Job ID = 6366693 SRX = SRX2228849 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:59 prefetch.2.10.7: 1) Downloading 'SRR4380305'... 2020-06-15T22:54:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:03 prefetch.2.10.7: 'SRR4380305' is valid 2020-06-15T22:56:03 prefetch.2.10.7: 1) 'SRR4380305' was downloaded successfully Read 8154140 spots for SRR4380305/SRR4380305.sra Written 8154140 spots for SRR4380305/SRR4380305.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: 00:01:41 8154140 reads; of these: 8154140 (100.00%) were unpaired; of these: 1505815 (18.47%) aligned 0 times 5616459 (68.88%) aligned exactly 1 time 1031866 (12.65%) aligned >1 times 81.53% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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] 1478034 / 6648325 = 0.2223 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 08:00:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.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 08:00:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:27: 1000000 INFO @ Tue, 16 Jun 2020 08:00:32: 2000000 INFO @ Tue, 16 Jun 2020 08:00:38: 3000000 INFO @ Tue, 16 Jun 2020 08:00:44: 4000000 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 08:00:50: 5000000 INFO @ Tue, 16 Jun 2020 08:00:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.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 08:00:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:00:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:00:51: #1 total tags in treatment: 5170291 INFO @ Tue, 16 Jun 2020 08:00:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:51: #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 08:00:51: #1 tags after filtering in treatment: 5170291 INFO @ Tue, 16 Jun 2020 08:00:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:52: #2 number of paired peaks: 583 WARNING @ Tue, 16 Jun 2020 08:00:52: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:52: #2 predicted fragment length is 175 bps INFO @ Tue, 16 Jun 2020 08:00:52: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 16 Jun 2020 08:00:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.05_model.r INFO @ Tue, 16 Jun 2020 08:00:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:58: 1000000 INFO @ Tue, 16 Jun 2020 08:01:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:06: 2000000 INFO @ Tue, 16 Jun 2020 08:01:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.05_summits.bed INFO @ Tue, 16 Jun 2020 08:01:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (645 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:13: 3000000 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 08:01:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.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 08:01:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:21: 4000000 INFO @ Tue, 16 Jun 2020 08:01:29: 1000000 INFO @ Tue, 16 Jun 2020 08:01:30: 5000000 INFO @ Tue, 16 Jun 2020 08:01:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:01:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:01:31: #1 total tags in treatment: 5170291 INFO @ Tue, 16 Jun 2020 08:01:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:31: #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 08:01:31: #1 tags after filtering in treatment: 5170291 INFO @ Tue, 16 Jun 2020 08:01:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:31: #2 number of paired peaks: 583 WARNING @ Tue, 16 Jun 2020 08:01:31: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:31: #2 predicted fragment length is 175 bps INFO @ Tue, 16 Jun 2020 08:01:31: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 16 Jun 2020 08:01:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.10_model.r INFO @ Tue, 16 Jun 2020 08:01:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:37: 2000000 INFO @ Tue, 16 Jun 2020 08:01:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.10_summits.bed INFO @ Tue, 16 Jun 2020 08:01:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (440 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:52: 4000000 INFO @ Tue, 16 Jun 2020 08:02:00: 5000000 INFO @ Tue, 16 Jun 2020 08:02:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:01: #1 total tags in treatment: 5170291 INFO @ Tue, 16 Jun 2020 08:02:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:01: #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 08:02:01: #1 tags after filtering in treatment: 5170291 INFO @ Tue, 16 Jun 2020 08:02:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:01: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:02:02: #2 number of paired peaks: 583 WARNING @ Tue, 16 Jun 2020 08:02:02: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:02: #2 predicted fragment length is 175 bps INFO @ Tue, 16 Jun 2020 08:02:02: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 16 Jun 2020 08:02:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.20_model.r INFO @ Tue, 16 Jun 2020 08:02:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228849/SRX2228849.20_summits.bed INFO @ Tue, 16 Jun 2020 08:02:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 1 millis CompletedMACS2peakCalling