Job ID = 6365834 SRX = ERX1999205 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:20:14 prefetch.2.10.7: 1) Downloading 'ERR1938672'... 2020-06-15T22:20:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:21:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:21:03 prefetch.2.10.7: 'ERR1938672' is valid 2020-06-15T22:21:04 prefetch.2.10.7: 1) 'ERR1938672' was downloaded successfully Read 9249716 spots for ERR1938672/ERR1938672.sra Written 9249716 spots for ERR1938672/ERR1938672.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: 00:02:16 9249716 reads; of these: 9249716 (100.00%) were unpaired; of these: 860373 (9.30%) aligned 0 times 4998673 (54.04%) aligned exactly 1 time 3390670 (36.66%) aligned >1 times 90.70% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 3458592 / 8389343 = 0.4123 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 07:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.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 07:25:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:25:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:25:59: 1000000 INFO @ Tue, 16 Jun 2020 07:26:04: 2000000 INFO @ Tue, 16 Jun 2020 07:26:09: 3000000 INFO @ Tue, 16 Jun 2020 07:26:14: 4000000 INFO @ Tue, 16 Jun 2020 07:26:18: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:26:18: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:26:18: #1 total tags in treatment: 4930751 INFO @ Tue, 16 Jun 2020 07:26:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:26:18: #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 07:26:18: #1 tags after filtering in treatment: 4930751 INFO @ Tue, 16 Jun 2020 07:26:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:26:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:26:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:26:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:26:19: #2 number of paired peaks: 3770 INFO @ Tue, 16 Jun 2020 07:26:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:26:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:26:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:26:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:26:19: #2 predicted fragment length is 56 bps INFO @ Tue, 16 Jun 2020 07:26:19: #2 alternative fragment length(s) may be 3,56,94,113 bps INFO @ Tue, 16 Jun 2020 07:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.05_model.r WARNING @ Tue, 16 Jun 2020 07:26:19: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:26:19: #2 You may need to consider one of the other alternative d(s): 3,56,94,113 WARNING @ Tue, 16 Jun 2020 07:26:19: #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 07:26:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:26:19: #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 07:26:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.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 07:26:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:26:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:26:30: 1000000 INFO @ Tue, 16 Jun 2020 07:26:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:26:36: 2000000 INFO @ Tue, 16 Jun 2020 07:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.05_summits.bed INFO @ Tue, 16 Jun 2020 07:26:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1075 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:26:42: 3000000 INFO @ Tue, 16 Jun 2020 07:26:47: 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 07:26:53: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:26:53: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:26:53: #1 total tags in treatment: 4930751 INFO @ Tue, 16 Jun 2020 07:26:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:26:53: #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 07:26:53: #1 tags after filtering in treatment: 4930751 INFO @ Tue, 16 Jun 2020 07:26:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:26:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:26:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:26:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:26:53: #2 number of paired peaks: 3770 INFO @ Tue, 16 Jun 2020 07:26:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:26:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:26:54: end of X-cor INFO @ Tue, 16 Jun 2020 07:26:54: #2 finished! INFO @ Tue, 16 Jun 2020 07:26:54: #2 predicted fragment length is 56 bps INFO @ Tue, 16 Jun 2020 07:26:54: #2 alternative fragment length(s) may be 3,56,94,113 bps INFO @ Tue, 16 Jun 2020 07:26:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.10_model.r WARNING @ Tue, 16 Jun 2020 07:26:54: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:26:54: #2 You may need to consider one of the other alternative d(s): 3,56,94,113 WARNING @ Tue, 16 Jun 2020 07:26:54: #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 07:26:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:26:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.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 07:26:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:26:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:26:59: 1000000 INFO @ Tue, 16 Jun 2020 07:27:04: 2000000 INFO @ Tue, 16 Jun 2020 07:27:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:27:09: 3000000 INFO @ Tue, 16 Jun 2020 07:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.10_summits.bed INFO @ Tue, 16 Jun 2020 07:27:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (371 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:27:13: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:27:18: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:27:18: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:27:18: #1 total tags in treatment: 4930751 INFO @ Tue, 16 Jun 2020 07:27:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:27:18: #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 07:27:18: #1 tags after filtering in treatment: 4930751 INFO @ Tue, 16 Jun 2020 07:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:27:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:27:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:27:19: #2 number of paired peaks: 3770 INFO @ Tue, 16 Jun 2020 07:27:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:27:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:27:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:27:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:27:19: #2 predicted fragment length is 56 bps INFO @ Tue, 16 Jun 2020 07:27:19: #2 alternative fragment length(s) may be 3,56,94,113 bps INFO @ Tue, 16 Jun 2020 07:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.20_model.r WARNING @ Tue, 16 Jun 2020 07:27:19: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:27:19: #2 You may need to consider one of the other alternative d(s): 3,56,94,113 WARNING @ Tue, 16 Jun 2020 07:27:19: #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 07:27:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:27:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:27:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:27:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999205/ERX1999205.20_summits.bed INFO @ Tue, 16 Jun 2020 07:27:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (118 records, 4 fields): 1 millis CompletedMACS2peakCalling