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (672 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:23: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:41:30: 5000000 INFO @ Tue, 16 Jun 2020 08:41:31: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:41:31: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:41:31: #1 total tags in treatment: 5213130 INFO @ Tue, 16 Jun 2020 08:41:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:31: #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 08:41:31: #1 tags after filtering in treatment: 5213130 INFO @ Tue, 16 Jun 2020 08:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:32: #2 number of paired peaks: 525 WARNING @ Tue, 16 Jun 2020 08:41:32: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:32: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 08:41:32: #2 alternative fragment length(s) may be 4,48,53,55,62,91 bps INFO @ Tue, 16 Jun 2020 08:41:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.20_model.r INFO @ Tue, 16 Jun 2020 08:41:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331188/SRX331188.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 1 millis CompletedMACS2peakCalling