Job ID = 6368213 SRX = SRX494896 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:17:51 prefetch.2.10.7: 1) Downloading 'SRR1198428'... 2020-06-16T00:17:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:47 prefetch.2.10.7: 1) 'SRR1198428' was downloaded successfully Read 45330527 spots for SRR1198428/SRR1198428.sra Written 45330527 spots for SRR1198428/SRR1198428.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: 00:09:40 45330527 reads; of these: 45330527 (100.00%) were unpaired; of these: 9825770 (21.68%) aligned 0 times 28093319 (61.97%) aligned exactly 1 time 7411438 (16.35%) aligned >1 times 78.32% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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_sort_core] merging from 16 files... [bam_rmdupse_core] 31226166 / 35504757 = 0.8795 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 09:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.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 09:43:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:55: 1000000 INFO @ Tue, 16 Jun 2020 09:44:01: 2000000 INFO @ Tue, 16 Jun 2020 09:44:06: 3000000 INFO @ Tue, 16 Jun 2020 09:44:12: 4000000 INFO @ Tue, 16 Jun 2020 09:44:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:44:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:44:14: #1 total tags in treatment: 4278591 INFO @ Tue, 16 Jun 2020 09:44:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:14: #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 09:44:14: #1 tags after filtering in treatment: 4278591 INFO @ Tue, 16 Jun 2020 09:44:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:14: #2 number of paired peaks: 1588 INFO @ Tue, 16 Jun 2020 09:44:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:14: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:44:14: #2 alternative fragment length(s) may be 3,50,580 bps INFO @ Tue, 16 Jun 2020 09:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.05_model.r WARNING @ Tue, 16 Jun 2020 09:44:15: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:15: #2 You may need to consider one of the other alternative d(s): 3,50,580 WARNING @ Tue, 16 Jun 2020 09:44:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:44:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:15: #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 09:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.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 09:44:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:25: 1000000 INFO @ Tue, 16 Jun 2020 09:44:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.05_summits.bed INFO @ Tue, 16 Jun 2020 09:44:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3896 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:31: 2000000 INFO @ Tue, 16 Jun 2020 09:44:37: 3000000 INFO @ Tue, 16 Jun 2020 09:44:43: 4000000 INFO @ Tue, 16 Jun 2020 09:44:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:44:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:44:44: #1 total tags in treatment: 4278591 INFO @ Tue, 16 Jun 2020 09:44:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:44: #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 09:44:44: #1 tags after filtering in treatment: 4278591 INFO @ Tue, 16 Jun 2020 09:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:45: #2 number of paired peaks: 1588 INFO @ Tue, 16 Jun 2020 09:44:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:45: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:44:45: #2 alternative fragment length(s) may be 3,50,580 bps INFO @ Tue, 16 Jun 2020 09:44:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.10_model.r WARNING @ Tue, 16 Jun 2020 09:44:45: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:45: #2 You may need to consider one of the other alternative d(s): 3,50,580 WARNING @ Tue, 16 Jun 2020 09:44:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:44:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:45: #3 Pre-compute pvalue-qvalue table... 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 09:44:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.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 09:44:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:56: 1000000 INFO @ Tue, 16 Jun 2020 09:44:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.10_summits.bed INFO @ Tue, 16 Jun 2020 09:44:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1613 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:03: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:45:10: 3000000 INFO @ Tue, 16 Jun 2020 09:45:16: 4000000 INFO @ Tue, 16 Jun 2020 09:45:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:18: #1 total tags in treatment: 4278591 INFO @ Tue, 16 Jun 2020 09:45:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:18: #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 09:45:18: #1 tags after filtering in treatment: 4278591 INFO @ Tue, 16 Jun 2020 09:45:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:19: #2 number of paired peaks: 1588 INFO @ Tue, 16 Jun 2020 09:45:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:19: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:45:19: #2 alternative fragment length(s) may be 3,50,580 bps INFO @ Tue, 16 Jun 2020 09:45:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.20_model.r WARNING @ Tue, 16 Jun 2020 09:45:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:19: #2 You may need to consider one of the other alternative d(s): 3,50,580 WARNING @ Tue, 16 Jun 2020 09:45:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:45:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:45:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494896/SRX494896.20_summits.bed INFO @ Tue, 16 Jun 2020 09:45:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (448 records, 4 fields): 2 millis CompletedMACS2peakCalling