Job ID = 6368392 SRX = SRX495071 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:32 prefetch.2.10.7: 1) Downloading 'SRR1198603'... 2020-06-16T00:14:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:48 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:48 prefetch.2.10.7: 1) 'SRR1198603' was downloaded successfully Read 12966659 spots for SRR1198603/SRR1198603.sra Written 12966659 spots for SRR1198603/SRR1198603.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: 00:02:22 12966659 reads; of these: 12966659 (100.00%) were unpaired; of these: 1923460 (14.83%) aligned 0 times 9220215 (71.11%) aligned exactly 1 time 1822984 (14.06%) aligned >1 times 85.17% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 4838677 / 11043199 = 0.4382 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 09:22:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.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 09:22:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:33: 1000000 INFO @ Tue, 16 Jun 2020 09:22:38: 2000000 INFO @ Tue, 16 Jun 2020 09:22:44: 3000000 INFO @ Tue, 16 Jun 2020 09:22:49: 4000000 INFO @ Tue, 16 Jun 2020 09:22:54: 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 09:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.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 09:22:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:00: 6000000 INFO @ Tue, 16 Jun 2020 09:23:01: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:23:01: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:23:01: #1 total tags in treatment: 6204522 INFO @ Tue, 16 Jun 2020 09:23:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:01: #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 09:23:01: #1 tags after filtering in treatment: 6204522 INFO @ Tue, 16 Jun 2020 09:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:02: #2 number of paired peaks: 766 WARNING @ Tue, 16 Jun 2020 09:23:02: Fewer paired peaks (766) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 766 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:02: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:23:02: #2 alternative fragment length(s) may be 90,103 bps INFO @ Tue, 16 Jun 2020 09:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.05_model.r INFO @ Tue, 16 Jun 2020 09:23:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:04: 1000000 INFO @ Tue, 16 Jun 2020 09:23:09: 2000000 INFO @ Tue, 16 Jun 2020 09:23:14: 3000000 INFO @ Tue, 16 Jun 2020 09:23:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:20: 4000000 INFO @ Tue, 16 Jun 2020 09:23:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.05_summits.bed INFO @ Tue, 16 Jun 2020 09:23:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1435 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:23:26: 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 09:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.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 09:23:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:31: 6000000 INFO @ Tue, 16 Jun 2020 09:23:32: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:23:32: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:23:32: #1 total tags in treatment: 6204522 INFO @ Tue, 16 Jun 2020 09:23:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:32: #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 09:23:33: #1 tags after filtering in treatment: 6204522 INFO @ Tue, 16 Jun 2020 09:23:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:33: #2 number of paired peaks: 766 WARNING @ Tue, 16 Jun 2020 09:23:33: Fewer paired peaks (766) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 766 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:33: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:23:33: #2 alternative fragment length(s) may be 90,103 bps INFO @ Tue, 16 Jun 2020 09:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.10_model.r INFO @ Tue, 16 Jun 2020 09:23:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:33: 1000000 INFO @ Tue, 16 Jun 2020 09:23:39: 2000000 INFO @ Tue, 16 Jun 2020 09:23:44: 3000000 INFO @ Tue, 16 Jun 2020 09:23:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:50: 4000000 INFO @ Tue, 16 Jun 2020 09:23:55: 5000000 INFO @ Tue, 16 Jun 2020 09:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.10_summits.bed INFO @ Tue, 16 Jun 2020 09:23:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (914 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:24:01: 6000000 INFO @ Tue, 16 Jun 2020 09:24:02: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:24:02: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:24:02: #1 total tags in treatment: 6204522 INFO @ Tue, 16 Jun 2020 09:24:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:02: #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 09:24:02: #1 tags after filtering in treatment: 6204522 INFO @ Tue, 16 Jun 2020 09:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:02: #2 number of paired peaks: 766 WARNING @ Tue, 16 Jun 2020 09:24:02: Fewer paired peaks (766) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 766 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:02: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:24:02: #2 alternative fragment length(s) may be 90,103 bps INFO @ Tue, 16 Jun 2020 09:24:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.20_model.r INFO @ Tue, 16 Jun 2020 09:24:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:24:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:24:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:24:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:24:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495071/SRX495071.20_summits.bed INFO @ Tue, 16 Jun 2020 09:24:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (457 records, 4 fields): 2 millis CompletedMACS2peakCalling