Job ID = 6366899 SRX = SRX257644 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:38 prefetch.2.10.7: 1) Downloading 'SRR800655'... 2020-06-15T23:05:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:10 prefetch.2.10.7: 'SRR800655' is valid 2020-06-15T23:06:10 prefetch.2.10.7: 1) 'SRR800655' was downloaded successfully Read 9699963 spots for SRR800655/SRR800655.sra Written 9699963 spots for SRR800655/SRR800655.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: 00:01:21 9699963 reads; of these: 9699963 (100.00%) were unpaired; of these: 176203 (1.82%) aligned 0 times 7900613 (81.45%) aligned exactly 1 time 1623147 (16.73%) aligned >1 times 98.18% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 4380260 / 9523760 = 0.4599 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 08:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.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 08:09:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:53: 1000000 INFO @ Tue, 16 Jun 2020 08:09:58: 2000000 INFO @ Tue, 16 Jun 2020 08:10:02: 3000000 INFO @ Tue, 16 Jun 2020 08:10:07: 4000000 INFO @ Tue, 16 Jun 2020 08:10:12: 5000000 INFO @ Tue, 16 Jun 2020 08:10:13: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:10:13: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:10:13: #1 total tags in treatment: 5143500 INFO @ Tue, 16 Jun 2020 08:10:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:13: #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 08:10:13: #1 tags after filtering in treatment: 5143500 INFO @ Tue, 16 Jun 2020 08:10:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:13: #2 number of paired peaks: 616 WARNING @ Tue, 16 Jun 2020 08:10:13: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:13: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 08:10:13: #2 alternative fragment length(s) may be 3,70,114 bps INFO @ Tue, 16 Jun 2020 08:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.05_model.r INFO @ Tue, 16 Jun 2020 08:10:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:13: #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 08:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.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 08:10:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:24: 1000000 INFO @ Tue, 16 Jun 2020 08:10:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:30: 2000000 INFO @ Tue, 16 Jun 2020 08:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.05_summits.bed INFO @ Tue, 16 Jun 2020 08:10:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (658 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:10:36: 3000000 INFO @ Tue, 16 Jun 2020 08:10:41: 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 08:10:47: 5000000 INFO @ Tue, 16 Jun 2020 08:10:48: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:10:48: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:10:48: #1 total tags in treatment: 5143500 INFO @ Tue, 16 Jun 2020 08:10:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:48: #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 08:10:48: #1 tags after filtering in treatment: 5143500 INFO @ Tue, 16 Jun 2020 08:10:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.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 08:10:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:48: #2 number of paired peaks: 616 WARNING @ Tue, 16 Jun 2020 08:10:48: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:48: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 08:10:48: #2 alternative fragment length(s) may be 3,70,114 bps INFO @ Tue, 16 Jun 2020 08:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.10_model.r INFO @ Tue, 16 Jun 2020 08:10:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:53: 1000000 INFO @ Tue, 16 Jun 2020 08:10:59: 2000000 INFO @ Tue, 16 Jun 2020 08:11:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:04: 3000000 INFO @ Tue, 16 Jun 2020 08:11:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.10_summits.bed INFO @ Tue, 16 Jun 2020 08:11:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:11:10: 4000000 INFO @ Tue, 16 Jun 2020 08:11:15: 5000000 INFO @ Tue, 16 Jun 2020 08:11:15: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:11:15: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:11:15: #1 total tags in treatment: 5143500 INFO @ Tue, 16 Jun 2020 08:11:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:15: #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 08:11:15: #1 tags after filtering in treatment: 5143500 INFO @ Tue, 16 Jun 2020 08:11:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:16: #2 number of paired peaks: 616 WARNING @ Tue, 16 Jun 2020 08:11:16: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:16: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 08:11:16: #2 alternative fragment length(s) may be 3,70,114 bps INFO @ Tue, 16 Jun 2020 08:11:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.20_model.r INFO @ Tue, 16 Jun 2020 08:11:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257644/SRX257644.20_summits.bed INFO @ Tue, 16 Jun 2020 08:11:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (209 records, 4 fields): 2 millis CompletedMACS2peakCalling