Job ID = 6366982 SRX = SRX257681 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:11:46 prefetch.2.10.7: 1) Downloading 'SRR800697'... 2020-06-15T23:11:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:39 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:39 prefetch.2.10.7: 'SRR800697' is valid 2020-06-15T23:12:39 prefetch.2.10.7: 1) 'SRR800697' was downloaded successfully Read 12195002 spots for SRR800697/SRR800697.sra Written 12195002 spots for SRR800697/SRR800697.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: 00:02:19 12195002 reads; of these: 12195002 (100.00%) were unpaired; of these: 1091721 (8.95%) aligned 0 times 9265840 (75.98%) aligned exactly 1 time 1837441 (15.07%) aligned >1 times 91.05% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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] 4329181 / 11103281 = 0.3899 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 08:18:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.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 08:18:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:24: 1000000 INFO @ Tue, 16 Jun 2020 08:18:29: 2000000 INFO @ Tue, 16 Jun 2020 08:18:35: 3000000 INFO @ Tue, 16 Jun 2020 08:18:41: 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 08:18:47: 5000000 INFO @ Tue, 16 Jun 2020 08:18:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.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 08:18:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:53: 6000000 INFO @ Tue, 16 Jun 2020 08:18:54: 1000000 INFO @ Tue, 16 Jun 2020 08:18:58: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:18:58: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:18:58: #1 total tags in treatment: 6774100 INFO @ Tue, 16 Jun 2020 08:18:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:58: #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 08:18:58: #1 tags after filtering in treatment: 6774100 INFO @ Tue, 16 Jun 2020 08:18:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:59: #2 number of paired peaks: 501 WARNING @ Tue, 16 Jun 2020 08:18:59: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:59: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:18:59: #2 alternative fragment length(s) may be 3,41 bps INFO @ Tue, 16 Jun 2020 08:18:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.05_model.r WARNING @ Tue, 16 Jun 2020 08:18:59: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:59: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Tue, 16 Jun 2020 08:18:59: #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 08:18:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:01: 2000000 INFO @ Tue, 16 Jun 2020 08:19:07: 3000000 INFO @ Tue, 16 Jun 2020 08:19:12: 4000000 INFO @ Tue, 16 Jun 2020 08:19:13: #3 Call peaks for each chromosome... 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 08:19:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.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 08:19:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:18: 5000000 INFO @ Tue, 16 Jun 2020 08:19:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.05_summits.bed INFO @ Tue, 16 Jun 2020 08:19:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (817 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:19:24: 1000000 INFO @ Tue, 16 Jun 2020 08:19:25: 6000000 INFO @ Tue, 16 Jun 2020 08:19:30: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:19:30: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:19:30: #1 total tags in treatment: 6774100 INFO @ Tue, 16 Jun 2020 08:19:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:30: #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 08:19:30: #1 tags after filtering in treatment: 6774100 INFO @ Tue, 16 Jun 2020 08:19:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:30: #2 number of paired peaks: 501 WARNING @ Tue, 16 Jun 2020 08:19:30: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:31: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:19:31: #2 alternative fragment length(s) may be 3,41 bps INFO @ Tue, 16 Jun 2020 08:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.10_model.r WARNING @ Tue, 16 Jun 2020 08:19:31: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:31: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Tue, 16 Jun 2020 08:19:31: #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 08:19:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:31: 2000000 INFO @ Tue, 16 Jun 2020 08:19:37: 3000000 INFO @ Tue, 16 Jun 2020 08:19:43: 4000000 INFO @ Tue, 16 Jun 2020 08:19:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:48: 5000000 INFO @ Tue, 16 Jun 2020 08:19:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.10_summits.bed INFO @ Tue, 16 Jun 2020 08:19:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (384 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:19:54: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:19:59: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:19:59: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:19:59: #1 total tags in treatment: 6774100 INFO @ Tue, 16 Jun 2020 08:19:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:59: #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 08:19:59: #1 tags after filtering in treatment: 6774100 INFO @ Tue, 16 Jun 2020 08:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:59: #2 number of paired peaks: 501 WARNING @ Tue, 16 Jun 2020 08:19:59: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:59: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:19:59: #2 alternative fragment length(s) may be 3,41 bps INFO @ Tue, 16 Jun 2020 08:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.20_model.r WARNING @ Tue, 16 Jun 2020 08:19:59: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:59: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Tue, 16 Jun 2020 08:19:59: #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 08:19:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:20:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257681/SRX257681.20_summits.bed INFO @ Tue, 16 Jun 2020 08:20:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 0 millis CompletedMACS2peakCalling